ko2name function doesn't work on some pathway numbers

[Ruiqi-CUB]

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 with ko2name even if they do have descriptions on KEGG website.

Here is an example with pathway map01521:

> ko2name("map01521")
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway"...
        ko name
1 map01521 <NA>

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!

[guidohooiveld]

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.

[Ruiqi-CUB]

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 <NA>

ko2name("hsa01521") Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/"... ko name 1 hsa01521 EGFR tyrosine kinase inhibitor resistance

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