BiblioI documentation.

Bio::DB BiblioI

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Summary

Bio::DB::BiblioI - An interface to a Bibliographic Query Service

Package variables

No package variables defined.

Included modules

Bio::Root::RootI

Inherit

Bio::Root::RootI

Synopsis

This is an interface module - you do not instantiate it.
Use Bio::Biblio module:

  use Bio::Biblio;
  my $biblio = new Bio::Biblio (@args);

Description

This interface describes the methods for accessing a bibliographic
repository, for quering it and for retrieving citations from it. The
retrieved citations are in XML format and can be converted to perl
objects using Bio::Biblio::IO.
The interface complies (with some simplifications) with the
specification described in the OpenBQS project. Its home page is at
http://industry.ebi.ac.uk/openBQS

Methods

BEGIN		Code
contains	Description	Code
destroy	Description	Code
exists	Description	Code
find	Description	Code
get_all	Description	Code
get_all_entries	Description	Code
get_all_ids	Description	Code
get_all_values	Description	Code
get_by_id	Description	Code
get_collection_id	Description	Code
get_count	Description	Code
get_entry_description	Description	Code
get_more	Description	Code
get_next	Description	Code
get_vocabulary_names	Description	Code
has_next	Description	Code
reset_retrieval	Description	Code

Methods description

contains

 Usage   : my $yes = $biblio->contains ($vocabulary_name, $value);
 Returns : 1 or undef
 Args    : $vocabulary_name defines a vocabulary where to look,
           and a $value defines what to look for

It returns 1 if the given controlled vocabulary contains the given
value.
For example, when you know, that a vocabulary
MEDLINE/JournalArticle/properties contains value COUNTRY you can
use it in the find method:

    $biblio->find ('United States', 'COUNTRY');

destroy

 Usage   : $biblio->destroy;
 Returns : nothing
 Args    : none

It sends a message to the remote server to forget (or free, or destroy
- whatever server choose to do) the query collection represented by
this object.
It throws an exception if this object does not represent any query
collection.

exists

 Usage   : my $exists = $biblio->exists;
 Returns : 1 or undef
 Args    : none

It returns 1 if the underlying query collection represented by the
$biblio object still exists (on the server side).
If you have a collection ID (e.g. stored or printed in a previous
session) but you do not have anymore a Bio::Biblio object representing
it this is how you can check the collection existence:

    use Bio::Biblio;
    print
      new Bio::Biblio (-collection_id => '1014324148861')->exists;

It throws an exception if this object does not represent any query
result - see explanation in method reset_retrieval elsewhere in
this document.

find

 Usage   : my $new_biblio = $biblio->find ($keywords, $attrs);
           my $new_biblio = $biblio->find ('perl', 'abstract');
           my $new_biblio = $biblio->find ( [ 'perl', 'Java' ] );
 Returns : new Bio::Biblio object representing a new query
           collection
 Args    : $keywords - what to look for (mandatory)
            - a comma-delimited list of keywords, or
            - an array reference with keywords as elements
           $attrs - where to look in (optional)
            - a comma-delimited list of attribute names, or
            - an array reference with attribute names as elements

This is the main query method. It looks for the $keywords in a default
set of attributes, or - if $attrs given - only in the given
attributes.
Because it returns a new Bio::Biblio object which can be again queried
it is possible to chain together several invocations:

    $biblio->find ('Brazma')->find ('Robinson')->get_collection_id;

get_all

 Usage   : my $all = $biblio->get_all;
 Returns : a (big) string with all citations in an XML format
 Args    : none

It returns an XML valid string (which means that individual citations
are also surrounded by a "set" XML tag) representing all citations
from the underlying query collection.
Note that some servers may limit the number of citations which can be
returned by this method. In such case you need either to refine
further your query collection (using find method) or to retrieve
results by iteration (methods has_next, get_next, get_more).
It throws an exception if this object does not represent any query
result - see explanation in method reset_retrieval elsewhere in
this document.

get_all_entries

 Usage   : $biblio->get_all_entries ($vocabulary_name);
 Returns : a hash reference - keys are vocabulary values
           and values are their descriptions
 Args    : $vocabulary_name defines a vocabulary whose entries
           are being returned

It returns pairs of values and their descriptions of the whole
vocabulary. It throws an exception if the vocabulary does not exist.
This is one way how to get it and print it:

    my $name = 'MEDLINE2002/JournalArticle/properties';
    use Data::Dumper;
    print Data::Dumper->Dump ( [$biblio->get_all_entries ($name)],
			       ['All entries']);

get_all_ids

 Usage   : my $r_ids = $biblio->get_all_ids;
 Returns : an array reference - each element has
           a citation identifier
 Args    : none

The identifiers of all citations in the underlying query collection
are returned. A usual pattern is to use them then in the get_by_id
method:

    my $biblio = $repository->find ('brazma')->find ('robinson');
    foreach my $id ( @{ $biblio->get_all_ids } ) {
        print $biblio->get_by_id ($id);
    }

It throws an exception if this object does not represent any query
result - see explanation in method reset_retrieval elsewhere in
this document.

get_all_values

 Usage   : $biblio->get_all_values ($vocabulary_name);
 Returns : an array reference - each element has a value (scalar)
           from the given controlled vocabulary
 Args    : $vocabulary_name defines a vocabulary whose values
           are being returned

It returns all values of the given vocabulary. It throws an exception
if the vocabulary does not exist.

get_by_id

 Usage   : my $citation = $biblio->get_by_id ('94033980');
 Returns : a citation in an XML format
 Args    : a citation identifier
           (e.g. for MEDLINE it is a MedlineID
            - at least for the time being)

