Question: Quick way to download KEGG pathway images
0
gravatar for Vijay Lakhujani
19 months ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

I have obtained the following ids for Vitis vinifera from UniprotKB retrieval utility by mapping Ensembl IDS.

vvi:100250200;
vvi:100254312;
vvi:100261308;
vvi:104880199;
vvi:100263187;
vvi:100260420;
vvi:100245574;
vvi:100244092;
vvi:100252790;
vvi:100262316;
vvi:100232889;
vvi:100253968;
vvi:100263079;

From this link, it seems obvious that these are indeed KEGG ids. However, I am having hard time identifying them via KEGG web portal.

This is indeed a trivial task and I found many discussions already on similar issues on Biostar. However, I am a little stuck here.

Can somebody please help?

download kegg image pathway • 973 views
ADD COMMENTlink modified 19 months ago by h.mon24k • written 19 months ago by Vijay Lakhujani4.0k

It appears that these are KEGG gene entries. How can then I obtain the pahtway IDS and then download the images?

ADD REPLYlink written 19 months ago by Vijay Lakhujani4.0k
1

Yes, they appear to be genes for this species (grape).

I have been able to look them up here and to view their sequence, amongst other information: http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&locale=en&serv=gn&dbkey=all&keywords=100250200&page=1

Here is the entry for vvi:100250200: http://www.genome.jp/dbget-bin/www_bget?vvi:100250200

If there is no link on the right-hand-side to 'KEGG Pathway', then I don't believe that a curated pathway exists that contains the gene.

ADD REPLYlink written 19 months ago by Kevin Blighe41k

in R:

library(KEGGREST)
library(png)
library(stringr)

with loop:

kegg_ids=read.csv("kegg_ids", header = F, stringsAsFactors = F)
kegg_pw=keggLink("pathway", kegg_ids[,1])
kegg_pw_ids=unique(str_split_fixed(kegg_pw,":", 2)[,2])

for (i in kegg_pw_ids) {
         #   print (paste(i))
              j=keggGet(i, "image")
              writePNG (j,target=paste(i,".png", sep=""))
            }

without loop:

kegg_ids=read.csv("kegg_ids", header = F, stringsAsFactors = F)
kegg_pw=keggLink("pathway", kegg_ids[,1])
kegg_pw_ids=unique(str_split_fixed(kegg_pw,":", 2)[,2])

sapply(kegg_pw_ids, function (x) writePNG(keggGet(x,"image"), target=paste(x,".png",sep="")))

output: (images are not posted)

    > kegg_ids
                  V1
    1  vvi:100250200
    2  vvi:100254312
    3  vvi:100261308
    4  vvi:104880199
    5  vvi:100263187
    6  vvi:100260420
    7  vvi:100245574
    8  vvi:100244092
    9  vvi:100252790
    10 vvi:100262316
    11 vvi:100232889
    12 vvi:100253968
    13 vvi:100263079

   > kegg_pw_ids
        [1] "vvi00710" "vvi01100" "vvi01200" "vvi04075" "vvi00500" "vvi00520" "vvi01110"
ADD REPLYlink modified 19 months ago • written 19 months ago by cpad011211k
1
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