Question: how to extract simple reactions from KEGG Pathway or similar database into a text file
0
gravatar for nicenewb
4.4 years ago by
nicenewb0
United Kingdom
nicenewb0 wrote:

I am having a huge amount of difficulty in an issue which seems as though it should be quite simple, due to the way the KEGG data seems to be available and my inability to grasp their short documentation. I have looked through github and available scripts for KEGG although none seem to cover my usage. I am comfortable scripting in Perl, and R, but have used PHP and Curl to access REST APIs in the past with no trouble. 

I would essentially like to download a large list in text format of all of the reactions in the human metabolic pathway, which are displayed beautifully in maps on the KEGG website.

Ideally the format would be as follows:

Compound Product Metabolism Enzyme
x y fatty acid degradation lipase
y z fatty acid degradation lipase

I seem to be making no headway and wondered if anybody had obtained anything similar before from the API or the .KPMG or .XML downloads which seem to be available. If anybody could give me an example I can extend this I believe to cover everything.

Thank you in advance for any help.

kegg • 1.6k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by nicenewb0
1

If you want to access the KEGG API you should take a look at these post Kegg Data Download and A New Rest Based Api For Kegg: Kyoto Encyclopedia Of Genes And Genomes

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by camachofrancine130
1
gravatar for nicenewb
4.4 years ago by
nicenewb0
United Kingdom
nicenewb0 wrote:

I have now worked out my problem, which came down to not properly understanding the response data. Essentially everything was returned in KMGL markup. Once you understand the architecture you can extract all the information.

ADD COMMENTlink written 4.4 years ago by nicenewb0
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