biblio::citation::parser::citebase(3pm) [debian man page]

Biblio::Citation::Parser::Citebase(3pm) 		User Contributed Perl Documentation		   Biblio::Citation::Parser::Citebase(3pm)

NAME

       Biblio::Citation::Parser::Citebase - Citebase's citation parsing module

DESCRIPTION

       This module is an updated (and hopefully improved) version of Zhuoan Jiao's citation-parsing modules.

SYNOPSIS

	       use Biblio::Citation::Parser::Citebase;
	       $parser = new Biblio::Citation::Parser::Citebase([$source_identifier]);
	       $metadata = $parser->parse($citation);
	       print "Author: ", $metadata->{aufirst}, " ", $metadata->{aulast}, "
";

       $p = new Biblio::Citation::Parser::Citebase([$citation],[$source_identifier]);
	   Create a new citation parser, optionally parsing $citation with $source_identifier. If a citation is given the return blessed hash will
	   contain the structured data.

       $md = $p->parse($citation, [$source_identifier]);
	   Parses a string, $citation, and returns a blessed hash of the structured data.

perl v5.10.1							    2009-11-15				   Biblio::Citation::Parser::Citebase(3pm)

Bio::Biblio::IO(3pm)					User Contributed Perl Documentation				      Bio::Biblio::IO(3pm)

NAME

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

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'} . "
";
	   }

	 #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".

SEE ALSO

       o   An example script examples/biblio.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).

       o   OpenBQS home page: http://www.ebi.ac.uk/~senger/openbqs

       o   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 one of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR

       Martin Senger (senger@ebi.ac.uk)

COPYRIGHT

       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.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are preceded with a _

   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

   _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).

perl v5.14.2							    2012-03-02						      Bio::Biblio::IO(3pm)