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

NAME
       Bio::Biblio - A Bibliographic Query Service module

SYNOPSIS
	 use Bio::Biblio;
	 my $biblio = Bio::Biblio->new();

	 print $biblio->find ('perl')->get_count . "\n";

	 my $collection = $biblio->find ('brazma', 'authors');
	 while ( $collection->has_next ) {
	     print $collection->get_next;
	 }

	 # The new() method can accept parameters, for example:

	 $biblio = Bio::Biblio->new
	   (-access	     => 'soap',
	    -location	     => 'http://www.ebi.ac.uk/openbqs/services/MedlineSRS',
	    -destroy_on_exit => '0');

	 # See below for some one-liners

DESCRIPTION
       This is a class whose instances can access bibliographic repositories.
       It allows to query a bibliographic database (such as MEDLINE) and then
       to retrieve resulting citations from it. The citations are returned in
       an XML format which is native to the repository but there are also
       supporting modules for converting them into Perl objects.

       The detailed descriptions of all query and retrieval methods are in
       Bio::DB::BiblioI (an interface). All those methods should be called on
       instances of this (Bio::Biblio) module.

       The module complies (with some simplifications) with the specification
       described in the OpenBQS project. Its home page is at
       <http://www.ebi.ac.uk/~senger/openbqs>.

       The module also gives an access to a set of controlled vocabularies and
       their values. It allows to introspect bibliographic repositories and to
       find what citation resource types (such as journal and book articles,
       patents or technical reports) are provided, and what attributes they
       have, eventually what attribute values are allowed.

       Here are some one-liners:

	 perl -MBio::Biblio -e 'print new Bio::Biblio->get_by_id ("12368254")'
	 perl -MBio::Biblio \
	      -e 'print join ("\n", @{ Bio::Biblio->new->find ("brazma")->get_all_ids })'
	 perl -MBio::Biblio \
	      -e 'print Bio::Biblio->new->find ("Java")->find ("perl")->get_count'

OVERVIEW OF CLASSES AND PACKAGES
       Bio::Biblio
	   This is the main class to be used by the end users. It loads a real
	   implementation for a particular access protocol according to the
	   argument -access. At the time of writing this documentation there
	   is only one available access module implementing all query and
	   retrieval methods:

	      -access => soap

	   This module implements all methods defined in the interface
	   Bio::DB::BiblioI (see Bio::DB::BiblioI) by delegating calls to a
	   loaded low-level module (e.g. see Bio::DB::Biblio::soap).

	   Note that there are other modules which do not use the SOAP
	   protocol and do not implement all query methods - nevertheless they
	   have retrieval methods and can be used in the same way:

	      -access => biofetch

	   Lacking documentation:

	      -access => eutils

       Bio::DB::BiblioI
	   This is an interface defining all methods that can be called on
	   Bio::Biblio instances.

       Bio::DB::Biblio::soap
	   This is a real implementation of all methods defined in
	   Bio::DB::BiblioI using SOAP protocol (calling a WebService based on
	   SOAP). This class should not be instantiated directly (use
	   Bio::Biblio instead). See Bio::DB::BiblioI for details.

       Bio::Biblio::IO
	   This module instantiates and uses a converter of the citations read
	   by any of the access methods mentioned above. See Bio::Biblio::IO
	   for details.

       Bio::Biblio::IO::medlinexml and Bio::Biblio::IO::medline2ref
	   A converter of MEDLINE citations in XML into Perl objects.

       Bio::Biblio::IO::pubmedxml and Bio::Biblio::IO::pubmed2ref
	   A converter of PUBMED citations in XML into Perl objects.

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:

	 http://bugzilla.open-bio.org/

AUTHOR
       Martin Senger (martin.senger@gmail.com)

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.

SEE ALSO
       ·   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

APPENDIX
       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 _.

   new
	Usage	: my $obj = Bio::Biblio->new(@args);
	Returns : Bio::Biblio object on success, or undef on failure
	Args	: This module recognizes and uses:

		    -access => 'soap'
		      It indicates what lower-level module to load.
		      Default is 'soap'.

		    -location => 'http://...'
		       It says where to find a bibliographic query service.
		       The format and contents of this argument is dependent
		       on the '-access' argument.

		       For 'soap' access it is a URL of a WebService.
		       Default is http://www.ebi.ac.uk/openbqs/services/MedlineSRS

		  Other arguments can be given here but they are
		  recognized by the lower-level module
		  (e.g. see Bio::DB::Biblio::soap).

       It builds, populates and returns a new Bio::Biblio object. This is how
       it is seen from the outside. But in fact, it builds, populates and
       returns a more specific lower-level object, for example
       Bio::DB::Biblio::soap object - which one it is depends on the parameter
       -access.

       The real initialization is done in the method _initialize of the lower-
       level object.

       This method can also be used for cloning an existing object and
       changing or adding new attributes to it in the same time. This is,
       however, not particulary useful for the casual users of this module,
       because the query methods (see Bio::DB::BiblioI) themselves already
       return cloned objects with more refined query collections. Anyway this
       is how the cloning can be done:

	 use Bio::Biblio;
	 my $biblio = Bio::Biblio->new();

	 # this will create a new object which will NOT send a 'destroy'
	 # message to the remote server when its life ends
	 my $clone = $biblio->new (-destroy-on-exit => '0');

   _load_access_module
	Usage	: $class->_load_access_module ($access)
	Returns : 1 on success, undef on failure
	Args	: 'access' 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::DB::Biblio::$access

       It prints an error on STDERR if it fails to find and load the module
       (for example, because of the compilation errors in the module).

   _guess_access
	Usage	: $class->_guess_access ($location)
	Returns : string with a guessed access protocol (e.g. 'soap')
	Args	: 'location' defines where to find a bibliographic service
		  in a protocol-dependent manner (e.g. for SOAP it is
		  a URL of a bibliographic WebService)

       It makes an expert guess what kind of access/transport protocol should
       be used based on the location of the service (e.g. if the location
       looks like an IOR then the access protocol is probably CORBA).

   VERSION and Revision
	Usage	: print $Bio::Biblio::VERSION;
		  print $Bio::Biblio::Revision;

perl v5.14.1			  2011-07-22			Bio::Biblio(3)
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