Bio::Annotation
OntologyTerm
Summary
Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Annotation::OntologyTerm;
use Bio::Annotation::Collection;
use Bio::Ontology::Term;
my $coll = new Bio::Annotation::Collection;
# this also implements a tag/value pair, where tag _and_ value are treated
# as ontology terms
my $annterm = new Bio::Annotation::OntologyTerm(-label => 'ABC1',
-tagname => 'Gene Name');
# ontology terms can be added directly - they implicitly have a tag
$coll->add_Annotation($annterm);
# implementation is by composition - you can get/set the term object
# e.g.
my $term = $annterm->term(); # term is-a Bio::Ontology::TermI
print "ontology term ",$term->name()," (ID ",$term->identifier(),
"), ontology ",$term->ontology()->name(),"\n";
$term = Bio::Ontology::Term->new(-name => 'ABC2', -ontology => 'Gene Name');
$annterm->term($term);
Description
Ontology term annotation object
Methods
Methods description
Title : new
Usage : my $sv = new Bio::Annotation::OntologyTerm;
Function: Instantiate a new OntologyTerm object
Returns : Bio::Annotation::OntologyTerm object
Args : -term => $term to initialize the term data field [optional]
Most named arguments that Bio::Ontology::Term accepts will work
here too. -label is a synonym for -name, -tagname is a synonym for
-ontology. |
Title : as_text
Usage : my $text = $obj->as_text
Function: return the string "Name: $v" where $v is the name of the term
Returns : string
Args : none |
Title : hash_tree
Usage : my $hashtree = $value->hash_tree
Function: For supporting the AnnotationI interface just returns the value
as a hashref with the key 'value' pointing to the value
Returns : hashrf
Args : none |
Title : tagname
Usage : $obj->tagname($newval)
Function: Get/set the tagname for this annotation value.
Setting this is optional. If set, it obviates the need to provide
a tag to AnnotationCollection when adding this object.
This is aliased to ontology() here.
Example :
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional) |
Title : term
Usage : $obj->term($newval)
Function: Get/set the Bio::Ontology::TermI implementing object.
We implement TermI by composition, and this method sets/gets the
object we delegate to.
Example :
Returns : value of term (a Bio::Ontology::TermI compliant object)
Args : new value (a Bio::Ontology::TermI compliant object, optional) |
Title : identifier
Usage : $term->identifier( "0003947" );
or
print $term->identifier();
Function: Set/get for the identifier of this Term.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional). |
Title : name
Usage : $term->name( "N-acetylgalactosaminyltransferase" );
or
print $term->name();
Function: Set/get for the name of this Term.
Returns : The name [scalar].
Args : The name [scalar] (optional). |
Title : definition
Usage : $term->definition( "Catalysis of ..." );
or
print $term->definition();
Function: Set/get for the definition of this Term.
Returns : The definition [scalar].
Args : The definition [scalar] (optional). |
Title : ontology
Usage : $term->ontology( $top );
or
$top = $term->ontology();
Function: Set/get for a relationship between this Term and
another Term (e.g. the top level of the ontology).
Returns : The ontology of this Term [TermI].
Args : The ontology of this Term [TermI or scalar -- which
becomes the name of the catagory term] (optional). |
Title : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the obsoleteness of this Term.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional). |
Title : comment
Usage : $term->comment( "Consider the term ..." );
or
print $term->comment();
Function: Set/get for an arbitrary comment about this Term.
Returns : A comment.
Args : A comment (optional). |
Title : get_synonyms()
Usage : @aliases = $term->get_synonyms();
Function: Returns a list of aliases of this Term.
Returns : A list of aliases [array of [scalar]].
Args : |
Title : add_synonym
Usage : $term->add_synonym( @asynonyms );
or
$term->add_synonym( $synonym );
Function: Pushes one or more synonyms into the list of synonyms.
