[Bioperl-l] Is it possible to retrieve full pubmed articles

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Apr 1 15:48:02 EDT 2009

Not all articles have full-text at Pubmed but if you know the article ID, you can usually get the whole article (if available) like this:

or as pdf

I'd just build a URL and use wget.

If you're searching Pubmed directly, use a query like this to ensure you only get articles with links to full text:

	cancer AND (free full text[sb])
eg 	http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=cancer+AND+(free+full+text[sb])

Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Miguel Pignatelli
> Sent: Thursday, 2 April 2009 6:16 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Is it possible to retrieve full pubmed articles
> Hi all,
> I have a list of PUBMED IDs and I am trying to retrieve automatically
> the *full article* in any format (not just the abstract). Is there any
> method in bioperl that allows this? any other solution?
> Currently I am trying to solve this using WWW::Mechanize, but do you
> know of any other method to do this?
> Any help would be appreciated,
> Thanks in advance,
> M;
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> Bioperl-l at lists.open-bio.org
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