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

[Zack Napalm]

solution:
install bioperl 1.5 (instead of 1.4) and all works fine ;-)

>From: "Zack Napalm" <fetter_fake at hotmail.com>
>To: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] pubmed article download and storing in object
>Date: Tue, 28 Jun 2005 13:09:12 +0000
>
>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
>>api.
>>
>>-allen
>>
>>On Mon, 27 Jun 2005, Zack Napalm wrote:
>>
>> > Hi,
>> > I am new at Bioperl and wondering whether there is a possibility to 
>>scrape
>> > 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 
>>object
>> > manually, if there is a appropriate function predefined.
>> >
>> > regards
>> > johnny
>> >
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