[Bioperl-l] get geneID for gene names

[Smithies, Russell]

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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