[Bioperl-l] Re: retreive medline records by title

Martin Senger senger at ebi.ac.uk
Mon Jul 19 09:39:55 EDT 2004

> My doubt is how to retreive all publication medline records for a
> species . i want to retrieve all the medline records having the
> species name in its title
   1) You can use either a provided script (let's say for testing first
before coding it into your own program/script) (everything on a single

perl ~/bioperl-live/scripts/biblio/biblio.PLS \
   -c - -find "Antheraea mylitta" -attrs title

   This will give you 15 citations. (But to be honest, you will get the
same 15 even without -attrs title - which means that either all citations
about Antheraea mylitta have it in the title, or there is a bug in the
Biblio code ... obviously if the later is true I would like to hear about
it in order to fix it).

   2) Or here is how to code it for yourself (it's practically identical
to the code you sent here - except an additional parameter in the find
method with the name 'title'):

#!/usr/bin/perl -w

use strict;
use Bio::Biblio;
use Bio::Biblio::IO;
use Data::Dumper;

my $count =1;
my @ids= @{ new Bio::Biblio->find ("Antheraea mylitta",
'title')->get_all_ids } ;

foreach my $ids (@ids) {
    print "$count","  ";
    print  $ids,"\n";
    $count ++;


Martin Senger

EMBL Outstation - Hinxton                Senger at EBI.ac.uk     
European Bioinformatics Institute        Phone: (+44) 1223 494636      
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger

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