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