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# $Id: OntologyTerm.pm,v 1.8 2003/10/13 20:02:43 lapp Exp $
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# BioPerl module for Bio::Annotation::OntologyTerm
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# Cared for by Hilmar Lapp <hlapp at gmx.net>
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# Copyright Hilmar Lapp
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# You may distribute this module under the same terms as perl itself
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# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
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# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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# You may distribute this module under the same terms as perl itself.
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# Refer to the Perl Artistic License (see the license accompanying this
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# software package, or see http://www.perl.com/language/misc/Artistic.html)
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# for the terms under which you may use, modify, and redistribute this module.
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# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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# POD documentation - main docs before the code
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Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
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use Bio::Annotation::OntologyTerm;
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use Bio::Annotation::Collection;
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use Bio::Ontology::Term;
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my $coll = new Bio::Annotation::Collection;
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# this also implements a tag/value pair, where tag _and_ value are treated
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my $annterm = new Bio::Annotation::OntologyTerm(-label => 'ABC1',
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-tagname => 'Gene Name');
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# ontology terms can be added directly - they implicitly have a tag
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$coll->add_Annotation($annterm);
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# implementation is by composition - you can get/set the term object
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my $term = $annterm->term(); # term is-a Bio::Ontology::TermI
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print "ontology term ",$term->name()," (ID ",$term->identifier(),
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"), ontology ",$term->ontology()->name(),"\n";
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$term = Bio::Ontology::Term->new(-name => 'ABC2', -ontology => 'Gene Name');
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$annterm->term($term);
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Ontology term annotation object
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bio.perl.org/MailList.html - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution. Bug reports can be submitted via email
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bioperl-bugs@bioperl.org
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http://bugzilla.bioperl.org/
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=head1 AUTHOR - Hilmar Lapp
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Email bioperl-l@bio.perl.org
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Email hlapp at gmx.net
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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# Let the code begin...
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package Bio::Annotation::OntologyTerm;
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# Object preamble - inherits from Bio::Root::Root
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use Bio::AnnotationI;
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use Bio::Ontology::TermI;
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use Bio::Ontology::Term;
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@ISA = qw(Bio::Root::Root Bio::AnnotationI Bio::Ontology::TermI);
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Usage : my $sv = new Bio::Annotation::OntologyTerm;
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Function: Instantiate a new OntologyTerm object
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Returns : Bio::Annotation::OntologyTerm object
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Args : -term => $term to initialize the term data field [optional]
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Most named arguments that Bio::Ontology::Term accepts will work
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here too. -label is a synonym for -name, -tagname is a synonym for
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my ($class,@args) = @_;
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my $self = $class->SUPER::new(@args);
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my ($term,$name,$label,$identifier,$definition,$ont,$tag) =
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$self->_rearrange([qw(TERM
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$self->name($name || $label) if $name || $label;
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$self->identifier($identifier) if $identifier;
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$self->definition($definition) if $definition;
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$self->ontology($ont || $tag) if $ont || $tag;
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=head1 AnnotationI implementing functions
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Usage : my $text = $obj->as_text
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Function: return the string "Name: $v" where $v is the name of the term
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return $self->tagname()."|".$self->name()."|".$self->identifier();
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Usage : my $hashtree = $value->hash_tree
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Function: For supporting the AnnotationI interface just returns the value
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as a hashref with the key 'value' pointing to the value
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$h->{'name'} = $self->name();
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$h->{'identifier'} = $self->identifier();
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$h->{'definition'} = $self->definition();
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$h->{'synonyms'} = [$self->get_synonyms()];
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Usage : $obj->tagname($newval)
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Function: Get/set the tagname for this annotation value.
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Setting this is optional. If set, it obviates the need to provide
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a tag to AnnotationCollection when adding this object.
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This is aliased to ontology() here.
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Returns : value of tagname (a scalar)
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Args : new value (a scalar, optional)
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return $self->ontology(@_) if @_;
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# if in get mode we need to get the name from the ontology
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my $ont = $self->ontology();
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return ref($ont) ? $ont->name() : $ont;
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=head1 Methods for Bio::Ontology::TermI compliance
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Usage : $obj->term($newval)
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Function: Get/set the Bio::Ontology::TermI implementing object.
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We implement TermI by composition, and this method sets/gets the
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object we delegate to.
