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Access Abstract From Pubmed Using Bio::Db::Eutilities

I am using Bio::DB::EUtilities to query the Pubmed DB with given PMIDs (Pubmed Id).

use Bio::DB::EUtilities;

use strict;
use warnings;

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

$factory -> get_Response(-file => 'pubmed_response.xml');

Is there a way to directly access the objects (e.g. abstract) instead of writing the response to file and using XML::Twig or so?

perl bioperl xml pubmed eutils
• 4,596 views • link
updated by Ram Ram • written by Mat • Mat

2 answers

You can just store the content of the response instead of writing it to a file. That would be:

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

Now, $xml can be parsed to get whatever information you want. For example, you could look for the 'Abstract' node in the XML:

This prints the abstract, though you could store it or do something else with it. You could also try getting different return types, as Sudeep mentioned.

EDIT: For reference, I also answered this question on Stack Overflow with more detail.

• 330 views • link
updated by Ram Ram • written by SES SES

This table tells that if you use rettype=abstract & retrymode=text you should probably get abstract as text. I've checked it using efetch but not using bioperl, see it here: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11748933,11700088&rettype=abstract&retmode=text

• 0 views • link
updated by Ram Ram • written by Sudeep Sudeep

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