[Bioperl-l] NCBI efetch: request limits and getting dates fast

Chris Fields cjfields at illinois.edu
Tue Apr 20 14:57:48 EDT 2010


Not sure about the upper limit with SOAP, but simple ol' EUtilities can take ~250-500 IDs (somewhere in that range) with a direct efetch/esummary/elink, and many many more if you use epost first.  I have been able to fetch a couple thousand with epost.  

As an example, this code works for me:

use Modern::Perl;
use Bio::DB::EUtilities;

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                     -db    => 'protein',
                                     -email => 'cjfields at bioperl.org',
                                     -term  => 'pyrR',
                                     -retmax => 250,
                                     -usehistory => 'y');

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil => 'esummary',
                       -history => $hist);

my %id_map;

while (my $ds = $eutil->next_DocSum) {
    my ($cdate) = $ds->get_contents_by_name('CreateDate');
    $id_map{$ds->get_id} = $cdate;
}

say join("\t", $_, $id_map{$_}) for sort keys %id_map;




On Apr 20, 2010, at 12:22 PM, Dave Messina wrote:

> Hi everyone,
> 
> I've got about 250 NCBI IDs that I'm pulling from NCBI using Bio::DB::SoapEUtilities. It works fine if I send 10 IDs at a time, but much more than that and I get an 'unspecified internal server error'.
> 
> I thought the limit with 500 IDs at a time — anyone have an idea whether that's true?
> 
> 
> And a separate, related question:
> 
> All I really want to get is the last-modified date for these records.
> 
> And it's kinda slow.
> 
> Using some code from the EUtilities_Web_Services HOWTO, I use the seq Fetch adaptor and the add_wanted_slot() Bio::Seq::SeqBuilder trick to get just the annotation part of a RichSeq object, and from there I pull out the dates using
> 
> $seq->annotation->get_Annotations('date_changed')
> 
> 
> Can someone suggest a faster way?
> 
> 
> Thanks,
> Dave
> 
> 
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