Bio::DB::Biblio::biofetch - a BioFetch-based access to a bibliographic citation retrieval


version 1.70


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.

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



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



 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


    * Only method get_by_id() is supported


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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 <>

This software is Copyright (c) by 2002 European Bioinformatics Institute and released under the license of the same terms as the perl 5 programming language system itself