#
# BioPerl module for Bio::Ontology::OBOEngine
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file
format from the Gene Ontology Consortium
=head1 SYNOPSIS
use Bio::Ontology::OBOEngine;
my $parser = Bio::Ontology::OBOEngine->new
( -file => "gene_ontology.obo" );
my $engine = $parser->parse();
=head1 DESCRIPTION
Needs Graph.pm from CPAN.
This module replaces SimpleGOEngine.pm, which is deprecated.
=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 lists 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
the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Sohel Merchant
Email: s-merchant@northwestern.edu
Address:
Northwestern University
Center for Genetic Medicine (CGM), dictyBase
Suite 1206,
676 St. Clair st
Chicago IL 60611
=head2 CONTRIBUTOR
Hilmar Lapp, hlapp at gmx.net
Chris Mungall, cjm at fruitfly.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Ontology::OBOEngine;
use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
use strict;
use Bio::Ontology::RelationshipType;
use Bio::Ontology::RelationshipFactory;
use Data::Dumper;
use constant TRUE => 1;
use constant FALSE => 0;
use constant IS_A => "IS_A";
use constant PART_OF => "PART_OF";
use constant RELATED_TO => "RELATED_TO";
use constant TERM => "TERM";
use constant TYPE => "TYPE";
use constant ONTOLOGY => "ONTOLOGY";
use constant REGULATES => "REGULATES";
use constant POSITIVELY_REGULATES => "POSITIVELY_REGULATES";
use constant NEGATIVELY_REGULATES => "NEGATIVELY_REGULATES";
use base qw(Bio::Root::Root Bio::Ontology::OntologyEngineI);
=head2 new
Title : new
Usage : $engine = Bio::Ontology::OBOEngine->new()
Function: Creates a new OBOEngine
Returns : A new OBOEngine object
Args :
=cut
sub new {
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
$self->init();
return $self;
} # new
=head2 init
Title : init()
Usage : $engine->init();
Function: Initializes this Engine.
Returns :
Args :
=cut
sub init {
my ( $self ) = @_;
$self->{ "_is_a_relationship" } = Bio::Ontology::RelationshipType->get_instance( IS_A );
$self->{ "_part_of_relationship" } = Bio::Ontology::RelationshipType->get_instance( PART_OF );
$self->{ "_related_to_relationship" } = Bio::Ontology::RelationshipType->get_instance( RELATED_TO );
$self->{'_regulates_relationship'} = Bio::Ontology::RelationshipType->get_instance(REGULATES);
$self->{'_positively_regulate'} = Bio::Ontology::RelationshipType->get_instance(POSITIVELY_REGULATES);
$self->{'_negatively_regulate'} = Bio::Ontology::RelationshipType->get_instance(NEGATIVELY_REGULATES);
$self->graph( Bio::Ontology::SimpleGOEngine::GraphAdaptor->new() ); # NG 05-02-16
# set defaults for the factories
$self->relationship_factory(Bio::Ontology::RelationshipFactory->new(
-type => "Bio::Ontology::Relationship"));
} # init
=head2 is_a_relationship
Title : is_a_relationship()
Usage : $IS_A = $engine->is_a_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "is-a"
relationships
Returns : Bio::Ontology::RelationshipType set to "IS_A"
Args :
=cut
sub is_a_relationship {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_is_a_relationship" };
} # is_a_relationship
=head2 part_of_relationship
Title : part_of_relationship()
Usage : $PART_OF = $engine->part_of_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "part-of"
relationships
Returns : Bio::Ontology::RelationshipType set to "PART_OF"
Args :
=cut
sub part_of_relationship {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_part_of_relationship" };
} # part_of_relationship
=head2 related_to_relationship
Title : related_to_relationship()
Usage : $RELATED_TO = $engine->related_to_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "related-to"
relationships
Returns : Bio::Ontology::RelationshipType set to "RELATED_TO"
Args :
=cut
sub related_to_relationship {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_related_to_relationship" };
} # related_to_relationship
=head2 regulates_relationship
Title : regulates_relationship()
Usage : $REGULATES = $engine->regulates_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "regulates"
relationships
Returns : Bio::Ontology::RelationshipType set to "REGULATES"
Args :
=cut
