Bio::DB::Biblio::biofetch(3) A BioFetch-based access to a bibliographic


Do not use this object directly, only access it through the Bio::Biblio module:

use Bio::Biblio;
my $biblio = Bio::Biblio->new(-access => 'biofetch');
my $ref = $biblio->get_by_id('20063307'));
my $ids = ['20063307', '98276153'];
my $refio = $biblio->get_all($ids);
while ($ref = $refio->next_bibref) {
print $ref->identifier, "\n";


This class uses BioFetch protocol based service to retrieve Medline references by their ID.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

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Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:


Heikki Lehvaslaiho (heikki-at-bioperl-dot-org)


Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.


This software is provided ``as is'' without warranty of any kind.


  • Only method get_by_id() is supported.


The main documentation details are to be found in Bio::DB::BiblioI.

Here is the rest of the object methods. Internal methods are preceded with an underscore _.


 Title   : get_by_id
 Usage   : $entry = $db->get__by_id('20063307')
 Function: Gets a Bio::Biblio::RefI object by its name
 Returns : a Bio::Biblio::Medline object
 Args    : the id (as a string) of the reference


  Title   : get_all
  Usage   : $seq = $db->get_all($ref);
  Function: Retrieves reference objects from the server 'en masse', 
            rather than one  at a time.  For large numbers of sequences, 
            this is far superior than get_by_id().
  Example :
  Returns : a stream of Bio::Biblio::Medline objects
  Args    : $ref : either an array reference, a filename, or a filehandle
            from which to get the list of unique ids/accession numbers.


 Title   : get_seq_stream
 Usage   : my $seqio = $self->get_seq_stream(%qualifiers)
 Function: builds a url and queries a web db
 Returns : a Bio::SeqIO stream capable of producing sequence
 Args    : %qualifiers = a hash qualifiers that the implementing class 
           will process to make a url suitable for web querying


 Title   : postprocess_data
 Usage   : $self->postprocess_data ( 'type' => 'string',
                                     'location' => \$datastr);
 Function: process downloaded data before loading into a Bio::SeqIO
 Returns : void
 Args    : hash with two keys - 'type' can be 'string' or 'file'
                              - 'location' either file location or string 
                                           reference containing data

VERSION and Revision

 Usage   : print $Bio::DB::Biblio::biofetch::VERSION;
           print $Bio::DB::Biblio::biofetch::Revision;


 Usage   : print $Bio::DB::Biblio::biofetch::DEFAULT_SERVICE;