It returns a citation - disregarding if the citation is or is not in
the underlying query collection (of course, it must be in the
repository).

get_collection_id

 Usage   : my $collection_id = $biblio->get_collection_id;
 Returns : string identifying a query collection
           represented by the $biblio object
 Args    : none

Every query collection is uniquely identify-able by its collection
ID. The returned value can be used to populate another $biblio object
and then to access that collection.

get_count

 Usage   : my $count = $biblio->get_count;
 Returns : integer
 Args    : none, or a string identifying a query collection

It returns a number of citations in the query collection represented
by the calling $biblio object, or in the collection whose ID is given
as an argument.

get_entry_description

 Usage   : $biblio->get_entry_description ($voc_name, $value);
 Returns : a string with a desciption
 Args    : $voc_name defines a vocabulary where to look,
           and a $value defines whose description to return

Each vocabulary entry has its value (mandatory attribute), and can
have a description (optional attribute). The description may be just a
human readable explanation of an attribute, or it can have more exact
meaning. For example, the server implementation of the bibliographic
query service provided by the EBI puts into attribute descriptions
words queryable and/or retrievable to distinguish the role of
the attributes.
It throws an exception if either vocabulary or value do not exist.

get_more

 Usage   : my $r_citations = $biblio->get_more (5);
 Returns : an array reference - each element has a citation
           in an XML format
 Args    : an integer 'how_many' citations to return;
           default is 1 - but it is assigned with warning

It returns the next how_many available citations from the
underlying query collection. It does not throw any exception if
'how_many' is more than currently available - it simply returns
less. However, it throws an exception if used again without calling
first reset_retrieval.
It also throws an exception if this object does not represent any
query result - see explanation in method reset_retrieval elsewhere
in this document.

get_next

 Usage   : my $citation = $biblio->get_next;
 Returns : a citation in an XML format
 Args    : none

It returns the next available citation from the underlying query
collection. It throws an exception if there are no more citations. In
order to avoid this use it together with the has_next method:

  my $result = $biblio->find ('brazma', 'authors');
  while ( $result->has_next ) {
      print $result->get_next;
  }

It also throws an exception if this object does not represent any
query result - see explanation in the reset_retrieval elsewhere in
this document.

get_vocabulary_names

 Usage   : print join ("\n", @{ $biblio->get_vocabulary_names });
 Returns : an array reference - each element has a name
           of a controlled vocabulary
 Args    : none

The controlled vocabularies allow to introspect bibliographic
repositories and to find what citation resource types (such as journal
and book articles, patents or technical reports) are provided by the
repository, what attributes they have, eventually what attribute
values are allowed.
This method returns names of all available controlled
vocabularies. The names can than be used in other methods dealing with
vocabularies: contains, get_entry_description,
get_all_values, and get_all_entries.

has_next

 Usage   : my $is = $biblio->has_next;
 Returns : 1 or undef
 Args    : none

It returns 1 if there is a next citation available in the underlying
query collection. Otherwise it returns undef.
It throws an exception if this object does not represent any query
result - see explanation in method reset_retrieval elsewhere in
this document.

reset_retrieval

 Usage   : $biblio->reset_retrieval;
 Returns : nothing
 Args    : none

It sets an iterator stored in the $biblio object back to its
beginning. After this, the retrieval methods has_next, get_next
and get_more start to iterate the underlying query collection
again from its start.
It throws an exception if this object does not represent any query
result (e.i. it does not contain a collection ID). Note that a
collection ID is created automatically when this object was returned
by a find method, or it can be assigned in a constructor using
argument -collection_id.

Methods code

BEGIN

BEGIN {

     $VERSION = do { my @r = (q$$Revision: 1.5 $ =~ /\d+/g); sprintf "%d.%-02d", @r };
    $Revision = q$$Id: BiblioI.pm,v 1.5 2002/10/22 07:45:13 lapp Exp $;

}

contains

prev

sub contains {

 shift->throw_not_implemented;

}

destroy

sub destroy {

 shift->throw_not_implemented;

}

exists

sub exists {

 shift->throw_not_implemented;

}

find

sub find {

 shift->throw_not_implemented;

}

get_all

sub get_all {

 shift->throw_not_implemented;

}

get_all_entries

sub get_all_entries {

 shift->throw_not_implemented;

}

get_all_ids

sub get_all_ids {

 shift->throw_not_implemented;

}

get_all_values

sub get_all_values {

 shift->throw_not_implemented;

}

get_by_id

sub get_by_id {

 shift->throw_not_implemented;

}

get_collection_id

sub get_collection_id {

   my ($self,@args) = @_;
   $self->throw_not_implemented();
}


# -----------------------------------------------------------------------------

}

get_count

sub get_count {

 shift->throw_not_implemented();

}

get_entry_description

sub get_entry_description {

 shift->throw_not_implemented;

}

get_more

sub get_more {

 shift->throw_not_implemented;

}

get_next

sub get_next {

 shift->throw_not_implemented;

}

get_vocabulary_names

sub get_vocabulary_names {

 shift->throw_not_implemented;

}

has_next

sub has_next {

 shift->throw_not_implemented;

}

reset_retrieval

next

sub reset_retrieval {

 shift->throw_not_implemented;

}

General documentation

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://bugzilla.bioperl.org/

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.

APPENDIX

This is actually the main documentation...
If you try to call any of these methods directly on this
Bio::DB::BiblioI object you will get a not implemented error
message. You need to call them on a Bio::Biblio object.

VERSION and Revision

 Usage   : print $Bio::DB::BiblioI::VERSION;
           print $Bio::DB::BiblioI::Revision;