Bio::DB::BiblioI(3)

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

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 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://www.ebi.ac.uk/~senger/openbqs/.

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.

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.

  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.

  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.

  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.

  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.

  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.

  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');

  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']);

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