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