NAME

Bio::Biblio - A Bibliographic Query Service module

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.

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 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.

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/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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.

SEE ALSO

• OpenBQS home page: http://industry.ebi.ac.uk/openBQS

• Comments to the Perl client: http://industry.ebi.ac.uk/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 = 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'); 

_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;

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq