diff variant_effect_predictor/Bio/Ontology/OntologyEngineI.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/Ontology/OntologyEngineI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: OntologyEngineI.pm,v 1.2.2.3 2003/03/27 10:07:56 lapp Exp $
+#
+# BioPerl module for OntologyEngineI
+#
+# Cared for by Peter Dimitrov <[e-mail]>
+#
+# (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
+
+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 doesn't 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 aren't, 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Peter Dimitrov
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=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 vars qw(@ISA);
+use strict;
+use Carp;
+use Bio::Root::RootI;
+
+@ISA = 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 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;
+}
+
+1;