sub regulates_relationship {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_regulates_relationship" };
} # is_a_relationship
=head2 positively_regulates_relationship
Title : positively_regulates_relationship()
Usage : $REGULATES = $engine->positively_regulates_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "positively_regulates"
relationships
Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES"
Args :
=cut
sub positively_regulates_relationship {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_positively_regulate" };
}
=head2 negatively_regulates_relationship
Title : negatively_regulates_relationship()
Usage : $REGULATES = $engine->negatively_regulates_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "negatively_regulates"
relationships
Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES"
Args :
=cut
sub negatively_regulates_relationship {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_negatively_regulate" };
}
=head2 add_term
Title : add_term
Usage : $engine->add_term( $term_obj );
Function: Adds a Bio::Ontology::TermI to this engine
Returns : true if the term was added and false otherwise (e.g., if the
term already existed in the ontology engine)
Args : Bio::Ontology::TermI
=cut
sub add_term {
my ( $self, $term ) = @_;
return FALSE if $self->has_term( $term );
my $goid = $self->_get_id($term);
$self->graph()->add_vertex( $goid );
$self->graph()->set_vertex_attribute( $goid, TERM, $term ); # NG 05-02-16
return TRUE;
} # add_term
=head2 has_term
Title : has_term
Usage : $engine->has_term( $term );
Function: Checks whether this engine contains a particular term
Returns : true or false
Args : Bio::Ontology::TermI
or
Term identifier (e.g. "GO:0012345")
=cut
sub has_term {
my ( $self, $term ) = @_;
$term = $self->_get_id( $term );
if ( $self->graph()->has_vertex( $term ) ) {
return TRUE;
}
else {
return FALSE;
}
} # has_term
=head2 add_relationship_type
Title : add_relationship_type
Usage : $engine->add_relationship_type( $type_name, $ont );
Function: Adds a new relationship type to the engine. Use
get_relationship_type($type_name) to retrieve.
Returns : true if successfully added, false otherwise
Args : relationship type name to add (scalar)
ontology to which to assign the relationship type
=cut
sub add_relationship_type{
my ($self,@args) = @_;
if(scalar(@_) == 3){
my $type_name = $args[0];
my $ont = $args[1];
$self->{ "_extra_relationship_types" }{$type_name} = Bio::Ontology::RelationshipType->get_instance($type_name,$ont);
#warn Dumper($self->{"_extra_relationship_types"}{$type_name});
return 1;
}
return 0;
}
=head2 get_relationship_type
Title : get_relationship_type
Usage : $engine->get_relationship_type( $type_name );
Function: Gets a Bio::Ontology::RelationshipI object corresponding
to $type_name
Returns : a Bio::Ontology::RelationshipI object
Args :
=cut
sub get_relationship_type{
my ($self,$type_name) = @_;
return $self->{ "_extra_relationship_types" }{$type_name};
}
=head2 add_relationship
Title : add_relationship
Usage : $engine->add_relationship( $relationship );
$engine->add_relatioship( $subject_term, $predicate_term,
$object_term, $ontology );
$engine->add_relatioship( $subject_id, $predicate_id,
$object_id, $ontology);
Function: Adds a relationship to this engine
Returns : true if successfully added, false otherwise
Args : The relationship in one of three ways:
a) subject (or child) term id, Bio::Ontology::TermI
(rel.type), object (or parent) term id, ontology
or
b) subject Bio::Ontology::TermI, predicate
Bio::Ontology::TermI (rel.type), object
Bio::Ontology::TermI, ontology
or
c) Bio::Ontology::RelationshipI-compliant object
=cut
# term objs or term ids
sub add_relationship {
my ( $self, $child, $type, $parent, $ont ) = @_;
if ( scalar( @_ ) == 2 ) {
$self->_check_class( $child, "Bio::Ontology::RelationshipI" );
$type = $child->predicate_term();
$parent = $child->object_term();
$ont = $child->ontology();
$child = $child->subject_term();
}
$self->_check_class( $type, "Bio::Ontology::TermI" );
my $parentid = $self->_get_id( $parent );
my $childid = $self->_get_id( $child );
my $g = $self->graph();
$self->add_term($child) unless $g->has_vertex( $childid );
$self->add_term($parent) unless $g->has_vertex( $parentid );
