biostars84811.pl - get pubmed abstract

biostars84811.pl

#!/usr/bin/env perl                                                                                                                                                

use 5.010;
use utf8;
use strict;
use warnings;
use Bio::DB::EUtilities;
use XML::LibXML;

my @ids = (23298400);
my $factory = Bio::DB::EUtilities->new(-eutil   => 'efetch',
                                       -email   => 'mymail@foo.bar',
                                       -db      => 'pubmed',
                                       -retmode => 'xml',
                                       -id      => \@ids);

my $xml = $factory->get_Response->content;

my $xml_parser = XML::LibXML->new();
my $dom = $xml_parser->parse_string($xml);
my $root = $dom->documentElement();

for my $node ($root->findnodes('//*[text()]')) {
    my $name = $node->nodeName();
    if ($name eq 'Abstract') {
        for my $child ($node->findnodes('*')) {
            binmode STDOUT, ":utf8";
            say $child->textContent();
        }
    }
}