[MOBY-l] GetPubmed service: calling from Perl, sample response

[Frank Gibbons]

Oops - sorry about that, Vijay, I was sure I had attached it. The list 
server told me my message looked suspicious, and perhaps it stripped it. 
Whatever the reason, here it is appended, the output is attached, since 
it's rather long.

-Frank

At 12:15 PM 4/1/2004, Vijay Narayanasamy wrote:
>Frank,
>
>The attachment PMid.pl is missing.
>
>Vijay
>
>Vijay Narayanasamy
>Project Programmer / Analyst
>Bioinformatics Program, Human and Molecular Genetics Center
>Medical College of Wisconsin
>8701, W. Watertown Plank Road
>Milwaukee, WI 53226
>414-456-8026
>vnarayan at mcw.edu
>http://brc.mcw.edu/
>
>-----Original Message-----
>From: Frank Gibbons [mailto:fgibbons at hms.harvard.edu]
>Sent: Thursday, April 01, 2004 9:59 AM
>To: moby-l at biomoby.org
>Subject: Re: [MOBY-l] help needed for GetPubmed service
>
>Martin,
>
>     Thanks for any advise, actually, if someone can get me any simple XML
> >object and tell me where to send it in order to get an answer and not an
> >errror I will be happy... :-)
>
>
>I'm attaching some Perl code (PMid.pl) that calls the GetPubmed service at
>prometheus. I wrote it last week, and just tried it right now, and it still
>works. I'm also appending the output from the service also (PM.txt).
>
>I hope this helps.
>
>-Frank
>
>
>
>PhD, Computational Biologist,
>Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
>Tel: 617-432-3555       Fax:
>617-432-3557       http://llama.med.harvard.edu/~fgibbons


================= Perl code to look up PubMed IDs at GetPubmed service 
===============
#!/home/fgibbons/bin/perl

use MOBY::Client::Central;
use MOBY::Client::Service;

my $Central = MOBY::Client::Central->new();

my ($Services, $REG) =
     $Central->findService( authURI => 'prometheus.brc.mcw.edu',
                            serviceName => 'GetPubmed'
                            );
unless ($Services) {
     print "Service discovery failed with the following errror: ",
     $REG->message;
     end
   }

my @PMids = ("9788350", "14730315", "12368250");
printf("%-35s\t\t %s\n%s\n", "Service", "provided by", "="x80);
foreach my $S ( @{$Services}) {
   printf("%-35s\t\t%s%s\n", $S->name, $S->authority, $S->description);
   my $WSDL = $Central->retrieveService($S);
   my $service = MOBY::Client::Service->new(service => $WSDL);
   foreach my $pmid (@PMids) {
       my $result =
           $service->execute( XMLinputlist => [
                                                  ['object0',
                                                   "<Object 
namespace='PMID' id='" . $pmid
                                                   . "' articleName='" . 
$pmid . "'/>"],
                                                  ]
                              ) || 'None';
       print "Result: ", $result, "\n";
   }
}





PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons 
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