[Bioperl-l] [bioperl newbie] Retrieving link to protein from PubChem
saikari78 at gmail.com
Tue Nov 10 06:41:11 EST 2009
Thanks again very much for your help and the script.
i've been trying it, however I fail to find any protein record linked to a
record in the pcsubstance database.
Do you think that its is because no links have been defined between the 2
databases, or that I am just unlucky and that no link exists for the
particular records I'm testing?
On Mon, Nov 9, 2009 at 4:41 PM, saikari keitele <saikari78 at gmail.com> wrote:
> Fabulous!. Huge help.
> 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:
>>> 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
>>> Thanks very much.
>> The below bioperl script returns the GI for proteins that correspond to
>> the substance passed on the command line; invoke using 'perl
>> pc_substance.pl substance_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:
>> #!/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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