Bio::EnsEMBL::OntologyTerm Class Reference

Inheritance diagram for Bio::EnsEMBL::OntologyTerm:

Public Member Functions
public Bio::EnsEMBL::OntologyTerm	new ()
public String	accession ()
public String	ontology ()
public String	name ()
public String	definition ()
public Boolean	is_root ()
public Boolean	is_obsolete ()
public Listref	synonyms ()
public Listref	subsets ()
public Listref	children ()
public Listref	descendants ()
public Listref	parents ()
public Listref	ancestors ()
public String	ontology_version ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Description

An ontology term object, used in querying for transcripts, genes,
and translations using the relevant adaptors and methods.

Definition at line 10 of file OntologyTerm.pm.

Member Function Documentation

accession()

public String Bio::EnsEMBL::OntologyTerm::accession

(

)

  Arg           : None

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

  Example       :

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

  Return type   : String

Code:

ancestors()

public Listref 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

Code:

children()

public Listref Bio::EnsEMBL::OntologyTerm::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

Code:

definition()

public String Bio::EnsEMBL::OntologyTerm::definition

(

)

  Arg           : None

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

  Example       :

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

  Return type   : String

Code:

descendants()

public Listref 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

Code:

is_obsolete()

public Boolean Bio::EnsEMBL::OntologyTerm::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)

Code:

is_root()

public Boolean Bio::EnsEMBL::OntologyTerm::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)

Code:

name()

public String Bio::EnsEMBL::OntologyTerm::name

(

)

  Arg           : None

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

  Example       :

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

  Return type   : String

Code:

Definition at line 184 of file OntologyTerm.pm.

new()

public Bio::EnsEMBL::OntologyTerm Bio::EnsEMBL::OntologyTerm::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

Code:

ontology()

public String Bio::EnsEMBL::OntologyTerm::ontology

(

)

  Arg           : None

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

  Example       :

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

  Return type   : String

Code:

ontology_version()

public String 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

Code:

parents()

public Listref 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

Code:

subsets()

public Listref Bio::EnsEMBL::OntologyTerm::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

Code:

synonyms()

public Listref Bio::EnsEMBL::OntologyTerm::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

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/OntologyTerm.pm