[Bioperl-l] Finding all bioactive substances through EUtils or PUG_SOAP

Chris Fields cjfields at illinois.edu
Wed Jul 15 14:11:47 EDT 2009

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:

> Hi,
> 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
> screening.
> 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
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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