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

[Smithies, Russell]

OK, I think I see what the problem is ;-)

This is the correct Pubmed link with a Pubmed UID: http://www.ncbi.nlm.nih.gov/pubmed/?term=23028701[uid] 
This is a link to the paper but with a GDS UID: http://www.ncbi.nlm.nih.gov/gds/?term=200039684[uid]

Not exactly sure how you'd convert between the two (elink maybe?) , but looks like it's giving the same answer.

--Russell

-----Original Message-----
From: Peng Yu [mailto:pengyu.ut at gmail.com] 
Sent: Monday, 15 June 2015 1:58 p.m.
To: Smithies, Russell
Cc: Fields, Christopher J; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] An example to query PMID given GEO accession number?

On Sun, Jun 14, 2015 at 8:33 PM, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:
> You need to specify you want to use history - it doesn't do it by default.
>
> my $factory = Bio::DB::EUtilities->new(
>         -eutil   => 'esearch',
>         -db      => 'gds',
>         -term    => "${geo}[ACCN] AND (gse[ETYP] OR gds[ETYP])",
>         -email   => 'x at y.com',
>         -usehistory => 'y',   <<<<============
> );

I still can't get the correct result (it should be 23028701). Could you try the code and see if it works on your machine?

$ ./main.pl
Query translation: GSE39684[ACCN] AND gse[ETYP] Count = 1
200039684
$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

use FindBin;
use lib "$FindBin::Bin/.";
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])", # whether
I use this line or the following line, the result is the same.
  -term    => "${geo}[ACCN] AND (gse[ETYP])",
  -email   => 'x at y.com',
  -usehistory => 'y',
);

# 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";


--
Regards,
Peng