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 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/.
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.
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;