# This prevents multi graphs.
if ( $g->has_edge( $parentid, $childid ) ) {
return FALSE;
}
$g->add_edge( $parentid, $childid );
$g->set_edge_attribute( $parentid, $childid, TYPE, $type ); # NG 05-02-16
$g->set_edge_attribute( $parentid, $childid, ONTOLOGY, $ont ); # NG 05-02-16
return TRUE;
} # add_relationship
=head2 get_relationships
Title : get_relationships
Usage : $engine->get_relationships( $term );
Function: Returns all relationships of a term, or all relationships in
the graph if no term is specified.
Returns : Relationship
Args : term id
or
Bio::Ontology::TermI
=cut
sub get_relationships {
my ( $self, $term ) = @_;
my $g = $self->graph();
# obtain the ID if term provided
my $termid;
if($term) {
$termid = $self->_get_id( $term );
# check for presence in the graph
if ( ! $g->has_vertex( $termid ) ) {
$self->throw( "no term with identifier \"$termid\" in ontology" );
}
}
# now build the relationships
my $relfact = $self->relationship_factory();
# we'll build the relationships from edges
my @rels = ();
my @edges = $termid ? $g->edges_at( $termid ) : $g->edges(); # NG 05-02-13
while(@edges) {
my ( $startid, $endid ) = @{ shift @edges }; # NG 05-02-16
my $rel = $relfact->create_object
(-subject_term => $self->get_terms($endid),
-object_term => $self->get_terms($startid),
-predicate_term => $g->get_edge_attribute($startid, $endid, TYPE),
-ontology => $g->get_edge_attribute($startid, $endid, ONTOLOGY));
push( @rels, $rel );
}
return @rels;
} # get_relationships
=head2 get_all_relationships
Title : get_all_relationships
Usage : @rels = $engine->get_all_relationships();
Function: Returns all relationships in the graph.
Returns : Relationship
Args :
=cut
sub get_all_relationships {
return shift->get_relationships(@_);
} # get_all_relationships
=head2 get_predicate_terms
Title : get_predicate_terms
Usage : $engine->get_predicate_terms();
Function: Returns the types of relationships this engine contains
Returns : Bio::Ontology::RelationshipType
Args :
=cut
sub get_predicate_terms {
my ( $self ) = @_;
my @a = (
$self->is_a_relationship(),
$self->part_of_relationship(),
$self->related_to_relationship(),
$self->regulates_relationship(),
$self->positively_regulates_relationship(),
$self->negatively_regulates_relationship(),
);
foreach my $termname (keys %{$self->{ "_extra_relationship_types" }}){
push @a, $self->{ "_extra_relationship_types" }{ $termname };
}
return @a;
} # get_predicate_terms
=head2 get_child_terms
Title : get_child_terms
Usage : $engine->get_child_terms( $term_obj, @rel_types );
$engine->get_child_terms( $term_id, @rel_types );
Function: Returns the children of this term
Returns : Bio::Ontology::TermI
Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
or
term id, Bio::Ontology::RelationshipType
if NO Bio::Ontology::RelationshipType is indicated: children
of ALL types are returned
=cut
sub get_child_terms {
my ( $self, $term, @types ) = @_;
return $self->_get_child_parent_terms_helper( $term, TRUE, @types );
} # get_child_terms
=head2 get_descendant_terms
Title : get_descendant_terms
Usage : $engine->get_descendant_terms( $term_obj, @rel_types );
$engine->get_descendant_terms( $term_id, @rel_types );
Function: Returns the descendants of this term
Returns : Bio::Ontology::TermI
Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
or
term id, Bio::Ontology::RelationshipType
if NO Bio::Ontology::RelationshipType is indicated:
