ensembl-hive
2.6
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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 () |
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.
public String Bio::EnsEMBL::OntologyTerm::accession | ( | ) |
Arg : None
Description : Returns the accession for the ontology term in question.
Example :
Return type : String
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 :
Return type : listref of Bio::EnsEMBL::OntologyTerm
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 :
Return type : listref of Bio::EnsEMBL::OntologyTerm
public String Bio::EnsEMBL::OntologyTerm::definition | ( | ) |
Arg : None
Description : Returns the definition for the ontology term in question.
Example :
Return type : String
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 :
Return type : listref of Bio::EnsEMBL::OntologyTerm
public Boolean Bio::EnsEMBL::OntologyTerm::is_obsolete | ( | ) |
Arg : None
Description : Returns true if the term is obsolete
Example :
Return type : Boolean (TRUE if it is obsolete, else FALSE)
public Boolean Bio::EnsEMBL::OntologyTerm::is_root | ( | ) |
Arg : None
Description : Returns true if the term is root of its ontology
Example :
Return type : Boolean (TRUE if it is a root, else FALSE)
public String Bio::EnsEMBL::OntologyTerm::name | ( | ) |
Arg : None
Description : Returns the name for the ontology term in question.
Example :
Return type : String
Definition at line 184 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 :
'-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
public String Bio::EnsEMBL::OntologyTerm::ontology | ( | ) |
Arg : None
Description : Returns the ontology for the ontology term in question.
Example :
Return type : String
public String Bio::EnsEMBL::OntologyTerm::ontology_version | ( | ) |
Arg : None
Description : Returns the version of the ontology from which this term originates.
Example :
Return type : string
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 :
Return type : listref of Bio::EnsEMBL::OntologyTerm
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 :
Return type : listref of strings
public Listref Bio::EnsEMBL::OntologyTerm::synonyms | ( | ) |
Arg : None
Description : Returns the list of synonyms defined for this term (if any).
Example :
Return type : Listref of strings