[Biopython] Entrez.efetch problem when querying pccompound database

[Peter]

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