[Biopython] Entrez.efetch problem when querying pccompound database

[saikari keitele]

Many thanks for your reply.
Does that mean that pccompound and pcassay databases can not be queried
programmatically, they just have to be queried manually?
Thanks again

On Fri, Oct 29, 2010 at 1:13 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Fri, Oct 29, 2010 at 12:26 PM, saikari keitele <saikari78 at gmail.com>
> wrote:
> > Hi,
> >
> > I'm using BioPython to query the NCBI pccompound database.
> > I'm trying to retrieve the molecular weight of a compound given its
> > InChIKey.
> > Gettting the ID of the compound with esearch works fine. For instance:
> >
> > Entrez.esearch(db="pccompound",
> > term='"BSYNRYMUTXBXSQ-UHFFFAOYSA-N"[InChIKey]')
> >
> > However, when I try to retrieve the record's content with efetch from the
> ID
> > returned by esearch, like this:
> >
> > Entrez.efetch(db="pcassay", id="2244")
> >
> > I get the following response:
> > ...
> > Error occurred: Report 'ASN1' not found in 'pccompound' presentation
> > ...
> >
> > I've tried to use other return types and return modes, like for instance
> >
> > Entrez.efetch(db="pcassay", id="2244", rettype="abstract",
> retmode="text")
> >
> > but I have not succeeded in retrieveing this compound's record's content.
> > Many thanks for any help on how to retrieve information on a compound
> from
> > pccompound.
> >
> > Best wishes
> >
> > Saikari
>
> If you go to the webpage for this,
> http://www.ncbi.nlm.nih.gov/pcassay?term=2244
> then you don't actually get any download links - rather it connects to the
> BioAssay server to retrieve data. My guess is the NCBI don't support
> efetch for the pcassay database - you'll have to email them and ask.
>
> Peter
>