How Many Human Pathways Exist In Kegg Database?
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4
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11.1 years ago
Woa ★ 2.9k

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?

kegg pathway database • 6.9k views
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7
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11.1 years ago
D-Horse ▴ 110

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.

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Many Thanks !!!!

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0
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+1 for KEGG API, that's a neat resource !

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5
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8.3 years ago
Prakki Rama ★ 2.6k

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

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3
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11.1 years ago
Joachim ★ 2.9k

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

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0
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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.

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

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9.6 years ago
wchknudt ▴ 50

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";
}
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8.3 years ago
Haluk ▴ 190

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

https://github.com/haluk/kegg

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