[Biopython] Record count in pcassay database

[bar tomas]

Thanks a lot!

On Tue, Jul 14, 2009 at 1:50 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

> 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
> > > _______________________________________________
> > > Biopython mailing list  -  Biopython at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biopython
> > >
>