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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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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::OntologyTerm

accession

Arg           : None

Description   : Returns the accession for the ontology term in question.

Example       : my $accession = $term->accession();

Return type   : String

ontology

Arg           : None

Description   : Returns the ontology for the ontology term in question.

Example       : my $ontology = $term->ontology();

Return type   : String

namespace

Arg           : None

Description   : Returns the namespace for the ontology term in question.

Example       : my $acc = $term->namespace();

Return type   : String

name

Arg           : None

Description   : Returns the name for the ontology term in question.

Example       : my $name = $term->name();

Return type   : String

definition

Arg           : None

Description   : Returns the definition for the ontology term in question.

Example       : my $definition = $term->definition();

Return type   : String

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)

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 strings

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

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

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

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

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

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