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Bio::EnsEMBL::OntologyTerm Class Reference
Inheritance diagram for Bio::EnsEMBL::OntologyTerm:

List of all members.


Class Summary

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.
 

Definition at line 12 of file OntologyTerm.pm.

Available Methods

public String accession ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Listref ancestors ()
public Listref children ()
public Int dbID ()
public String definition ()
public Listref descendants ()
public get_all_DAS_Features ()
public Boolean is_stored ()
public String name ()
public Bio::EnsEMBL::OntologyTerm new ()
public String ontology ()
public Listref parents ()
public Listref subsets ()
public Listref synonyms ()

Method Documentation

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:
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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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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:
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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:
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public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

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:
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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:
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public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
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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:
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Definition at line 183 of file OntologyTerm.pm.

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:
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Reimplemented from Bio::EnsEMBL::Storable.

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