/ 
Bio-Biblio-1.70
River stage zero No dependents
/ Bio::Biblio::IO

NAME

Bio::Biblio::IO - Handling the bibliographic references

VERSION

version 1.70

SYNOPSIS

  use Bio::Biblio::IO;

  # getting citations from a file
  $in = Bio::Biblio::IO->new ('-file' => 'myfile.xml' ,
                              '-format' => 'medlinexml');
# --- OR ---

  # getting citations from a string
  $in = Bio::Biblio::IO->new ('-data' => '<MedlineCitation>...</MedlineCitation>' ,
                              '-format' => 'medlinexml');
#--- OR ---

  # getting citations from a string if IO::String is installed
  use IO::String;
  $in = Bio::Biblio::IO->new ('-fh' => IO::String->new ($citation),
                              '-format' => 'medlinexml');

  $in = Bio::Biblio::IO->new(-fh => $io_handle , '-format' => 'medlinexml');

#--- OR ---

  # getting citations from any IO handler
  $in = Bio::Biblio::IO->new('-fh' => $io_handle ,
                             '-format' => 'medlinexml');


  # now, having $in, we can read all citations
  while ( my $citation = $in->next_bibref() ) {
      &do_something_with_citation ($citation);
  }

#--- OR ---

  # again reading all citation but now a callback defined in your
  # code is used (note that the reading starts already when new()
  # is called)
  $io = Bio::Biblio::IO->new('-format'   => 'medlinexml',
                             '-file'     => $testfile,
                             '-callback' => \&callback);
  sub callback {
      my $citation = shift;
      print $citation->{'_identifier'} . "\n";
  }

#Now, to actually get a citation in an XML format,
#use I<Bio::Biblio> module which returns an XML string:

  use Bio::Biblio;
  use Bio::Biblio::IO;
  my $xml = Bio::Biblio->new->get_by_id ('12368254');
  my $reader = Bio::Biblio::IO->new ('-data' => $xml,
                                     '-format' => 'medlinexml');

  while (my $citation = $reader->next_bibref()) {
     #... do something here with $citation
     }

#And, finally, the resulting citation can be received in different
#output formats:

  $io = Bio::Biblio::IO->new('-format' => 'medlinexml',
                             '-result' => 'raw');
#--- OR ---

  $io = Bio::Biblio::IO->new('-format' => 'medlinexml',
                             '-result' => 'medline2ref');

#--- OR ---

  $io = Bio::Biblio::IO->new('-format' => 'pubmedxml',
                             '-result' => 'pubmed2ref');

DESCRIPTION

Bio::Biblio::IO is a handler module for accessing bibliographic citations. The citations can be in different formats - assuming that there is a corresponding module knowing that format in Bio::Biblio::IO directory (e.g. Bio::Biblio::IO::medlinexml). The format (and the module name) is given by the argument -format.

Once an instance of Bio::Biblio::IO class is available, the citations can be read by calling repeatedly method next_bibref:

while (my $citation = $reader->next_bibref()) {
   ... do something here with $citation
   }

However, this may imply that all citations were already read into the memory. If you expect a huge amount of citations to be read, you may choose a callback option. Your subroutine is specified in the new() method and is called everytime a new citation is available (see an example above in SYNOPSIS).

The citations returned by next_bibref or given to your callback routine can be of different formats depending on the argument -result. One result type is raw and it is represented by a simple, not blessed hash table:

$io = Bio::Biblio::IO->new('-result' => 'raw');

What other result formats are available depends on the module who reads the citations in the first place. At the moment, the following ones are available:

$io = Bio::Biblio::IO->new('-result' => 'medline2ref');

This is a default result format for reading citations by the medlinexml module. The medlinexml module is again the default one. Which means that you can almost omit arguments (you still need to say where the citations come from):

$io = Bio::Biblio::IO->new('-file' => 'data/medline_data.xml');

Another result format available is for PUBMED citations (which is a super-set of the MEDLINE citations having few more tags):

$io = Bio::Biblio::IO->new('-format' => 'pubmedxml',
                           '-result' => 'pubmed2ref',
                           '-data'   => $citation);

Or, because pubmed2ref is a default one for PUBMED citations, you can say just:

$io = Bio::Biblio::IO->new('-format' => 'pubmedxml',
                           '-data'   => $citation);

Both medline2ref and pubmed2ref results are objects defined in the directory Bio::Biblio.

ATTRIBUTES

fh

METHODS

new

newFh

next_bibref

Usage   : $citation = stream->next_bibref
Function: Reads the next citation object from the stream and returns it.
Returns : a Bio::Biblio::Ref citation object, or something else
          (depending on the '-result' argument given in the 'new()'
          method).
Args    : none

DESTROY

TIEHANDLE

READLINE

INTERNAL METHODS

_initialize

_load_format_module

Usage   : $class->_load_format_module ($format)
Returns : 1 on success, undef on failure
Args    : 'format' should contain the last part of the
          name of a module who does the real implementation

It does (in run-time) a similar thing as

require Bio::Biblio::IO::$format

It throws an exception if it fails to find and load the module (for example, because of the compilation errors in the module).

_guess_format

Usage   : $class->_guess_format ($filename)
Returns : string with a guessed format of the input data (e.g. 'medlinexml')
Args    : a file name whose extension can help to guess its format

It makes an expert guess what kind of data are in the given file (but be prepare that $filename may be empty).

SEE ALSO

  • An example script eg/biblio-soap.pl

    It has many options and its own help. The relevant options to this IO module are -f (specifying what file to read) and -O (specifying what result format to achieve).

  • OpenBQS home page

    http://www.ebi.ac.uk/~senger/openbqs/

  • Comments to the Perl client

    http://www.ebi.ac.uk/~senger/openbqs/Client_perl.html

FEEDBACK

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org

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:

https://redmine.open-bio.org/projects/bioperl/

LEGAL

Authors

Martin Senger <senger@ebi.ac.uk>

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