Open Ruiqi-CUB opened 1 year ago
If you look at the KEGG REST API that is called by the function ko2name
(this site: https://rest.kegg.jp/list/pathway/), you will notice that the pathway you mention (map01521
) is indeed not listed on that page. Yet, you will see that human pathway hsa01521
is present (thus hsa
, not map
).
Why there is no 'general' pathway defined I do not know.... maybe because map01521 is specific for a human disease?? So it seems the cause of the problem is at KEGG, and not the ko2name
function.
> ko2name("map01521")
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/"...
ko name
1 map01521 <NA>
>
> ko2name("hsa01521")
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/"...
ko name
1 hsa01521 EGFR tyrosine kinase inhibitor resistance
>
[[added]] If you check the section "Pathway Identifiers" at the KEGG pathway web page (https://www.genome.jp/kegg/pathway.html) its seems that it indeed has something to do with a difference between reference and organism-specific pathways. What exactly I don't know, but you could consider asking KEGG. Please reply back if you do so. :)
Pathway Identifiers
Each pathway map is identified by the combination of 2-4 letter prefix code and 5 digit number
(see [KEGG Identifier](https://www.genome.jp/kegg/kegg3.html)).
The prefix has the following meaning:
map
manually drawn reference pathway
ko
reference pathway highlighting KOs
ec
reference metabolic pathway highlighting EC numbers
rn
reference metabolic pathway highlighting reactions
<org>
organism-specific pathway generated by converting KOs to gene identifiers
and the numbers starting with the following:
011
global map (lines linked to KOs)
012
overview map (lines linked to KOs)
010
chemical structure map (no KO expansion)
07
drug structure map (no KO expansion)
other
regular map (boxes linked to KOs)
are used for different types of maps.
I contacted KEGG and they just fixed the issu.
On Fri, Mar 3, 2023 at 3:08 AM Guido Hooiveld @.***> wrote:
If you look at the KEGG REST API that is called by the function ko2name (this site: https://rest.kegg.jp/list/pathway/), you will notice that the pathway you mention (map01521) is indeed not listed on that page. Yet, you will see that human pathway hsa01521 is present (thus hsa, not map). Why there is no 'general' pathway defined I do not know.... So it seems the cause of the problem is at KEGG, and not the ko2name function.
ko2name("map01521") Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/"... ko name 1 map01521
ko2name("hsa01521") Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/"... ko name 1 hsa01521 EGFR tyrosine kinase inhibitor resistance
— Reply to this email directly, view it on GitHub https://github.com/YuLab-SMU/clusterProfiler/issues/545#issuecomment-1453280793, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILIQFZMVDAXKXD2GAE63W2G7IJANCNFSM6AAAAAAVMWGL2I . You are receiving this because you authored the thread.Message ID: @.***>
-- Ruiqi Li PhD Candidate Dept. of Ecology and Evolutionary Biology University of Colorado Boulder [image: A button with "Hear my name" text for name playback in email signature] https://www.name-coach.com/ruiqi-li
Hi Dr. Yu!
I was trying to use
ko2name
fuction to get the name of pathways with pathway numbers. I found a lot of pathway numbers don't work withko2name
even if they do have descriptions on KEGG website.Here is an example with pathway map01521:
Here is the KEGG website showing that the name for map01521 is "EGFR tyrosine kinase inhibitor resistance".
Could you please help me have a look? Thanks a lot!