=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =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 [-ONTOLOGY] : String The ontology that the term belongs to. Arg [-NAMESPACE] : String The namespace of the ontology term. Arg [-NAME] : String The name of the ontology term. Arg [-SUBSETS] : (optional) Listref of strings The subsets within the ontology to which this term belongs. Arg [-DEFINITION] : (optional) String The definition of the ontology term. Arg [-SYNONYMS] : (optional) Listref of strings The synonyms of this 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:0021785', '-ontology' => 'GO', '-namespace' => 'biological_process', '-name' => 'branchiomotor neuron axon guidance', '-definition' => 'The process in which a branchiomotor ' . 'neuron growth cone is directed to a specific target site. ' . 'Branchiomotor neurons are located in the hindbrain and ' . 'innervate branchial arch-derived muscles that control jaw ' . 'movements, facial expression, the larynx, and the pharynx.', '-synonyms' => [ 'BMN axon guidance', 'branchial motor axon guidance', 'special visceral motor neuron axon guidance' ] # ... 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, $ontology, $ontology_version,$namespace, $name, $definition, $is_root, $is_obsolete, $subsets ) = rearrange( [ 'ACCESSION', 'ONTOLOGY', 'ONTOLOGY_VERSION', 'NAMESPACE', 'NAME', 'DEFINITION', 'IS_ROOT', 'IS_OBSOLETE', 'SUBSETS' ], @_ ); $this->{'accession'} = $accession; $this->{'ontology'} = $ontology; $this->{'ontology_version'} = $ontology_version; $this->{'namespace'} = $namespace; $this->{'name'} = $name; $this->{'definition'} = $definition; $this->{'is_root'} = $is_root; $this->{'is_obsolete'}= $is_obsolete; $this->{'subsets'} = [ @{$subsets} ]; $this->{'child_terms_fetched'} = 0; $this->{'parent_terms_fetched'} = 0; return $this; } =head2 accession Arg : None Description : Returns the accession for the ontology term in question. Example : my $accession = $term->accession(); Return type : String =cut sub accession { my ($this) = @_; return $this->{'accession'}; } =head2 ontology Arg : None Description : Returns the ontology for the ontology term in question. Example : my $ontology = $term->ontology(); Return type : String =cut sub ontology { my ($this) = @_; return $this->{'ontology'}; } =head2 namespace Arg : None Description : Returns the namespace for the ontology term in question. Example : my $acc = $term->namespace(); Return type : String =cut sub namespace { my ($this) = @_; return $this->{'namespace'}; } =head2 name Arg : None Description : Returns the name for the ontology term in question. Example : my $name = $term->name(); Return type : String =cut sub name { my ($this) = @_; return $this->{'name'}; } =head2 definition Arg : None Description : Returns the definition for the ontology term in question. Example : my $definition = $term->definition(); Return type : String =cut sub definition { my ($this) = @_; return $this->{'definition'}; } =head2 is_root Arg : None Description : Returns true if the term is root of its ontology Example : my $is_root = $term->is_root(); Return type : Boolean (TRUE if it is a root, else FALSE) =cut sub is_root { my ($this) = @_; return $this->{'is_root'}; } =head2 is_obsolete Arg : None Description : Returns true if the term is obsolete Example : my $is_obsolete = $term->is_obsolete(); Return type : Boolean (TRUE if it is obsolete, else FALSE) =cut sub is_obsolete { my ($this) = @_; return $this->{'is_obsolete'}; } =head2 synonyms Arg : None Description : Returns the list of synonyms defined for this term (if any). Example : my @synonyms = @{ $term->synonyms() }; Return type : Listref of strings =cut sub synonyms { my ($this) = @_; if ( !exists( $this->{'synonyms'} ) ) { $this->{'synonyms'} = $this->adaptor()->_fetch_synonyms_by_dbID( $this->dbID() ); } return $this->{'synonyms'}; } =head2 subsets Arg : None Description : Returns a list of subsets that this term is part of. The list might be empty. Example : my @subsets = @{ $term->subsets() }; Return type : listref of strings =cut sub subsets { my ($this) = @_; return $this->{'subsets'}; } =head2 children Arg : (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 = @{ $this->adaptor()->fetch_all_by_parent_term($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 @descendants = @{ $term->descendants() }; Return type : listref of Bio::EnsEMBL::OntologyTerm =cut sub descendants { my ($this) = @_; return $this->adaptor()->fetch_all_by_ancestor_term($this); } =head2 parents Arg : (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 = @{ $this->adaptor()->fetch_all_by_child_term($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 @ancestors = @{ $term->ancestors() }; Return type : listref of Bio::EnsEMBL::OntologyTerm =cut sub ancestors { my ($this) = @_; return $this->adaptor()->fetch_all_by_descendant_term($this); } =head2 ontology_version Arg : None Description : Returns the version of the ontology from which this term originates. Example : my $version = $term->ontology_version() ; Return type : string =cut sub ontology_version{ my ($this) = @_; return $this->{ontology_version}; } 1;