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

[Peng Yu]

On Tue, Jun 9, 2015 at 3:09 PM, Smithies, Russell
<Russell.Smithies at agresearch.co.nz> wrote:
> 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";

Why can't I get the correct PMID?

~$ ./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])",
  -term    => "${geo}[ACCN] AND (gse[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";


-- 
Regards,
Peng