[Biopython] Parsing records off PubMed vs. PubMedCentral.

Fri Nov 20 10:49:09 UTC 2009

On Thu, Nov 19, 2009 at 11:03 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Now, according to the documentation for EFetch, PMC should support
> rettype="medline" (just like PubMed):
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
>
>>>> print Entrez.efetch(db="pmc",id="2682512", retmode="medline", rettype="text").read()
> <html>
> <body>
> <br/><h2>Error occurred: Report 'text' not found in 'pmc'
> presentation</h2><br/><ul title="some params from request:">
> ...
> </html>
>
> Odd. I also tried the XML from EFetch for PMC, but it fails to
> validate. I wonder if this in an NCBI glitch? I have emailed them
> about this.
>

I had a reply from someone at the NCBI, who had also noticed a
problem, and has reported this to the EFetch developers.

> In the meantime, I would suggest you just use PubMed not PMC - it
> covers more journals but in less depth.

Peter