[Biopython] Record count in pcassay database

Brad Chapman chapmanb at 50mail.com
Tue Jul 14 07:30:09 EDT 2009


Hello;

> I'm using Biopython to access Entrez databases.
> I've retrieved information of the pcassay database with the following code:
> 
> 
> handle=Entrez.einfo(db=*"pcassay"*)
> record=Entrez.read(handle)
> print record[*'DbInfo'*][*'Count'*]
> 
> Printing the record count of pcassay gives :
> *1659*
> Such a limited number of records seems impossible.
> Am I using Biopython incorrectly ?

That count looks right to me if I manually browse the PubChem
BioAssay database:

http://www.ncbi.nlm.nih.gov/pcassay?term=all[filt]

It looks like you are retrieving the top level assay records. The
counts for total compounds assayed will be much higher but you would
need to examine individual records of interest to determine those.

Hope this helps,
Brad


More information about the Biopython mailing list