[Bioperl-l] An example to query PMID given GEO accession number?

[Smithies, Russell]

And to get back the Pubmed data you need to use the history.

--------------------------------

my $hist  = $factory->next_History || die 'No history data returned';
$factory->set_parameters(-eutil   => 'efetch',
                         -rettype => 'xml',
                         -history => $hist);
$factory->get_Response(-file => "$geo.xml");


----------------------------------

--Russell


-----Original Message-----
From: bioperl-l-bounces+russell.smithies=agresearch.co.nz at mailman.open-bio.org [mailto:bioperl-l-bounces+russell.smithies=agresearch.co.nz at mailman.open-bio.org] On Behalf Of Smithies, Russell
Sent: Wednesday, 10 June 2015 8:09 a.m.
To: Fields, Christopher J; Peng Yu
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] An example to query PMID given GEO accession number?

It's all a matter of knowing the database and how to format the query.

--Russell

---------------------------------------

#!/usr/bin/perl

use strict;
use warnings;

use Bio::DB::EUtilities;

# want to get PMID 23028701
my $geo        = "GSE39684";
my $factory = Bio::DB::EUtilities->new(
        -eutil   => 'esearch',
        -db      => 'gds',
        -term    => "${geo}[ACCN] AND (gse[ETYP] OR gds[ETYP])",
        -email   => 'x at y.com',
);

# query terms are mapped; what's the actual query?
print "Query translation: ",$factory->get_query_translation,"\n";
# query hits
print "Count = ",$factory->get_count,"\n"; # UIDs my @ids = $factory->get_ids; print "@ids\n";

-------------------------------------------------

-----Original Message-----
From: bioperl-l-bounces+russell.smithies=agresearch.co.nz at mailman.open-bio.org [mailto:bioperl-l-bounces+russell.smithies=agresearch.co.nz at mailman.open-bio.org] On Behalf Of Fields, Christopher J
Sent: Wednesday, 10 June 2015 3:52 a.m.
To: Peng Yu
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] An example to query PMID given GEO accession number?

Should be feasible via elink, possibly starting with using a search term against GEO, then using the link between GEO and pubmed (via GEO’s UID) to get related PMIDs.

chris

> On Jun 9, 2015, at 9:47 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> 
> Hi,
> 
> I am looking for an example to to query GEO to get the PMID associated 
> with a GEO accession number.
> 
> For example, GSE39684 has the associated PMID 23028701. Can this be 
> done with bioperl? Does anybody have an example script for doing so?
> Thanks.
> 
> --
> Regards,
> Peng
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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