Re: An example to query PMID given GEO accession number?
"Fields, Christopher J" <[email protected]>
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 <[email protected]> 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@mailman.open-bio.org [mailto:bioperl-l-bounces+russell.smithies=agresearch.co.nz@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: [email protected] > 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 => '[email protected]', > ); > > # 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@mailman.open-bio.org [mailto:bioperl-l-bounces+russell.smithies=agresearch.co.nz@mailman.open-bio.org] On Behalf Of Fields, Christopher J > Sent: Wednesday, 10 June 2015 3:52 a.m. > To: Peng Yu > Cc: [email protected] > 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 <[email protected]> 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 >> [email protected] >> http://mailman.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l