[Biopython] Entrez.efetch problem when querying pccompound database

[saikari keitele]

Many thanks! By using esummary as you suggest I can retrieve all the
information from pccompound and pcassay with BioPython.
For instance, for retrieving the molecular weight of a compound given its
InChIKey :


handle=Entrez.esearch(db="pccompound",
term='"BSYNRYMUTXBXSQ-UHFFFAOYSA-N"[InChIKey]')

records = Entrez.read(handle)

molWeight = Entrez.read(Entrez.esummary(db="pccompound",
id=records["IdList"][0]))[0]['MolecularWeight']

Thanks again.

On Mon, Nov 1, 2010 at 2:50 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Try using esummary instead of efetch to get that information
> programmatically.  Some database information can't be retrieved via efetch
> (I think pcassay/pccomopund are two of those), but the summary of the
> information for any database is retrievable.
>
> Using the BioPerl eutil interface, one does this to just dump the returned
> information.  One can also get at the various bits of that data
> programmatically as well using generic constructs, but you have to know the
> tag names for the data you are looking for.  There should be an analogous
> Biopython way to do this.
>
> ===================================
>
> use Bio::DB::EUtilities;
>
> my $term = '"BSYNRYMUTXBXSQ-UHFFFAOYSA-N"[InChIKey]';
>
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -term  => $term,
>                                     -email => 'cjfields at bioperl.org',
>                                     -db    => 'pccompound',
>                                     -usehistory => 'y');
>
> my $hist = $eutil->next_History || die "Can't retrieve history data";
>
> $eutil->set_parameters(-eutil     => 'esummary',
>                         -history   => $hist);
>
> $eutil->print_all;
>
> ===================================
>
> chris
>
> On Nov 1, 2010, at 6:24 AM, saikari keitele wrote:
>
> > 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
> >>
> > _______________________________________________
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>
>