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

[Smithies, Russell]

Try this: http://www.pubmedcentral.nih.gov/about/ftp.html#Obtaining_DOIs

Use ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz to associate PMC articles with a PMC ID, a PubMed ID, and the corresponding DOI.

PMC-ids.csv.gz is a comma separated file with the following fields:

    * Journal Title
    * ISSN
    * Electronic ISSN
    * Publication Year
    * Volume
    * Issue
    * Page
    * DOI (if available)
    * PMC ID
    * PubMed ID (if available)
    * Manuscript ID (if available)
    * Release Date (Mmm DD YYYY or live)

--Russell

> -----Original Message-----
> From: Miguel Pignatelli [mailto:miguel.pignatelli at uv.es]
> Sent: Thursday, 2 April 2009 11:14 a.m.
> To: Smithies, Russell
> Cc: 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] Is it possible to retrieve full pubmed articles
> 
> Thanks for the response,
> 
> I have PMIDs extracted from Genbank flat files, is there a way to
> convert PMIDs to PMCIDs?
> I found this page:
> 
> http://www.ncbi.nlm.nih.gov/sites/pmctopmid
> 
> Is it possible to download the underlying conversion table for local
> use?
> 
> Thank you very much in advance,
> 
> M;
> 
> 
> El 01/04/2009, a las 21:48, Smithies, Russell escribió:
> 
> > 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:
> >
> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1307096&tool=pmcentr
> ez
> >
> > or as pdf
> > http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1307096&blobtype=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,
> > Mosgiel,
> > New Zealand
> > T  +64 3 489 3809
> > F  +64 3 489 9174
> > www.agresearch.co.nz
> >
> >
> >
> >
> >> -----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;
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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