Is there any quick way to annotate KO terms using a script or tool?

Question

[arsilan324]

Hi all, I have a list of KO IDs, and their frequency which I want to annotate. Can you please help me suggesting how can I do so. I have started this manually but it is taking time. But I would appreciate any computational method doing this.

KO-Term KO-freq Annotation
K13457  49  RPM1, RPS3; disease resistance protein RPM1
K03233  25  EEF1G; elongation factor 1-gamma
K00430  18  E1.11.1.7; peroxidase [EC:1.11.1.7]
K00660  14  CHS; chalcone synthase [EC:2.3.1.74]
K03283  13  HSPA1s; heat shock 70kDa protein 1/2/6/8
K05658  13  ABCB1, CD243; ATP-binding cassette, subfamily B (MDR/TAP), member 1 [EC:3.6.3.44]
K10775  13  
K05909  12  
K14376  12  
K19986  12  
K00549  11  
K00799  11  
K15559  11

Thanks in advance! Arslan

Answer 1

[Pierre Lindenbaum]

using togows: http://togows.dbcls.jp/site/en/rest.html

$ echo -e  "K13457\nK03233\nK00430\nK00660" | while read K; do echo -n "${K} " && wget -q -O -  "http://togows.dbcls.jp/entry/orthology/${K}/name"  | tr "\n" " " && wget -q -O -  "http://togows.dbcls.jp/entry/orthology/${K}/definition"  ; done


K13457 RPM1, RPS3 disease resistance protein RPM1
K03233 EEF1G elongation factor 1-gamma
K00430 E1.11.1.7 peroxidase [EC:1.11.1.7]
K00660 CHS chalcone synthase [EC:2.3.1.74]

[pedrorodrigues]

Hi Pierre, I am new to togows, but your solution is the best I have found so far, in particular if you have thousands of KO ids to query! Nevertheless, I am not succeeding in running your example. I removed "q" from wget and what I see is a lot of 404 not found. Most likely there is something wrong that I am doing, and I was wondering if perhaps you could help me identify my mistake. Here is how the output on screen looks like - thank you in advance!

K13457 --2018-09-15 13:30:07--  http://togows.dbcls.jp/entry/orthology/K13457/name
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:08 ERROR 404: Not Found.

--2018-09-15 13:30:08--  http://togows.dbcls.jp/entry/orthology/K13457/definition
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:08 ERROR 404: Not Found.

K03233 --2018-09-15 13:30:08--  http://togows.dbcls.jp/entry/orthology/K03233/name
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:08 ERROR 404: Not Found.

--2018-09-15 13:30:08--  http://togows.dbcls.jp/entry/orthology/K03233/definition
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:08 ERROR 404: Not Found.

K00430 --2018-09-15 13:30:08--  http://togows.dbcls.jp/entry/orthology/K00430/name
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:08 ERROR 404: Not Found.

--2018-09-15 13:30:08--  http://togows.dbcls.jp/entry/orthology/K00430/definition
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:09 ERROR 404: Not Found.

K00660 --2018-09-15 13:30:09--  http://togows.dbcls.jp/entry/orthology/K00660/name
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:09 ERROR 404: Not Found.

--2018-09-15 13:30:09--  http://togows.dbcls.jp/entry/orthology/K00660/definition
Resolving togows.dbcls.jp togows.dbcls.jp)... 133.39.78.80
Connecting to togows.dbcls.jp togows.dbcls.jp)|133.39.78.80|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-09-15 13:30:09 ERROR 404: Not Found.

[Pierre Lindenbaum]

'looks like the site is broken...

Answer 2

[Sej Modha]

If you paste the list of KO IDs in the text box provided on https://www.genome.jp/kegg/ko.html and search for 'Get title' it should return the annotations.

ko:K13457    RPM1, RPS3; disease resistance protein RPM1
ko:K03233    EEF1G; elongation factor 1-gamma
ko:K00430    E1.11.1.7; peroxidase [EC:1.11.1.7]
ko:K00660    CHS; chalcone synthase [EC:2.3.1.74]
ko:K03283    HSPA1s; heat shock 70kDa protein 1/2/6/8
ko:K05658    ABCB1, CD243; ATP-binding cassette, subfamily B (MDR/TAP), member 1 [EC:3.6.3.44]
ko:K10775    PAL; phenylalanine ammonia-lyase [EC:4.3.1.24]
ko:K05909    E1.10.3.2; laccase [EC:1.10.3.2]
ko:K14376    PAP; poly(A) polymerase [EC:2.7.7.19]
ko:K19986    EXOC8, SEC84; exocyst complex component 8
ko:K00549    metE; 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase [EC:2.1.1.14]
ko:K00799    GST, gst; glutathione S-transferase [EC:2.5.1.18]
ko:K15559    RTT103; regulator of Ty1 transposition protein 103