#
# BioPerl module for OntologyEngineI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Peter Dimitrov <dimitrov@gnf.org>
#
# (c) Peter Dimitrov
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# 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.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy
=head1 SYNOPSIS
# see documentation of methods
=head1 DESCRIPTION
This describes the minimal interface an ontology query engine should
provide. It intentionally does not make explicit references to the
ontology being a DAG, nor does it mandate that the ontology be a
vocabulary. Rather, it tries to generically express what should be
accessible (queriable) about an ontology.
The idea is to allow for different implementations for different
purposes, which may then differ as to which operations are efficient
and which are not, and how much richer the functionality is on top of
this minimalistic set of methods. Check modules in the Bio::Ontology
namespace to find out which implementations exist. At the time of
writing, there is a SimpleOntologyEngine (which does not use
Graph.pm), and a Graph.pm-based implementation in SimpleGOEngine.
Ontology parsers in Bio::OntologyIO are required to return an
implementation of this interface.
=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
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Peter Dimitrov
Email dimitrov@gnf.org
=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::OntologyEngineI;
use strict;
use Carp;
use base qw(Bio::Root::RootI);
=head2 add_term
Title : add_term
Usage : add_term(TermI term): TermI
Function: Adds TermI object to the ontology engine term store
Example : $oe->add_term($term)
Returns : its argument.
Args : object of class TermI.
=cut
sub add_term{
shift->throw_not_implemented();
}
=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
sub add_relationship{
shift->throw_not_implemented();
}
=head2 add_relationship_type
Title : add_relationship_type
Usage : add_relationship_type(scalar,OntologyI ontology)
Function: Adds a relationshiptype object to the ontology engine.
Example :
Returns : 1 on success, undef on failure
Args : The name(scalar) of the relationshiptype, and the OntologyI
it is to be added to.
=cut
sub add_relationship_type{
shift->throw_not_implemented();
}
=head2 get_relationship_type
Title : get_relationship_type
Usage : get_relationship_type(scalar): RelationshipTypeI
Function: Get a relationshiptype object from the ontology engine.
Example :
Returns : A RelationshipTypeI object.
Args : The name (scalar) of the RelationshipTypeI object desired.
=cut
sub get_relationship_type{
shift->throw_not_implemented();
}
=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
sub get_relationships{
shift->throw_not_implemented();
}
=head2 get_predicate_terms
Title : get_predicate_terms
Usage : get_predicate_terms(): TermI
Function:
Example :
Returns :
Args :
=cut
sub get_predicate_terms{
shift->throw_not_implemented();
}
=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
sub get_child_terms{
shift->throw_not_implemented();
}
=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
sub get_descendant_terms{
shift->throw_not_implemented();
}
=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
sub get_parent_terms{
shift->throw_not_implemented();
}
=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
sub get_ancestor_terms{
shift->throw_not_implemented();
}
=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
sub get_leaf_terms{
shift->throw_not_implemented();
}
=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 ancestors.
Example : @root_terms = $obj->get_root_terms()
Returns : Array of TermI objects.
Args :
=cut
sub get_root_terms{
shift->throw_not_implemented();
}
=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::ObjectFactory
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::ObjectFactory
compliant object)
Args :
=cut
sub term_factory{
return shift->throw_not_implemented();
}
=head1 Decorator Methods
These methods come with a default implementation that uses the
abstract methods defined for this interface. This may not be very
efficient, and hence implementors are encouraged to override these
methods if they can provide more efficient implementations.
=cut
=head2 get_all_terms
Title : get_all_terms
Usage : get_all_terms: TermI
Function: Retrieves all terms from the ontology.
This is more a decorator method. We provide a default
implementation here that loops over all root terms and gets
all descendants for each root term. The overall union of
terms is then made unique by name and 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.
Engine implementations that can provide a more efficient
method for obtaining all terms should definitely override
this.
Example : @terms = $obj->get_all_terms()
Returns : Array of TermI objects.
Args :
=cut
sub get_all_terms{
my $self = shift;
# get all root nodes
my @roots = $self->get_root_terms();
# accumulate all descendants for each root term
my @terms = map { $self->get_descendant_terms($_); } @roots;
# add on the root terms themselves
push(@terms, @roots);
# make unique by name and ontology
my %name_map = map { ($_->name."@".$_->ontology->name, $_); } @terms;
# done
return values %name_map;
}
=head2 find_terms
Title : find_terms
Usage : ($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
sub find_terms{
my $self = shift;
my %params = @_;
@params{ map { lc $_; } keys %params } = values %params; # lowercase keys
my @terms = grep {
my $ok = exists($params{-identifier}) ?
$_->identifier() eq $params{-identifier} : 1;
$ok && ((! exists($params{-name})) ||
($_->name() eq $params{-name}));
} $self->get_all_terms();
return @terms;
}
=head1 Experimental API method proposals
Ontologies are a very new domain in bioperl, and we are not sure yet
what we will want to do on and with ontologies in which
situation. The methods from here on downwards are solely API
descriptions to solicit comment and feedback; the chance of any of
those being actually implemented already is very slim.
Disclaimer: As long as an API method stays in this section, it is
subject to change, possibly even radical change or complete
deletion. If it's not implemented yet (most likely it isn't),
implement yourself at your own risk.
So far for the disclaimer. The reason the API description is here,
however, is to solicit feedback. Please feel encouraged to share your
opinion, regardless of what it is (a notable difference of this API
method to others is that there is actually no working code behind it
- so the defense line is non-existent for practical purposes).
=cut
=head2 common_ancestor_path
Title : common_ancestor_path
Usage :
Function: Get the paths from two terms A and B to term C, such that
there is no other term D to which A and B would have a shorter
path, provided there is a term C to which both A and B are
connected by a path.
Note that the path to the common ancestor between A and A
exists, has distance zero, and predicate "identity".
The search for the common ancestor C can be further
constrained by supplying a predicate term. If supplied, the
predicates of the two paths (A,C) and (B,C) must have a
common ancestor identical to the predicate, or that has a
path to the predicate.
Example :
Returns : The path of the first term to the common ancestor in scalar
context, and both paths in list context. Paths are
Bio::Ontology::PathI compliant objects.
Args : The two terms (Bio::Ontology::TermI objects), and optionally
a constraining common predicate (Bio::Ontology::TermI object).
The latter may also be given as a scalar, in which case it
is treated as a boolean that, if TRUE, means that the two paths
must have identical predicates in order to be returned.
=cut
sub common_ancestor_path{
return shift->throw_not_implemented();
}
1;