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

[Fields, Christopher J]

Yep (and thanks for the more explicit answer :).  

Sometimes it takes playing around with parameters to get what you need, but in general anything that is doable via the Entrez interface is possible via eutils.

chris

> On Jun 9, 2015, at 3:20 PM, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:
> 
> 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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