Retrieve all compound ID, Description from a ko ID

Question

[jkim]

Hello,

I am trying to get, reaction IDs, descriptions, compound IDs and their descriptions from ko IDs (e.g. K00163). I went through Biostars and KEGG rest APIs, but I can't find an answer.

For example, I have a K00163. My goal is ko:K00507 has R02222 (Reaction ID, description) has C00001(compound),C00007 (IDs, Definitions)
ko:K00507 has R12173 (Reaction ID, description) has C00999,C21072...(IDs, Definitions)

The kegg rest api doesn't have the chemical reaction info. I tried some other ways but can't find ways.

The url has some patterns.
https://www.genome.jp/dbget-bin/get_linkdb?-t+7+ko:K00163
https://www.genome.jp/dbget-bin/get_linkdb?-t+compound+rn:R02222

Maybe I could use some html parser and html libraries (like request) so request a ko ID html and parse it and then get reaction IDs html and parse it over and over again, but it doesn't seem a nice way.

Is there a nice way of doing it?
Thank you in advance.

Answer 1

[AK]

Hi jkkim,

You can use KEGGREST package in R:

library(KEGGREST)

ko <- "K00163"

reactions <- keggLink("reaction", ko)
compounds <- keggLink("compound", reactions)

df <-
  data.frame(
    ko = rep(ko, length(compounds)),
    rn = names(compounds),
    rn_desc = keggList(names(compounds)),
    cpd = compounds,
    cpd_desc = keggList(compounds)
  )

You'll get a dataframe like this:

Hope it helps.

Answer 2

[Sej Modha]

It is possible to download KEGG KO records in the flat file format using KEGG API and then parse the text file for any data.

For example, http://rest.kegg.jp/get/ko:K00507 and http://rest.kegg.jp/get/ko:K00163

[jkim]

Thank you. I tried that way before, but it doesn't have the chemical reaction information.

[Sej Modha]

Please do not delete the post after members of the community have provided feedback on your post.

[jkim]

I am sorry. For some reason, I removed the post. Sorry again.