descendants of ALL types are returned
=cut
sub get_descendant_terms {
my ( $self, $term, @types ) = @_;
my %ids = ();
my @ids = ();
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a term with an identifier of \"$term\"" );
}
$self->_get_descendant_terms_helper( $term, \%ids, \@types );
while( ( my $id ) = each ( %ids ) ) {
push( @ids, $id );
}
return $self->get_terms( @ids );
} # get_descendant_terms
=head2 get_parent_terms
Title : get_parent_terms
Usage : $engine->get_parent_terms( $term_obj, @rel_types );
$engine->get_parent_terms( $term_id, @rel_types );
Function: Returns the parents of this term
Returns : Bio::Ontology::TermI
Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
or
term id, Bio::Ontology::RelationshipType
if NO Bio::Ontology::RelationshipType is indicated:
parents of ALL types are returned
=cut
sub get_parent_terms {
my ( $self, $term, @types ) = @_;
return $self->_get_child_parent_terms_helper( $term, FALSE, @types );
} # get_parent_terms
=head2 get_ancestor_terms
Title : get_ancestor_terms
Usage : $engine->get_ancestor_terms( $term_obj, @rel_types );
$engine->get_ancestor_terms( $term_id, @rel_types );
Function: Returns the ancestors of this term
Returns : Bio::Ontology::TermI
Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
or
term id, Bio::Ontology::RelationshipType
if NO Bio::Ontology::RelationshipType is indicated:
ancestors of ALL types are returned
=cut
sub get_ancestor_terms {
my ( $self, $term, @types ) = @_;
my %ids = ();
my @ids = ();
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a term with an identifier of \"$term\"" );
}
$self->_get_ancestor_terms_helper( $term, \%ids, \@types );
while( ( my $id ) = each ( %ids ) ) {
push( @ids, $id );
}
return $self->get_terms( @ids );
} # get_ancestor_terms
=head2 get_leaf_terms
Title : get_leaf_terms
Usage : $engine->get_leaf_terms();
Function: Returns the leaf terms
Returns : Bio::Ontology::TermI
Args :
=cut
sub get_leaf_terms {
my ( $self ) = @_;
my @a = $self->graph()->sink_vertices();
return $self->get_terms( @a );
}
=head2 get_root_terms()
Title : get_root_terms
Usage : $engine->get_root_terms();
Function: Returns the root terms
Returns : Bio::Ontology::TermI
Args :
=cut
sub get_root_terms {
my ( $self ) = @_;
my @a = $self->graph()->source_vertices();
return $self->get_terms( @a );
}
=head2 get_terms
Title : get_terms
Usage : @terms = $engine->get_terms( "GO:1234567", "GO:2234567" );
Function: Returns term objects with given identifiers
Returns : Bio::Ontology::TermI, or the term corresponding to the
first identifier if called in scalar context
Args : term ids
=cut
sub get_terms {
my ( $self, @ids ) = @_;
my @terms = ();
foreach my $id ( @ids ) {
if ( $self->graph()->has_vertex( $id ) ) {
push( @terms, $self->graph()->get_vertex_attribute( $id, TERM ) ); # NG 05-02-16
}
}
return wantarray ? @terms : shift(@terms);
} # get_terms
=head2 get_all_terms
Title : get_all_terms
Usage : $engine->get_all_terms();
Function: Returns all terms in this engine
Returns : Bio::Ontology::TermI
Args :
=cut
sub get_all_terms {
my ( $self ) = @_;
return( $self->get_terms( $self->graph()->vertices() ) );
} # get_all_terms
=head2 find_terms
Title : find_terms
Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263");
Function: Find term instances matching queries for their attributes.
This implementation can efficiently resolve queries by
identifier.
