This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Retriving compounds name from KEGG IDs

Dear all, I have list of KEGG IDs for metabolites (compounds) and I want to get the name of the all the compounds from that list. So please suggest me what should I do??? Thanks

gene
• 9,617 views • link
updated by Biostar Biostar • written by glady glady

yes something like that but for my list of IDs. Thanks

• 1 views • link
written by glady glady

Sorry, but what you are asking for are 10 lines of code in python(maximum) and even less in R

• 1 views • link
written by Girolamo Girolamo

It is more helpful to provide actual code rather than a statement about how small the needed code is.

• 1 views • link
written by GenoMax GenoMax

Can you please post your sample input ?

• 1 views • link
written by EagleEye EagleEye

3 answers

I hope this helps,

1.make a file 'sample.list' with the list of compound IDs you have,

cat sample.list

C00001

C00002

C00003

C00004

C00005

C00006

C00007

2.And then run the following CURL command below.

curl -g -s -S http://rest.kegg.jp/list/compound | grep -f sample.list | sed "s/cpd\://" > sample_extracted.table.txt

SAMPLE OUTPUT:

C00001  H2O; Water
C00002  ATP; Adenosine 5'-triphosphate
C00003  NAD+; NAD; Nicotinamide adenine dinucleotide; DPN; Diphosphopyridine nucleotide; Nadide; beta-NAD+
C00004  NADH; DPNH; Reduced nicotinamide adenine dinucleotide
C00005  NADPH; TPNH; Reduced nicotinamide adenine dinucleotide phosphate
C00006  NADP+; NADP; Nicotinamide adenine dinucleotide phosphate; beta-Nicotinamide adenine dinucleotide phosphate; TPN; Triphosphopyridine nucleotide; beta-NADP+
C00007  Oxygen; O2

I assume, I understand your question properly.

• 1 views • link
written by EagleEye EagleEye

Dear EagleEye thank you for your comments

And you got me right. I am trying to run the above command but in windows it is saying that grep is not recognized as internal or external command., so is there any alternative for that. please let me know.

Thanks

• 1 views • link
written by glady glady

You can install cygwin to get a unix like environment on windows or better still run linux in a virtual machine (e.g. virtual box).

• 1 views • link
written by GenoMax GenoMax

You can follow as genomax2 suggested or simple is to run on Linux.

• 1 views • link
written by EagleEye EagleEye

Please upvote if this helps, so that other people know that the problem has been solved.

• 1 views • link
written by EagleEye EagleEye

Thank you for the reply.

I just upvoted. Thanks

• 1 views • link
written by glady glady

You can either search for them in the KEGG database website, or use something more automated like the KEGG REST API (in this specific case you need the "get" method).

Suppose you are interested in the following three compound IDs:

  • C00818
  • C00140
  • C00259

Simply go to this webpage (have a look at how the URL has been constructed): http://rest.kegg.jp/get/C00259+C00140+C00818

• 1 views • link
written by mgalactus mgalactus

Dear Mgalactus, thank you for your reply. The method you suggested, gives the details of the compounds in query. but I have a list of more than 2000 metabolites IDs. In that case its very difficult to get the name and details. So is there any way to get the result output in tabular format like as in *.csv format.

Thanks in advance

• 1 views • link
written by glady glady

like this? http://rest.kegg.jp/list/compound

• 1 views • link
written by Girolamo Girolamo

Log in to answer this question.

More posts like this