[Bioperl-l] [bioperl newbie] Retrieving link to protein from PubChem

saikari keitele saikari78 at gmail.com
Mon Nov 9 11:41:20 EST 2009


Fabulous!. Huge help.
saikari

On Mon, Nov 9, 2009 at 4:27 PM, Chris Fields <cjfields at illinois.edu> wrote:

>  On Nov 9, 2009, at 10:05 AM, saikari keitele wrote:
>
> Hi,
>>
>> I'm using Bioperl to retrieve records from PubChem.
>> I'm trying to find a way-but have been unsuccessful- to retrieve from a
>> compound record, the reference to the protein(s) that can synthesize the
>> compound.
>> Thanks very much.
>>
>> saikari
>>
>
> The below bioperl script returns the GI for proteins that correspond to the
> substance passed on the command line; invoke using 'perl pc_substance.plsubstance_requested'.  It probably needs more fiddling to catch everything
> but it should get you started.
>
> For other bits and pieces (such as how to retrieve the raw sequence files),
> please see the EUtilities HOWTO:
>
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
>
> chris
>
> ----------------------------------------
>
> #!/usr/bin/perl -w
>
> use 5.010;
> use strict;
> use warnings;
> use Bio::DB::EUtilities;
>
> my $substance = shift;
>
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -db => 'pcsubstance',
>                                     -term => $substance,
>                                     -usehistory => 'y');
>
> my $hist = $eutil->next_History || die;
>
> $eutil->reset_parameters(-eutil => 'elink',
>                       -history => $hist,
>                       -db      => 'protein',
>                       -dbfrom  => 'pcsubstance',
>                       -retmax  => 1000);
>
> say join(',',$eutil->get_ids);
>


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