[Bioperl-l] Finding all bioactive substances through EUtils or PUG_SOAP
cjfields at illinois.edu
Wed Jul 15 18:37:45 UTC 2009
Posted a modified example of this to the EUtilities cookbook:
On Jul 15, 2009, at 1:11 PM, Chris Fields wrote:
> Tomas B.,
> Just so you know, this isn't really a bioperl-specific question,
> though you may be able to use bioperl tools to do what you want.
> I'll run with the latter assumption.
> I'm not too familiar with pubchem and related, but using einfo you
> can get relevant information on the databases. The available
> databases are:
> Lots of filters available, summarized here:
> My guess is you would have to query the database pcassay with
> esearch and the appropriate filter to find the IDs active for a
> particular assay, then use elink from pcassay to either pccompound
> or pcsubstance to get what you want.
> Using Bio::DB::EUtilities (below) this worked to get the compound
> IDs, you could probably get more information using esummary (not
> sure if you can retrieve all info on them).
> #!/usr/bin/perl -w
> use strict;
> use warnings;
> use Bio::DB::EUtilities;
> my $term = '"Luciferase Profiling Assay"';
> my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
> -db => 'pcassay',
> -term => $term,
> -verbose => 1,
> -retmax => 100);
> my @ids = $factory->get_ids;
> # note the linkname, can use same for pcsubstance
> $factory->reset_parameters(-eutil => 'elink',
> -db => 'pccompound',
> -dbfrom => 'pcassay',
> -linkname => 'pcassay_pccompound_active',
> -id => \@ids);
> On Jul 15, 2009, at 8:40 AM, bar tomas wrote:
>> Could you give me a hint on how to query Entrez databases to find all
>> substances that have been found to be bioactive through a bioassay
>> I've looked at the wsdl file for querying pubchem (*
>> http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl* ) but
>> have found
>> no service for retrieving substance ids.
>> Is there a way to do this with EUtils or a http query with
>> parameters ?
>> Thanks a lot.
>> Tomas B.
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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