Bio Biblio
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Summary
Bio::Biblio - A Bibliographic Query Service module
Package variables
No package variables defined.
Included modules
Bio::DB::BiblioI
Bio::Root::Root
Inherit
Bio::DB::BiblioI Bio::Root::Root
Synopsis
  use Bio::Biblio;
  my $biblio = new Bio::Biblio;

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

  my $collection = $biblio->find ('brazma', 'authors');
  while ( $collection->has_next ) {
      print $collection->get_next;
  }
Here are some one-liners:
  perl -MBio::Biblio -e 'print new Bio::Biblio->get_by_id ("94033980")' 
  perl -MBio::Biblio \
       -e 'print join ("\n", @{ new Bio::Biblio->find ("brazma")->get_all_ids })' 
  perl -MBio::Biblio \
       -e 'print new Bio::Biblio->find ("Java")->find ("perl")->get_count'
The new method can get parameters, for example:
  my $biblio = Bio::Biblio 
    (-access          => 'soap',
     -location        => 'http://industry.ebi.ac.uk/soap/openBQS',
     -destroy_on_exit => '0');
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://industry.ebi.ac.uk/openBQS. There are also links to
available servers providing access to the bibliographic repositories
(namely to MEDLINE).
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.
Methods
BEGIN Code
_guess_accessDescriptionCode
_load_access_moduleDescriptionCode
newDescriptionCode
Methods description
_guess_accesscode    nextTop
 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).
_load_access_modulecodeprevnextTop
 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).
newcodeprevnextTop
 Usage   : my $obj = new Bio::Biblio (@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://industry.ebi.ac.uk/soap/openBQS

           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 = new Bio::Biblio;

  # 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');
Methods code
BEGINTop
BEGIN {
     $VERSION = do { my @r = (q$$Revision: 1.7 $ =~ /\d+/g); sprintf "%d.%-02d", @r };
    $Revision = q$$Id: Biblio.pm,v 1.7 2002/10/22 07:45:09 lapp Exp $;
}
_guess_accessdescriptionprevnextTop
sub _guess_access {
#   my ($class, $location) = @_;
   return 'soap';
}
_load_access_moduledescriptionprevnextTop
sub _load_access_module {
  my ($access) = @_;
  my ($module, $load, $m);

  $module = "_<Bio/DB/Biblio/$access.pm";
  $load = "Bio/DB/Biblio/$access.pm";

  return 1 if $main::{$module};
  eval {
    require $load;
  };

  if ( $@ ) {
    Bio::Root::Root->throw (<<END);
$load: $access cannot be found or loaded
Exception $@
For more information about the Biblio system please see the Bio::Biblio docs.
END
  ;
    return;
  }
  return 1;
}

# -----------------------------------------------------------------------------
}
newdescriptionprevnextTop
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;
  
    # if $caller is an object, or if it is an underlying
    # 'real-work-doing' class (e.g. Bio::DB::Biblio::soap) then
    # we want to call SUPER to create and bless an object

    if ($class =~ /Bio::DB::Biblio::(\S+)/) {
	my ($self) = $class->SUPER::new (@args);

	# now the $self is an empty object - we will populate it from
	# the $caller - if $caller is an object

	if (ref ($caller)) {
	    %{ $self } = %{ $caller };
	}

	# and finally add values from '@args' into the newly created
	# object (the values will overwrite the values copied above)

	$self->_initialize (@args);
	return $self;

    # this is called only the first time when somebody calls: 'new
    # Bio::Biblio (...)', and it actually loads a 'real-work-doing'
    # module and call this new() method again (unless the loaded
    # module has its own new() method)

    } else { 
	my %param = @args;
	@param { map { lc $_ } keys %param } = values %param; # lowercase keys
	my $access =
	    $param {'-access'} || 
	    $class->_guess_access ( $param {'-location'} ) ||
	    'soap';
	$access = "\L$access";	# normalize capitalization to lower case

	# load module with the real implementation - as defined in $access
	return undef unless (&_load_access_module ($access));

	# this will call this same method new() - but rather its the
	# upper (object) branche
	return "Bio::DB::Biblio::$access"->new (@args);
    }
}

# -----------------------------------------------------------------------------
}
General documentation
OVERVIEW OF CLASSES AND PACKAGESTop
    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 is also another module (and perhaps more) which does
not use SOAP protocol and do not implement all query methods -
nevertheless it has retrieval methods and it can be used in the same
way:
   -access => biofetch
    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.
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml  - About the mailing lists
Reporting BugsTop
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHORTop
Martin Senger (senger@ebi.ac.uk)
COPYRIGHTTop
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.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
SEE ALSOTop
    *(1)
    OpenBQS home page: http://industry.ebi.ac.uk/openBQS
    *(2)
    Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
APPENDIXTop
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 _.
VERSION and RevisionTop
 Usage   : print $Bio::Biblio::VERSION;
           print $Bio::Biblio::Revision;