[Bioperl-l] get geneID for gene names

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed May 2 19:12:14 EDT 2012


If you're looking for gene information, why are you searching UniSTS?
Unless I've overlooked something, wouldn't it be more useful to search the "gene" database and tighten up your query a bit?

#!/bin/perl 
use strict;
use warnings;

use Bio::DB::EUtilities;

my $factory = Bio::DB::EUtilities->new(
    -eutil      => 'esearch',
    -db         => 'gene',
    -term       => '(copg[Gene Name]) AND mouse[Organism]',
    -email      => 'hnorpois at mpipsykl.mpg.de',
    -usehistory => 'y'
);

my $hist = $factory->next_History || die "No history data returned";

$factory->set_parameters(
    -eutil   => 'efetch',
    -history => $hist
);

print $factory->get_Response->content;


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hermann Norpois
Sent: Thursday, 3 May 2012 9:01 a.m.
To: Fields, Christopher J
Cc: <bioperl-l at lists.open-bio.org>
Subject: Re: [Bioperl-l] get geneID for gene names

Thank you very much. But there still is a problem.

This is my output:
525211,210532,167498,142652

I get some ids (the first one is the UniSTS ID, the following ... I do not
know) but there is no gene ID. If you compare to the following link:
http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=525211 The gene ID should be 54161<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=54161>
.

This is my (your) script:

#!/bin/perl -w

use Bio::DB::EUtilities;

my $name = "Copg";
my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                     -db     => 'unists',
                                     -term   => "$name AND Mus musculus
[ORGN]",
                                     -email  => 'hnorpois at mpipsykl.mpg.de',
                                     );

print join(',',$factory->get_ids)."\n";



2012/5/2 Fields, Christopher J <cjfields at illinois.edu>

> Also, a small but very significant bug is in the below.  Can you spot it?
>
> The '-term' value is in single quotes, these need to be double-quotes 
> to interpolate $name.  Otherwise, it is literally looking for '$name'.
>
> chris
>
> On May 2, 2012, at 12:55 PM, Christopher Fields wrote:
>
> > Hermann,
> >
> > The below works for me (note I'm using esearch, not efetch).  To
> actually get the records you will use efetch and the IDs obtained below.
> >
> > chris
> >
> > ------------------------------
> > my $name = "Copg";
> > my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
> >                                      -db     => 'unists',
> >                                      -term   => '$name AND mouse [ORGN]',
> >                                      -email  => '<EMAIL_HERE>',
> >                                      );
> >
> > print join(',',$factory->get_ids)."\n";
> >
> >
> > On May 2, 2012, at 12:42 PM, Hermann Norpois wrote:
> >
> >> Hello,
> >>
> >> I wish to get gene IDs for gene names (e.g. bdnf, copg). I thought 
> >> it
> was a
> >> good idea to use Bio::DB::EUtilities (see below) and addressed 
> >> UNISTS as database because there it was quite easy to find the gene 
> >> ID. So far I
> was
> >> unable to retrieve the gene ID from UNISTS. Could anybody give me a 
> >> hint how to proceed? The cookbook ... Yes, I was trying.
> >>
> >> #!/bin/perl -w
> >>
> >> use Bio::DB::EUtilities;
> >>
> >> my $name = "Copg";
> >> my $factory = Bio::DB::EUtilities->new(-eutil  => 'efetch',
> >>                                      -db     => 'unists',
> >>                                      -term   => '$name AND mouse
> [ORGN]',
> >>                                      -email  => '
> hnorpois at mpipsykl.mpg.de'
> >>                                      )
> >>
> >>
> >> Thank you
> >> Hermann Norpois
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
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