[Biopython] efetch only returns 20 records of pubmed

[ming.xue at boehringer-ingelheim.com]

Hi David,

Thanks for the quick tips and I certainly missed the tutorials. But I had
more serious problem as I think I got denied. During my test of the examples
in the section 8.15 of the Tutorials, my simple command of
Entrez.einfo(db='pubmed') failed at 9:45 pm US EDT but the same command
worked fine on my personal computer with a different IP. I emailed NCBI for
clarification.

Thanks,
Ming

-----Original Message-----
From: biopython-bounces at lists.open-bio.org
[mailto:biopython-bounces at lists.open-bio.org] On Behalf Of David Winter
Sent: Monday, March 12, 2012 6:55 PM
To: biopython at lists.open-bio.org
Subject: Re: [Biopython] efetch only returns 20 records of pubmed

Hi Min,

I think "retmax" is the parameter you are looking for. If you plan on 
making some huge query, be sure to do it outside of peak times (US) and 
think about using the WebEnv features ("Using the history and WebEnv" 
section of the tutorial: 
http://biopython.org/DIST/docs/tutorial/Tutorial) if you want to 
download a lot of data.

Cheers,
David

On 3/13/2012 11:18 AM, ming.xue at boehringer-ingelheim.com wrote:
> Hello,
>
> I used the biopython 1.5.9 to download some pubmed abstracts. The query
from
> browser showed 409580 records. But I only got the count of 20 from
> record["IdList"] and they matched the records on the first page from
browser.
> Am I blocked by NCBI or there is a parameter for page I missed?
>
> from Bio import Entrez
> Entrez.email = 'my.email at domain.com'
>
> query = Entrez.esearch(db="pubmed", term="publisher[sb]")
> record = Entrez.read(query)
> print len(record["IdList"])
>
> Thanks for your comments,
> Ming
>
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>

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