Question: How Many Human Pathways Exist In Kegg Database?
4
gravatar for Woa
8.5 years ago by
Woa2.7k
United States
Woa2.7k wrote:

How to know how many Human pathways exist in the KEGG database?

If I search THIS PAGE with 'hsa'(Homo sapiens) in the organism field and keeping the keyword field blank it returns 236. Is this the correct way to find it?

pathway database kegg • 5.3k views
ADD COMMENTlink modified 5.7 years ago by Haluk170 • written 8.5 years ago by Woa2.7k
7
gravatar for D-Horse
8.5 years ago by
D-Horse110
Germany
D-Horse110 wrote:

Hi, I think you could use the APIs in KEGG.For example to get the total numbers of genes in hsa00010.The code is written in Perl:

#!/usr/bin/env perl
use SOAP::Lite +trace => [qw(debug)];
my $serv = SOAP::Lite -> service("http://soap.genome.jp/KEGG.wsdl");
my $result = $serv->get_genes_by_pathway('path:hsa00010');
my $count = 0;
foreach (@{$result}){
    print $_,"\n";
    $count += 1;
}
print $count,"\n";

The answer is 65.

ADD COMMENTlink written 8.5 years ago by D-Horse110

Many Thanks !!!!

ADD REPLYlink written 8.5 years ago by Woa2.7k

+1 for KEGG API, that's a neat resource !

ADD REPLYlink written 8.5 years ago by Khader Shameer18k
5
gravatar for Prakki Rama
5.7 years ago by
Prakki Rama2.3k
Singapore
Prakki Rama2.3k wrote:

KEGG now operates with REST instead of SOAP. Could be done in a feasible way. But I did this:

wget -O http://rest.kegg.jp/link/pathway/hsa >HSA.txt ##Saving the file
cut -d "      " -f 2 HSA.txt | cut -d ":" -f 2 | sort -u | wc -l ## counting the pathways in Human
283 (pathways in Human in KEGG at present)

~Prakki Datta

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Prakki Rama2.3k
3
gravatar for Joachim
8.5 years ago by
Joachim2.8k
San Francisco, California
Joachim2.8k wrote:

Yes, this is the correct number of pathways for human in KEGG and it is also the right way to find them.

ADD COMMENTlink written 8.5 years ago by Joachim2.8k

Many thanks. I've a further question: for a particular pathway like http://www.genome.jp/dbget-bin/www_bget?pathway+hsa00010, I wish to get the total no. of genes involved in that pathway. Is there an easy way to find it? Thanks in advance.

ADD REPLYlink modified 11 weeks ago by RamRS25k • written 8.5 years ago by Woa2.7k

I guess D-Horse was faster with providing an answer.. :)

ADD REPLYlink written 8.5 years ago by Joachim2.8k
1
gravatar for wchknudt
7.1 years ago by
wchknudt50
wchknudt50 wrote:

You are correct. The answer now is 260.

You can also use perl script to do this:

#!/usr/bin/env perl

use SOAP::Lite;
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';

$results = SOAP::Lite
-> service($wsdl)
-> list_pathways("hsa");

my $file_name = "kegg_hsa_pathways.txt";

if (open (OUTFILE, '>'.$file_name))
{
    foreach $path (@{$results}) {
        print OUTFILE "$path->{entry_id}\t$path->{definition}\n";
    }
    close(OUTFILE);

    print "Content writtent to $file_name!"
}
else{
    die "Error: Error occur in  writing to file\n";
}
ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by wchknudt50
0
gravatar for Haluk
5.7 years ago by
Haluk170
Lincoln, Nebraska
Haluk170 wrote:

If you need their graphs, I generated them in dot format.

https://github.com/haluk/kegg

ADD COMMENTlink written 5.7 years ago by Haluk170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1699 users visited in the last hour