[Bioperl-l] pubmed article download and storing in object

Zack Napalm fetter_fake at hotmail.com
Tue Jun 28 09:09:12 EDT 2005

how does this work exactly? the bioperl documentation seems very poor 
concerning structure and content.
i have tried the following easy piece of code:

my $biblio = new Bio::Biblio;
my $bibResult = $biblio->find('p53');
my $cit = $bibResult->get_next();
print "$_\n" for @{$cit};

just a lot of numbers in an array come back, but no xml file => if i try to 
print $cit directly, just byte[]=ARRAY(0x...) is printed

when i try to use Bio::DB::Biblio::eutils, the interpreter says, that this 
eutils.pm isn't installed. all moduls i use work properly, though. in the 
bioperl documentation is mentioned, that you shouldn't use this modul 
directly, but use it via my $biblio = new Bio::Biblio (-access => 
'eutils');, which doesn't work either (eutils.pm not installed again).

how can i get a proper xml file back? is there a nice bioperl documentation 
out there?

>From: Allen Day <allenday at ucla.edu>
>To: Zack Napalm <fetter_fake at hotmail.com>
>CC: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] pubmed article download and storing in object
>Date: Mon, 27 Jun 2005 11:26:30 -0700 (PDT)
>try Bio::DB::Biblio::eutils.  it doesn't give back an object, but gives
>back an xml document.
>to any volunteers out there looking for something to contribute: this
>would be an easy place to jump in and add something useful to bioperl.
>you'd have a chance to learn a bit of pubmed query language and xml dom
>On Mon, 27 Jun 2005, Zack Napalm wrote:
> > Hi,
> > I am new at Bioperl and wondering whether there is a possibility to 
> > articles from PubMed automatically, and put them into an
> > Bio::Biblio::PubmedArticle object.
> > I don't want to scrape them via LWP::Simple get and put them into an 
> > manually, if there is a appropriate function predefined.
> >
> > regards
> > johnny
> >
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