Example :
Returns : an array of zero or more Bio::Ontology::TermI objects
Args : Named parameters. The following parameters should be recognized
by any implementations:
-identifier query by the given identifier
-name query by the given name
=cut
sub find_terms{
my ($self,@args) = @_;
my @terms;
my ($id,$name) = $self->_rearrange([qw(IDENTIFIER NAME)],@args);
if(defined($id)) {
@terms = $self->get_terms($id);
} else {
@terms = $self->get_all_terms();
}
if(defined($name)) {
@terms = grep { $_->name() eq $name; } @terms;
}
return @terms;
}
=head2 find_identically_named_terms
Title : find_identically_named_terms
Usage : ($term) = $oe->find_identically_named_terms($term0);
Function: Find term instances where names match the query term
name exactly
Example :
Returns : an array of zero or more Bio::Ontology::TermI objects
Args : a Bio::Ontology::TermI object
=cut
sub find_identically_named_terms{
my ($self,$qterm) = @_;
$self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." )
unless defined $qterm and $qterm->isa("Bio::Ontology::TermI");
my %matching_terms;
foreach my $term ($self->get_all_terms) {
$matching_terms{$term->identifier} = $term and next
if $term->name eq $qterm->name;
}
return values %matching_terms;
}
=head2 find_identical_terms
Title : find_identical_terms
Usage : ($term) = $oe->find_identical_terms($term0);
Function: Find term instances where name or synonym
matches the query exactly
Example :
Returns : an array of zero or more Bio::Ontology::TermI objects
Args : a Bio::Ontology::TermI object
=cut
sub find_identical_terms{
my ($self,$qterm) = @_;
$self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." )
unless defined $qterm and $qterm->isa("Bio::Ontology::TermI");
my %matching_terms;
foreach my $qstring ($qterm->name, $qterm->each_synonym) {
foreach my $term ($self->get_all_terms) {
foreach my $string ( $term->name, $term->each_synonym() ) {
$matching_terms{$term->identifier} = $term and next
if $string eq $qstring;
}
}
}
return values %matching_terms;
}
=head2 find_similar_terms
Title : find_similar_terms
Usage : ($term) = $oe->find_similar_terms($term0);
Function: Find term instances where name or synonym, or part of one,
matches the query.
Example :
Returns : an array of zero or more Bio::Ontology::TermI objects
Args : a Bio::Ontology::TermI object
=cut
sub find_similar_terms{
my ($self,$qterm) = @_;
$self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." )
unless defined $qterm and $qterm->isa("Bio::Ontology::TermI");
my %matching_terms;
foreach my $qstring ($qterm->name, $qterm->each_synonym) {
foreach my $term ($self->get_all_terms) {
foreach my $string ( $term->name, $term->each_synonym() ) {
$matching_terms{$term->identifier} = $term and next
if $string =~ /\Q$qstring\E/ or $qstring =~ /\Q$string\E/;
}
}
}
return values %matching_terms;
}
=head2 relationship_factory
Title : relationship_factory
Usage : $fact = $obj->relationship_factory()
Function: Get/set 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 : on set, a Bio::Factory::ObjectFactoryI compliant object
=cut
sub relationship_factory{
my $self = shift;
return $self->{'relationship_factory'} = shift if @_;
return $self->{'relationship_factory'};
}
=head2 term_factory
Title : term_factory
Usage : $fact = $obj->term_factory()
Function: Get/set the object factory to be used when term objects are
created by the implementation on-the-fly.
Note that this ontology engine implementation does not
create term objects on the fly, and therefore setting this
attribute is meaningless.
Example :
Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
compliant object)
Args : on set, a Bio::Factory::ObjectFactoryI compliant object
=cut
sub term_factory{
my $self = shift;
if(@_) {
$self->warn("setting term factory, but ".ref($self).
