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

[Chris Fields]

Posted a modified example of this to the EUtilities cookbook:

http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_find_all_active_compounds.2Fsubstances_for_a_particular_bioassay.3F

chris

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:
>
> pcassay
> pccompound
> pcsubstance
>
> Lots of filters available, summarized here:
>
> http://pubchem.ncbi.nlm.nih.gov/help.html#PubChem_index
>
> 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).
>
> chris
>
> ==========================================
> #!/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);
>
> $factory->print_all;
> ==========================================
>
> chris
>
> 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.
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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