Bio::EnsEMBL
OntologyTerm
Toolbar
Summary
Bio::EnsEMBL::OntologyTerm
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
No synopsis!
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.
Methods
Methods description
Arg : (optional) String
The new accession of this ontology term.
Description : Accesses and/or assigns the accession for the
ontology term in question.
Example : my $accession = $term->accession();
Return type : String |
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 @desc = @{ $term->descendants() };
Return type : listref of Bio::EnsEMBL::OntologyTerm |
Args : (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 |
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 @desc = @{ $term->descendants() };
Return type : listref of Bio::EnsEMBL::OntologyTerm |
Arg : (optional) String
The new name of this ontology term.
Description : Accesses and/or assigns the name for the ontology
term in question.
Example : my $name = $term->name();
Return type : String |
Arg : (optional) String
The new namespace of this ontology term.
Description : Accesses and/or assigns the namespace for the
ontology term in question.
Example : my $acc = $term->namespace();
Return type : String |
Arg [-ACCESSION] : String
The accession of the ontology term.
Arg [-NAMESPACE] : String
The namespace of the ontology term.
Arg [-NAME] : String
The name of the ontology term.
Arg [-DEFINITION] : (optional) String
The definition of the ontology 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:0030326',
'-namespace' => 'biological_process',
'-name' => 'embryonic limb morphogenesis',
'-definition' => 'The process, occurring in the embryo, '
. 'by which the anatomical structures of the limb '
. 'are generated and organized. '
. 'Morphogenesis pertains to the creation of form. '
. 'A limb is an appendage of an animal '
. 'used for locomotion or grasping.'
# ... other arguments required by Bio::EnsEMBL::Storable.
);
Return type : Bio::EnsEMBL::OntologyTerm |
Args : (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 |
Methods code
sub accession
{ my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'accession'} = $value }
return $this->{'accession'};} | sub ancestors
{ my ($this) = @_;
return $this->adaptor()->fetch_all_by_child_term($this);
}
1; } | sub children
{ my ( $this, @relations ) = @_;
my @terms = @{ $this->adaptor()->fetch_by_parent_term($this) };
if (@relations) {
@terms = ();
foreach my $relation (@relations) {
if ( exists( $this->{'children'}{$relation} ) ) {
push( @terms, @{ $this->{'children'}{$relation} } );
}
}
}
return\@ terms;} | sub defintion
{ my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'defintion'} = $value }
return $this->{'definition'};} | sub descendants
{ my ($this) = @_;
return $this->adaptor()->fetch_all_by_parent_term($this); } | sub name
{ my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'name'} = $value }
return $this->{'name'};} | sub namespace
{ my ( $this, $value ) = @_;
if ( defined($value) ) { $this->{'namespace'} = $value }
return $this->{'namespace'};} | sub new
{ my $proto = shift(@_);
my $this = $proto->SUPER::new(@_);
my ( $accession, $namespace, $name, $definition ) =
rearrange( [ 'ACCESSION', 'NAMESPACE', 'NAME', 'DEFINITION' ], @_ );
$this->{'accession'} = $accession;
$this->{'namespace'} = $namespace;
$this->{'name'} = $name;
$this->{'definition'} = $definition;
$this->{'child_terms_fetched'} = 0;
$this->{'parent_terms_fetched'} = 0;
return $this;} | sub parents
{ my ( $this, @relations ) = @_;
my @terms = @{ $this->adaptor()->fetch_by_child_term($this) };
if (@relations) {
@terms = ();
foreach my $relation (@relations) {
if ( exists( $this->{'parents'}{$relation} ) ) {
push( @terms, @{ $this->{'parents'}{$relation} } );
}
}
}
return\@ terms;} | General documentation
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
Arg : (optional) String
The new definition of this ontology term.
Description : Accesses and/or assigns the definition for the
ontology term in question.
Example : my $definition = $term->definition();
Return type : String