Bio::DB::Biblio::soap - a SOAP-based access to a bibliographic query service


version 1.70


Do not use this object directly, it is recommended to access it and use it through the Bio::Biblio module:

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


This object contains the real implementation of a Bibliographic Query Service as defined in Bio::DB::BiblioI - using a SOAP protocol to access a WebService (a remote server) that represents a bibliographic repository.

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



 Usage   : print $Bio::DB::Biblio::soap::DEFAULT_SERVICE;
           print $Bio::DB::Biblio::soap::DEFAULT_NAMESPACE;



 Usage   : my $obj = Bio::Biblio->new(-access => 'soap' ...);
           (_initialize is internally called from this constructor)
 Returns : nothing interesting
 Args    : This module recognises and uses following arguments:

             -namespace => 'urn'
               The namespace used by the WebService that is being
               accessed. It is a string which guarantees its world-wide
               uniqueness - therefore it often has a style of a URL -
               but it does not mean that such pseudo-URL really exists.

               ## TODO: This namespace is no longer valid (check for deprecation
               ## or update)

               Default is ''.

             -destroy_on_exit => '0'
                Default value is '1' which means that all Bio::Biblio
                objects - when being finalised - will send a request
                to the remote WebService to forget the query collections
                they represent.

                If you change it to '0' make sure that you know the
                query collection identification - otherwise you will
                not be able to re-established connection with it.
                This can be done by calling method get_collection_id.

              -collection_id => '...'
                It defines what query collection will this object work
                with. Use this argument when you know a collection ID
                of an existing query collection and when you wish to
                re-established connection with it.

                By default, the collection IDs are set automatically
                by the query methods - they return Bio::Biblio objects
                already having a collection ID.

                A missing or undefined collection ID means that the
                object represents the whole bibliographic repository
                (which again means that some methods, like get_all,
                will be probably refused).

              -soap => a SOAP::Lite object
                Usually all Bio::Biblio objects share an instance of
                the underlying SOAP::Lite module. But you are free
                to have more - perhaps with different characteristics.

                See the code for attributes of the default SOAP::Lite

              -httpproxy => 'http://server:port'
                 In addition to the 'location' parameter, you may need
                 to specify also a location/URL of a HTTP proxy server
                 (if your site requires one).

           Additionally, the main module Bio::Biblio recognises
              -access => '...'
              -location => '...'

It populates calling object with the given arguments, and then - for some attributes and only if they are not yet populated - it assigns some default values.

This is an actual new() method (except for the real object creation and its blessing which is done in the parent class Bio::Root::Root in method _create_object).

Note that this method is called always as an object method (never as a class method) - and that the object who calls this method may already be partly initiated (from Bio::Biblio::new method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Biblio::new method, not this one.


    * Methods returning a boolean value (has_next, exists and contains) can be used only with SOAP::Lite version 0.52 and newer (probably due to a bug in the older SOAP::Lite). * It does not use WSDL. * More testing and debugging needed to ensure that returned citations are properly transferred even if they contain foreign characters.


Mailing lists

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Please direct usage questions or support issues to the mailing list:

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:



Martin Senger <>

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