How to get a list of all KEGG ko terms vs names?
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2.5 years ago
tianshenbio ▴ 150

I want to map a list of KEGG terms with their corresponding names. Is it possible to get a list of all KEGG terms and their descriptions/names?

kegg annotation rna-seq • 2.2k views
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23 months ago
Arsenal ▴ 160

Hi.

I am not sure if you already figured it out, but, I know two easy ways of getting KO names/descriptions and use them afterwards to map their names to the respective KO IDs.

1 - The elegant way: Get title

  • If you happen to have a list of KOs, you can map their names using the lower field at "KO (KEGG ORTHOLOGY) Database" page (https://www.genome.jp/kegg/ko.html); enter your IDs (separated by either new lines, spaces, or both) and click "Get title":

get KOs title

  • This opens a new browser tab with the KOs description/names:

get KOs title 2

2 - The not-so-elegant way: Copy from page

  • If you wish to get all the descriptions/names from once, open the "KEGG Orthology (KO)" link in the "KO (KEGG ORTHOLOGY) Database" page (https://www.genome.jp/kegg/ko.html): get KOs title 3

  • Click in the rightmost arrow at top of the list (wait the complete page load): get KOs title 4

  • Then copy everything! it may lag a litle because the page is a bit heavy (55k+ lines, currently) get KOs title 5

  • Now you can paste in a text file (in my example I used notepad++, but any other text editor should work):

get KOs title 6

  • Save as tab-delimited file or any other usefull format and get whichever description you want.

Tips

1 - Avoid using excel IF you are not REALLY sure excel won't mess up the entered data. If you are REALLY sure it is ok, you can open the file as a speadsheet and use it as a database in formulas like VLOOKUP to map the descriptions to any KOs list you have (comment if you need me to show you how).

2 - In unix systems, you can easily get the description from the text file using grep, awk, sed, etc. This is much better if you wanna map the descriptions within a script/pipeline/program, etc.

I'm glad if this answer helps anyone. Cheers

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Entering edit mode

Hey Arsenal,

I just made a post about this, but since its somewhat related, do you have an idea how I can get the functional category ( different level of the heirarchy) rather than the specific gene function? I'm trying to summarize the annotations by saying for example there are 243 genes related to "Carbohydrate metabolism"

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20 months ago
szymon • 0

My group prepared a very nice tool based on KEGG ( see https://dariusz-izak-doktorat.github.io/ )

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