[Biopython] efetch only returns 20 records of pubmed
David Winter
winda002 at student.otago.ac.nz
Mon Mar 12 22:55:20 UTC 2012
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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