Bio::Annotation OntologyTerm
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Summary
Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
Package variables
No package variables defined.
Included modules
Bio::AnnotationI
Bio::Ontology::Term
Bio::Ontology::TermI
Bio::Root::Root
Inherit
Bio::AnnotationI Bio::Ontology::TermI Bio::Root::Root
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
add_dblinkDescriptionCode
add_secondary_idDescriptionCode
add_synonymDescriptionCode
as_textDescriptionCode
commentDescriptionCode
definitionDescriptionCode
get_dblinksDescriptionCode
get_secondary_idsDescriptionCode
get_synonymsDescriptionCode
hash_treeDescriptionCode
identifierDescriptionCode
is_obsoleteDescriptionCode
nameDescriptionCode
newDescriptionCode
ontologyDescriptionCode
remove_dblinksDescriptionCode
remove_secondary_idsDescriptionCode
remove_synonymsDescriptionCode
tagnameDescriptionCode
termDescriptionCode
Methods description
add_dblinkcode    nextTop
 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]].
add_secondary_idcodeprevnextTop
 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]
add_synonymcodeprevnextTop
 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]].
as_textcodeprevnextTop
 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
commentcodeprevnextTop
 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).
definitioncodeprevnextTop
 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).
get_dblinkscodeprevnextTop
 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    :
get_secondary_idscodeprevnextTop
 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    :
get_synonymscodeprevnextTop
 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    :
hash_treecodeprevnextTop
 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
identifiercodeprevnextTop
 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).
is_obsoletecodeprevnextTop
 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).
namecodeprevnextTop
 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).
newcodeprevnextTop
 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.
ontologycodeprevnextTop
 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).
remove_dblinkscodeprevnextTop
 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    :
remove_secondary_idscodeprevnextTop
 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    :
remove_synonymscodeprevnextTop
 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    :
tagnamecodeprevnextTop
 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)
termcodeprevnextTop
 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)
Methods code
add_dblinkdescriptionprevnextTop
sub add_dblink {
    return shift->term->add_dblink(@_);
} # add_dblink
}
add_secondary_iddescriptionprevnextTop
sub add_secondary_id {
    return shift->term->add_secondary_id(@_);
} # add_secondary_id
}
add_synonymdescriptionprevnextTop
sub add_synonym {
    return shift->term()->add_synonym(@_);
} # add_synonym
}
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   return $self->tagname()."|".$self->name()."|".$self->identifier();
}
commentdescriptionprevnextTop
sub comment {
    return shift->term()->comment(@_);
} # comment
}
definitiondescriptionprevnextTop
sub definition {
    return shift->term()->definition(@_);
} # definition
}
get_dblinksdescriptionprevnextTop
sub get_dblinks {
    return shift->term->get_dblinks(@_);
} # get_dblinks
}
get_secondary_idsdescriptionprevnextTop
sub get_secondary_ids {
    return shift->term->get_secondary_ids(@_);
} # get_secondary_ids
}
get_synonymsdescriptionprevnextTop
sub get_synonyms {
    return shift->term()->get_synonyms(@_);
} # get_synonyms
}
hash_treedescriptionprevnextTop
sub hash_tree {
   my ($self) = @_;
   
   my $h = {};
   $h->{'name'} = $self->name();
   $h->{'identifier'} = $self->identifier();
   $h->{'definition'} = $self->definition();
   $h->{'synonyms'} = [$self->each_synonym()];
}
identifierdescriptionprevnextTop
sub identifier {
    return shift->term()->identifier(@_);
} # identifier
}
is_obsoletedescriptionprevnextTop
sub is_obsolete {
    return shift->term()->is_obsolete(@_);
} # is_obsolete
}
namedescriptionprevnextTop
sub name {
    return shift->term()->name(@_);
} # name
}
newdescriptionprevnextTop
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;
}
ontologydescriptionprevnextTop
sub ontology {
    return shift->term()->ontology(@_);
}
remove_dblinksdescriptionprevnextTop
sub remove_dblinks {
    return shift->term->remove_dblinks(@_);
} # remove_dblinks
}
remove_secondary_idsdescriptionprevnextTop
sub remove_secondary_ids {
    return shift->term->remove_secondary_ids(@_);
} # remove_secondary_ids


1;
}
remove_synonymsdescriptionprevnextTop
sub remove_synonyms {
    return shift->term()->remove_synonyms(@_);
} # remove_synonyms
}
tagnamedescriptionprevnextTop
sub tagname {
    my $self = shift;

    return $self->ontology(@_) if @_;
    # if in get mode we need to get the name from the ontology
    my $ont = $self->ontology();
    return ref($ont) ? $ont->name() : $ont;
}
termdescriptionprevnextTop
sub term {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'term'} = $value;
    }
    if(! exists($self->{'term'})) {
	$self->{'term'} = Bio::Ontology::Term->new();
    }
    return $self->{'term'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
  http://bio.perl.org/MailList.html  - About the mailing lists
Reporting BugsTop
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/
AUTHOR - Hilmar LappTop
Email bioperl-l@bio.perl.org
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
AnnotationI implementing functionsTop
Methods for Bio::Ontology::TermI complianceTop