Raw content of Bio::EnsEMBL::OntologyTerm
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::OntologyTerm
=head1 DESCRIPTION
An ontology term object, (most often) created by
Bio::EnsEMBL::DBSQL::GOTermAdaptor and used in querying for
transcripts, genes, and translations using the relevant adaptors and
methods.
=head1 METHODS
=cut
package Bio::EnsEMBL::OntologyTerm;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use base qw( Bio::EnsEMBL::Storable );
=head2 new
Arg [-ACCESSION] : String
The accession of the ontology term.
Arg [-NAMESPACE] : String
The namespace of the ontology term.
Arg [-NAME] : String
The name of the ontology term.
Arg [-DEFINITION] : (optional) String
The definition of the ontology term.
Arg : Further arguments required for parent class
Bio::EnsEMBL::Storable.
Description : Creates an ontology term object.
Example :
my $term = Bio::EnsEMBL::OntologyTerm->new(
'-accession' => 'GO:0030326',
'-namespace' => 'biological_process',
'-name' => 'embryonic limb morphogenesis',
'-definition' => 'The process, occurring in the embryo, '
. 'by which the anatomical structures of the limb '
. 'are generated and organized. '
. 'Morphogenesis pertains to the creation of form. '
. 'A limb is an appendage of an animal '
. 'used for locomotion or grasping.'
# ... other arguments required by Bio::EnsEMBL::Storable.
);
Return type : Bio::EnsEMBL::OntologyTerm
=cut
sub new {
my $proto = shift(@_);
my $this = $proto->SUPER::new(@_);
my ( $accession, $namespace, $name, $definition ) =
rearrange( [ 'ACCESSION', 'NAMESPACE', 'NAME', 'DEFINITION' ], @_ );
$this->{'accession'} = $accession;
$this->{'namespace'} = $namespace;
$this->{'name'} = $name;
$this->{'definition'} = $definition;
$this->{'child_terms_fetched'} = 0;
$this->{'parent_terms_fetched'} = 0;
return $this;
}
=head2 accession
Arg : (optional) String
The new accession of this ontology term.
Description : Accesses and/or assigns the accession for the
ontology term in question.
Example : my $accession = $term->accession();
Return type : String
=cut
sub accession {
my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'accession'} = $value }
return $this->{'accession'};
}
=head2 namespace
Arg : (optional) String
The new namespace of this ontology term.
Description : Accesses and/or assigns the namespace for the
ontology term in question.
Example : my $acc = $term->namespace();
Return type : String
=cut
sub namespace {
my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'namespace'} = $value }
return $this->{'namespace'};
}
=head2 name
Arg : (optional) String
The new name of this ontology term.
Description : Accesses and/or assigns the name for the ontology
term in question.
Example : my $name = $term->name();
Return type : String
=cut
sub name {
my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'name'} = $value }
return $this->{'name'};
}
=head2 definition
Arg : (optional) String
The new definition of this ontology term.
Description : Accesses and/or assigns the definition for the
ontology term in question.
Example : my $definition = $term->definition();
Return type : String
=cut
sub defintion {
my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'defintion'} = $value }
return $this->{'definition'};
}
=head2 children
Args : (optional) List of strings
The type of relations to retrieve children for.
Description : Returns the children terms of this ontology term.
Example : my @children =
@{ $term->children( 'is_a', 'part_of' ) };
Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub children {
my ( $this, @relations ) = @_;
my @terms = @{ $this->adaptor()->fetch_by_parent_term($this) };
if (@relations) {
@terms = ();
foreach my $relation (@relations) {
if ( exists( $this->{'children'}{$relation} ) ) {
push( @terms, @{ $this->{'children'}{$relation} } );
}
}
}
return \@terms;
}
=head2 descendants
Arg : None
Description : Returns the complete set of 'is_a' and 'part_of'
descendant terms of this ontology term, down to
and including any leaf terms.
Example : my @desc = @{ $term->descendants() };
Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub descendants {
my ($this) = @_;
return $this->adaptor()->fetch_all_by_parent_term($this);
}
=head2 parents
Args : (optional) List of strings
The type of relations to retrieve parents for.
Description : Returns the parent terms of this ontology term.
Example : my @parents =
@{ $term->parents( 'is_a', 'part_of' ) };
Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub parents {
my ( $this, @relations ) = @_;
my @terms = @{ $this->adaptor()->fetch_by_child_term($this) };
if (@relations) {
@terms = ();
foreach my $relation (@relations) {
if ( exists( $this->{'parents'}{$relation} ) ) {
push( @terms, @{ $this->{'parents'}{$relation} } );
}
}
}
return \@terms;
}
=head2 ancestors
Arg : None
Description : Returns the complete set of 'is_a' and 'part_of'
ancestor terms of this ontology term, up to and
including the root term.
Example : my @desc = @{ $term->descendants() };
Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub ancestors {
my ($this) = @_;
return $this->adaptor()->fetch_all_by_child_term($this);
}
1;
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