" does not create terms on-the-fly");
return $self->{'term_factory'} = shift;
}
return $self->{'term_factory'};
}
=head2 graph
Title : graph()
Usage : $engine->graph();
Function: Returns the Graph this engine is based on
Returns : Graph
Args :
=cut
sub graph {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_check_class( $value, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor' ); # NG 05-02-16
$self->{ "_graph" } = $value;
}
return $self->{ "_graph" };
} # graph
# Internal methods
# ----------------
# Checks the correct format of a GOBO-formatted id
# Gets the id out of a term or id string
sub _get_id {
my ( $self, $term ) = @_;
my $id = $term;
if ( ref($term) ) {
# use TermI standard API
$self->throw(
"Object doesn't implement Bio::Ontology::TermI. " . "Bummer." )
unless $term->isa("Bio::Ontology::TermI");
$id = $term->identifier();
# if there is no ID, we need to fake one from ontology name and name
# in order to achieve uniqueness
if ( !$id ) {
$id = $term->ontology->name() if $term->ontology();
$id = $id ? $id . '|' : '';
$id .= $term->name();
}
}
return $id
# if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/);
if $term->isa("Bio::Ontology::OBOterm") || ( $id =~ /^\w+:\w+$/ );
# prefix with something if only numbers
# if($id =~ /^\d+$/) {
# $self->warn(ref($self).": identifier [$id] is only numbers - ".
# "prefixing with 'GO:'");
# return "GO:" . $id;
# }
# we shouldn't have gotten here if it's at least a remotely decent ID
$self->throw( ref($self) . ": non-standard identifier '$id'\n" )
unless $id =~ /\|/;
return $id;
} # _get_id
# Helper for getting children and parent terms
sub _get_child_parent_terms_helper {
my ( $self, $term, $do_get_child_terms, @types ) = @_;
foreach my $type ( @types ) {
$self->_check_class( $type, "Bio::Ontology::TermI" );
}
my @relative_terms = ();
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a term with an identifier of \"$term\"" );
}
my @all_relative_terms = ();
if ( $do_get_child_terms ) {
@all_relative_terms = $self->graph()->successors( $term );
}
else {
@all_relative_terms = $self->graph()->predecessors( $term );
}
foreach my $relative ( @all_relative_terms ) {
if ( scalar( @types ) > 0 ) {
foreach my $type ( @types ) {
my $relative_type;
if ( $do_get_child_terms ) {
$relative_type = $self->graph()->get_edge_attribute ($term, $relative, TYPE ); # NG 05-02-16
}
else {
$relative_type = $self->graph()->get_edge_attribute ($relative, $term, TYPE ); # NG 05-02-16
}
if ( $relative_type->equals( $type ) ) {
push( @relative_terms, $relative );
}
}
}
else {
push( @relative_terms, $relative );
}
}
return $self->get_terms( @relative_terms );
} # get_child_terms
# Recursive helper
sub _get_descendant_terms_helper {
my ( $self, $term, $ids_ref, $types_ref ) = @_;
my @child_terms = $self->get_child_terms( $term, @$types_ref );
if ( scalar( @child_terms ) < 1 ) {
return;
}
foreach my $child_term ( @child_terms ) {
my $child_term_id = $self->_get_id($child_term->identifier());
$ids_ref->{ $child_term_id } = 0;
$self->_get_descendant_terms_helper( $child_term_id, $ids_ref, $types_ref );
}
} # _get_descendant_terms_helper
# Recursive helper
sub _get_ancestor_terms_helper {
my ( $self, $term, $ids_ref, $types_ref ) = @_;
my @parent_terms = $self->get_parent_terms( $term, @$types_ref );
if ( scalar( @parent_terms ) < 1 ) {
return;
}
foreach my $parent_term ( @parent_terms ) {
my $parent_term_id = $self->_get_id($parent_term->identifier());
$ids_ref->{ $parent_term_id } = 0;
$self->_get_ancestor_terms_helper( $parent_term_id, $ids_ref, $types_ref );
}
} # get_ancestor_terms_helper
sub _check_class {
my ( $self, $value, $expected_class ) = @_;
if ( ! defined( $value ) ) {
$self->throw( "Found [undef] where [$expected_class] expected" );
}
elsif ( ! ref( $value ) ) {
$self->throw( "Found [scalar] where [$expected_class] expected" );
}
elsif ( ! $value->isa( $expected_class ) ) {
$self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" );
}
} # _check_class
#################################################################
# aliases
#################################################################
*get_relationship_types = \&get_predicate_terms;
1;