NAME

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

VERSION

version 1.70

SYNOPSIS

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

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

DESCRIPTION

This interface describes the methods for accessing a bibliographic repository, for querying 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://www.ebi.ac.uk/~senger/openbqs/.

ATTRIBUTES

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.

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
  Bio::Biblio->new(-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.

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');

METHODS

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.

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;

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.

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_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_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_by_id

Usage   : my $citation = $biblio->get_by_id ('12368254');
Returns : a citation in an XML format
Args    : a citation identifier (PMID for Medline)

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_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.

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.

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.

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_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_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 $name = 'MEDLINE2005/JournalArticle/properties';
use Data::Dumper;
print Data::Dumper->Dump ( [$biblio->get_all_entries ($name)],
                           ['All entries']);

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/

LEGAL

Authors

Martin Senger <martin.senger@gmail.com>

Copyright and License

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

cpanm Bio::Biblio

perl -MCPAN -e shell
install Bio::Biblio