How to get a list of all KEGG ko terms vs names?
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?
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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
(www.genome.jp/kegg/ko.html); enter your IDs (separated by
either new lines, spaces, or both) and click “Get title”:
- This opens a new browser tab with the KOs description/names:
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
Click in the rightmost arrow at top of the list (wait the
complete page load):
Then copy everything! it may lag a litle because the page is a bit heavy (55k+ lines, currently)
Now you can paste in a text file (in my example I used notepad++, but any
other text editor should work):
- Save as tab-delimited file or any other usefull format and get
whichever description you want.
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
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.
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