LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] 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-2.0Unless 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.
CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::OntologyTerm
DESCRIPTION
An ontology term object, used in querying for transcripts, genes, and translations using the relevant adaptors and methods.
METHODS
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::OntologyTermaccession
Arg : None
Description : Returns the accession for the ontology term in question.
Example : my $accession = $term->accession();
Return type : Stringontology
Arg : None
Description : Returns the ontology for the ontology term in question.
Example : my $ontology = $term->ontology();
Return type : Stringnamespace
Arg : None
Description : Returns the namespace for the ontology term in question.
Example : my $acc = $term->namespace();
Return type : Stringname
Arg : None
Description : Returns the name for the ontology term in question.
Example : my $name = $term->name();
Return type : Stringdefinition
Arg : None
Description : Returns the definition for the ontology term in question.
Example : my $definition = $term->definition();
Return type : Stringis_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)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)synonyms
Arg : None
Description : Returns the list of synonyms defined for this term
(if any).
Example : my @synonyms = @{ $term->synonyms() };
Return type : Listref of stringssubsets
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 stringschildren
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::OntologyTermdescendants
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::OntologyTermparents
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::OntologyTermancestors
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::OntologyTermontology_version
Arg : None
Description : Returns the version of the ontology from which this term
originates.
Example : my $version = $term->ontology_version() ;
Return type : string