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

[Brian Osborne]

Zack,

There are *some* examples in the examples/biblio/biblio_examples.pl script.
If you come up with some more please send them our way, I can add them.

Do  you have XML::Twig installed? If not that could explain the error using
"eutils".


Brian O.


On 6/28/05 9:09 AM, "Zack Napalm" <fetter_fake at hotmail.com> wrote:

> 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
>>> 
>>> _________________________________________________________________
>>> Sie suchen E-Mails, Dokumente oder Fotos? Die neue MSN Suche Toolbar mit
>>> Windows-Desktopsuche liefert in sekundenschnelle Ergebnisse. Jetzt neu!
>>> http://desktop.msn.de/ Jetzt gratis downloaden!
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> _________________________________________________________________
> Die neue MSN Suche Toolbar mit Windows-Desktopsuche. Suchen Sie gleichzeitig
> im Web, Ihren E-Mails und auf Ihrem PC! Jetzt neu! http://desktop.msn.de/
> Jetzt gratis downloaden!
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l