[Bioperl-l] module for pubchem queries

Chris Fields cjfields at uiuc.edu
Fri Apr 4 17:25:41 EDT 2008


Do you need something to access eutils via BioPerl, or are you looking  
for a specific set of classes?  I wrote an interface to eutils  
(Bio::DB::EUtilities), you could do something like this:

#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::DB::EUtilities;

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                      -term => 'dihydroorotate',
                                      -db => 'pcsubstance',
                                      -retmax => 1000);

print join(',',$eutil->get_ids)."\n";

chris

On Apr 2, 2008, at 7:24 AM, Robert Citek wrote:

> Hello all,
>
> I have a list of chemical compounds that have some kind of interaction
> with proteins or genes.  The current list contains names or SMILES and
> I would like to get the CID number for those compounds.  Currently,
> I'm using perl to query the NCBI's eutils[1], which works great.  But
> I was just curious to know of there was a bioperl module to do
> something similar.  A quick google didn't turn up anything, so I
> thought I'd ask.
>
> [1] http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
>
> Regards,
> - Robert
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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