How to get KEGG pathway names from a list of 'ko' IDs?

Question

I have a list of ko IDs from which I want to get the pathway names. How can I get that? I have tried this link, but it does not give me any result. What to do?

  ko00010   ko00030 ko00061 ko00120 ko00121 ko00190 ko00195 ko00230 ko00250 ko00253 ko00270 ko00300 ko00330 ko00400 ko00401 ko00410 ko00430 ko00450 ko00460 ko00471 ko00472 ko00500 ko00511 ko00520 ko00521 ko00523 ko00531 ko00550 ko00562 ko00604 ko00620 ko00625 ko00640

Thanks

Answer 1

You can use the KEGG API:

ko_list="ko00010 ko00030 ko00061 ko00120 ko00121
         ko00190 ko00195 ko00230 ko00250 ko00253
         ko00270 ko00300 ko00330 ko00400 ko00401
         ko00410 ko00430 ko00450 ko00460 ko00471
         ko00472 ko00500 ko00511 ko00520 ko00521
         ko00523 ko00531 ko00550 ko00562 ko00604
         ko00620 ko00625 ko00640"

for i in ${ko_list}
do
    hit=$(curl -# http://rest.kegg.jp/list/pathway | grep -w "${i/ko/map}")
    echo -e "${i}\t${hit}" | cut -f1,3 >> ko_pathways.txt
done

Or if your list is too long you can change the input and use a file with a list of ids.

while read line
do
    hit=$(curl -# http://rest.kegg.jp/list/pathway | grep -w "${line/ko/map}")
    echo -e "${line}\t${hit}" | cut -f1,3 >> ko_pathways.txt
done < ko_list.txt

The result will be something like:

 ko00010    Glycolysis / Gluconeogenesis
 ko00030    Pentose phosphate pathway
 ko00061    Fatty acid biosynthesis
 ko00120    Primary bile acid biosynthesis
 ko00121    Secondary bile acid biosynthesis