#
# BioPerl module for Bio::Ontology::OntologyI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2003.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::OntologyI - Interface for an ontology implementation
=head1 SYNOPSIS
# see method documentation
=head1 DESCRIPTION
This describes the minimal interface an ontology implementation must
provide. In essence, it represents a namespace with description on top
of the query interface OntologyEngineI.
This interface inherits from L<Bio::Ontology::OntologyEngineI>.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Ontology::OntologyI;
use strict;
use base qw(Bio::Ontology::OntologyEngineI);
=head1 Methods defined in this interface.
=cut
=head2 name
Title : name
Usage : $obj->name($newval)
Function: Get/set the name of this ontology.
Example :
Returns : value of name (a scalar)
Args :
=cut
sub name{
shift->throw_not_implemented();
}
=head2 authority
Title : authority
Usage : $auth = $obj->authority()
Function: Get/set the authority for this ontology, for instance the
DNS base for the organization granting the name of the
ontology and identifiers for the terms.
This attribute is optional and should not generally
expected by applications to have been set. It is here to
follow the rules for namespaces, which ontologies serve as
for terms.
Example :
Returns : value of authority (a scalar)
Args :
=cut
sub authority{
shift->throw_not_implemented();
}
=head2 identifier
Title : identifier
Usage : $id = $obj->identifier()
Function: Get an identifier for this ontology.
This is primarily intended for look-up purposes. Clients
should not expect the value to be modifiable, and it may
not be allowed to set its value from outside. Also, the
identifier's uniqueness may only hold within the scope of a
particular application's run time, i.e., it may be a memory
location.
Example :
Returns : value of identifier (a scalar)
Args :
=cut
sub identifier{
shift->throw_not_implemented();
}
=head2 definition
Title : definition
Usage : $def = $obj->definition()
Function: Get a descriptive definition for this ontology.
Example :
Returns : value of definition (a scalar)
Args :
=cut
sub definition{
shift->throw_not_implemented();
}
=head2 close
Title : close
Usage :
Function: Release any resources this ontology may occupy. In order
to efficiently release used memory or file handles, you
should call this method once you are finished with an
ontology.
Example :
Returns : TRUE on success and FALSE otherwise
Args : none
=cut
sub close{
shift->throw_not_implemented();
}
=head1 Methods inherited from L<Bio::Ontology::OntologyEngineI>
Their documentations are copied here for completeness. In most use
cases, you will want to access the query methods of an ontology, not
just the name and description ...
=cut
=head2 add_term
Title : add_term
Usage : add_term(TermI term): TermI
Function: Adds TermI object to the ontology engine term store.
For ease of use, if the ontology property of the term
object was not set, an implementation is encouraged to set
it to itself upon adding the term.
Example : $oe->add_term($term)
Returns : its argument.
Args : object of class TermI.
=cut
=head2 add_relationship
Title : add_relationship
Usage : add_relationship(RelationshipI relationship): RelationshipI
Function: Adds a relationship object to the ontology engine.
Example :
Returns : Its argument.
Args : A RelationshipI object.
=cut
=head2 get_relationships
Title : get_relationships
Usage : get_relationships(TermI term): RelationshipI
Function: Retrieves all relationship objects from this ontology engine,
or all relationships of a term if a term is supplied.
Example :
Returns : Array of Bio::Ontology::RelationshipI objects
Args : None, or a Bio::Ontology::TermI compliant object for which
to retrieve the relationships.
=cut
=head2 get_predicate_terms
Title : get_predicate_terms
Usage : get_predicate_terms(): TermI[]
Function:
Example :
Returns :
Args :
=cut
=head2 get_child_terms
Title : get_child_terms
Usage : get_child_terms(TermI term, TermI predicate_terms): TermI
Function: Retrieves all child terms of a given term, that satisfy a
relationship among those that are specified in the second
argument or undef otherwise. get_child_terms is a special
case of get_descendant_terms, limiting the search to the
direct descendants.
Example :
Returns : Array of TermI objects.
Args : First argument is the term of interest, second is the list
of relationship type terms.
=cut
=head2 get_descendant_terms
Title : get_descendant_terms
Usage : get_descendant_terms(TermI term, TermI rel_types): TermI
Function: Retrieves all descendant terms of a given term, that
satisfy a relationship among those that are specified in
the second argument or undef otherwise.
Example :
Returns : Array of TermI objects.
Args : First argument is the term of interest, second is the list
of relationship type terms.
=cut
=head2 get_parent_terms
Title : get_parent_terms
Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI
Function: Retrieves all parent terms of a given term, that satisfy a
relationship among those that are specified in the second
argument or undef otherwise. get_parent_terms is a special
case of get_ancestor_terms, limiting the search to the
direct ancestors.
Example :
Returns : Array of TermI objects.
Args : First argument is the term of interest, second is the list
of relationship type terms.
=cut
=head2 get_ancestor_terms
Title : get_ancestor_terms
Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI
Function: Retrieves all ancestor terms of a given term, that satisfy
a relationship among those that are specified in the second
argument or undef otherwise.
Example :
Returns : Array of TermI objects.
Args : First argument is the term of interest, second is the list
of relationship type terms.
=cut
=head2 get_leaf_terms
Title : get_leaf_terms
Usage : get_leaf_terms(): TermI
Function: Retrieves all leaf terms from the ontology. Leaf term is a
term w/o descendants.
Example : @leaf_terms = $obj->get_leaf_terms()
Returns : Array of TermI objects.
Args :
=cut
=head2 get_root_terms()
Title : get_root_terms
Usage : get_root_terms(): TermI
Function: Retrieves all root terms from the ontology. Root term is a
term w/o descendants.
Example : @root_terms = $obj->get_root_terms()
Returns : Array of TermI objects.
Args :
=cut
=head2 get_all_terms
Title : get_all_terms
Usage : get_all_terms: TermI
Function: Retrieves all terms from the ontology.
We do not mandate an order here in which the terms are
returned. In fact, the default implementation will return
them in unpredictable order.
Example : @terms = $obj->get_all_terms()
Returns : Array of TermI objects.
Args :
=cut
=head2 find_terms
Title : find_terms
Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263");
Function: Find term instances matching queries for their attributes.
An implementation may not support querying for arbitrary
attributes, but can generally be expected to accept
-identifier and -name as queries. If both are provided,
they are implicitly intersected.
Example :
Returns : an array of zero or more Bio::Ontology::TermI objects
Args : Named parameters. The following parameters should be recognized
by any implementation:
-identifier query by the given identifier
-name query by the given name
=cut
=head1 Factory for relationships and terms
=cut
=head2 relationship_factory
Title : relationship_factory
Usage : $fact = $obj->relationship_factory()
Function: Get (and set, if the implementation supports it) the object
factory to be used when relationship objects are created by
the implementation on-the-fly.
Example :
Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI
compliant object)
Args :
=cut
sub relationship_factory{
return shift->throw_not_implemented();
}
=head2 term_factory
Title : term_factory
Usage : $fact = $obj->term_factory()
Function: Get (and set, if the implementation supports it) the object
factory to be used when term objects are created by
the implementation on-the-fly.
Example :
Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
compliant object)
Args :
=cut
sub term_factory{
return shift->throw_not_implemented();
}
1;