Returns :
Args : One synonym [scalar] or a list of synonyms [array of [scalar]]. |
Title : remove_synonyms()
Usage : $term->remove_synonyms();
Function: Deletes (and returns) the synonyms of this Term.
Returns : A list of synonyms [array of [scalar]].
Args : |
Title : get_dblinks()
Usage : @ds = $term->get_dblinks();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args : |
Title : add_dblink
Usage : $term->add_dblink( @dbls );
or
$term->add_dblink( $dbl );
Function: Pushes one or more dblinks
into the list of dblinks.
Returns :
Args : One dblink [scalar] or a list of
dblinks [array of [scalars]]. |
Title : remove_dblinks()
Usage : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : |
Title : get_secondary_ids
Usage : @ids = $term->get_secondary_ids();
Function: Returns a list of secondary identifiers of this Term.
Secondary identifiers mostly originate from merging terms,
or possibly also from splitting terms.
Returns : A list of secondary identifiers [array of [scalar]]
Args : |
Title : add_secondary_id
Usage : $term->add_secondary_id( @ids );
or
$term->add_secondary_id( $id );
Function: Adds one or more secondary identifiers to this term.
Returns :
Args : One or more secondary identifiers [scalars] |
Title : remove_secondary_ids
Usage : $term->remove_secondary_ids();
Function: Deletes (and returns) the secondary identifiers of this Term.
Returns : The previous list of secondary identifiers [array of [scalars]]
Args : |
Methods code
sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($term,$name,$label,$identifier,$definition,$ont,$tag) =
$self->_rearrange([qw(TERM
NAME
LABEL
IDENTIFIER
DEFINITION
ONTOLOGY
TAGNAME)],
@args);
if($term) {
$self->term($term);
} else {
$self->name($name || $label) if $name || $label;
$self->identifier($identifier) if $identifier;
$self->definition($definition) if $definition;
}
$self->ontology($ont || $tag) if $ont || $tag;
return $self;} | sub as_text
{ my ($self) = @_;
return $self->tagname()."|".$self->name()."|".$self->identifier(); } | sub hash_tree
{ my ($self) = @_;
my $h = {};
$h->{'name'} = $self->name();
$h->{'identifier'} = $self->identifier();
$h->{'definition'} = $self->definition();
$h->{'synonyms'} = [$self->each_synonym()];} | sub tagname
{ my $self = shift;
return $self->ontology(@_) if @_;
my $ont = $self->ontology();
return ref($ont) ? $ont->name() : $ont;} | sub term
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'term'} = $value;
}
if(! exists($self->{'term'})) {
$self->{'term'} = Bio::Ontology::Term->new();
}
return $self->{'term'};} | sub identifier
{ return shift->term()->identifier(@_);
}
} | sub name
{ return shift->term()->name(@_);
}
} | sub definition
{ return shift->term()->definition(@_);
}
} | sub ontology
{ return shift->term()->ontology(@_); } | sub is_obsolete
{ return shift->term()->is_obsolete(@_);
}
} | sub comment
{ return shift->term()->comment(@_);
}
} | sub get_synonyms
{ return shift->term()->get_synonyms(@_);
}
} | sub add_synonym
{ return shift->term()->add_synonym(@_);
}
} | sub remove_synonyms
{ return shift->term()->remove_synonyms(@_);
}
} | sub get_dblinks
{ return shift->term->get_dblinks(@_);
}
} | sub add_dblink
{ return shift->term->add_dblink(@_);
}
} | sub remove_dblinks
{ return shift->term->remove_dblinks(@_);
}
} | sub get_secondary_ids
{ return shift->term->get_secondary_ids(@_);
}
} | sub add_secondary_id
{ return shift->term->add_secondary_id(@_);
}
} | sub remove_secondary_ids
{ return shift->term->remove_secondary_ids(@_);
}
} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
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Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
| AnnotationI implementing functions | Top |
| Methods for Bio::Ontology::TermI compliance | Top |