[Biopython] Record count in pcassay database

[Brad Chapman]

Hello;

> Thanks very much for your reply.
> By the way in your http query you specify *term=all[filt]*
> I've just tried the same with BioPython and it does retireve all records:

It looked like you were getting all the records with your previous
query as well.

> handle = Entrez.esearch(db=*"pcassay"*, term=*"ALL[filt]"*)
> Is 'filt' the standard wildcard for Entrez queries ?

I don't know too much about PubChem queries but had just clicked on the
"All BioAssays" link from the main page:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay

The documentation linked to from there:

http://pubchem.ncbi.nlm.nih.gov/help.html#PubChem_index

can probably provide additional direction. Thanks,
Brad

> 
> Thanks.
> 
> On Tue, Jul 14, 2009 at 12:30 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> 
> > 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
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