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Returns : value of term (a Bio::Ontology::TermI compliant object)
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Args : new value (a Bio::Ontology::TermI compliant object, optional)
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my ($self,$value) = @_;
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if( defined $value) {
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$self->{'term'} = $value;
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if(! exists($self->{'term'})) {
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$self->{'term'} = Bio::Ontology::Term->new();
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return $self->{'term'};
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Usage : $term->identifier( "0003947" );
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print $term->identifier();
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Function: Set/get for the identifier of this Term.
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Returns : The identifier [scalar].
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Args : The identifier [scalar] (optional).
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return shift->term()->identifier(@_);
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Usage : $term->name( "N-acetylgalactosaminyltransferase" );
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Function: Set/get for the name of this Term.
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Returns : The name [scalar].
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Args : The name [scalar] (optional).
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return shift->term()->name(@_);
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Usage : $term->definition( "Catalysis of ..." );
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print $term->definition();
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Function: Set/get for the definition of this Term.
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Returns : The definition [scalar].
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Args : The definition [scalar] (optional).
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return shift->term()->definition(@_);
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Usage : $term->ontology( $top );
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$top = $term->ontology();
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Function: Set/get for a relationship between this Term and
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another Term (e.g. the top level of the ontology).
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Returns : The ontology of this Term [TermI].
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Args : The ontology of this Term [TermI or scalar -- which
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becomes the name of the catagory term] (optional).
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return shift->term()->ontology(@_);
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Usage : $term->is_obsolete( 1 );
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if ( $term->is_obsolete() )
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Function: Set/get for the obsoleteness of this Term.
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Returns : the obsoleteness [0 or 1].
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Args : the obsoleteness [0 or 1] (optional).
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return shift->term()->is_obsolete(@_);
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Usage : $term->comment( "Consider the term ..." );
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print $term->comment();
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Function: Set/get for an arbitrary comment about this Term.
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Args : A comment (optional).
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return shift->term()->comment(@_);
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Title : get_synonyms()
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Usage : @aliases = $term->get_synonyms();
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Function: Returns a list of aliases of this Term.
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Returns : A list of aliases [array of [scalar]].
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return shift->term()->get_synonyms(@_);
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Usage : $term->add_synonym( @asynonyms );
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$term->add_synonym( $synonym );
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Function: Pushes one or more synonyms into the list of synonyms.
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Args : One synonym [scalar] or a list of synonyms [array of [scalar]].
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return shift->term()->add_synonym(@_);
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=head2 remove_synonyms
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Title : remove_synonyms()
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Usage : $term->remove_synonyms();
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Function: Deletes (and returns) the synonyms of this Term.
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Returns : A list of synonyms [array of [scalar]].
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sub remove_synonyms {
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return shift->term()->remove_synonyms(@_);
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Title : get_dblinks()
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Usage : @ds = $term->get_dblinks();
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Function: Returns a list of each dblinks of this GO term.
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Returns : A list of dblinks [array of [scalars]].
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return shift->term->get_dblinks(@_);
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Usage : $term->add_dblink( @dbls );
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$term->add_dblink( $dbl );
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Function: Pushes one or more dblinks
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into the list of dblinks.
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Args : One dblink [scalar] or a list of
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dblinks [array of [scalars]].
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return shift->term->add_dblink(@_);
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=head2 remove_dblinks
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Title : remove_dblinks()
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Usage : $term->remove_dblinks();
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Function: Deletes (and returns) the definition references of this GO term.
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Returns : A list of definition references [array of [scalars]].
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return shift->term->remove_dblinks(@_);
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=head2 get_secondary_ids
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Title : get_secondary_ids
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Usage : @ids = $term->get_secondary_ids();
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Function: Returns a list of secondary identifiers of this Term.
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Secondary identifiers mostly originate from merging terms,
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or possibly also from splitting terms.
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Returns : A list of secondary identifiers [array of [scalar]]
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sub get_secondary_ids {
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return shift->term->get_secondary_ids(@_);
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} # get_secondary_ids
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=head2 add_secondary_id
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Title : add_secondary_id
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Usage : $term->add_secondary_id( @ids );
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$term->add_secondary_id( $id );
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Function: Adds one or more secondary identifiers to this term.
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Args : One or more secondary identifiers [scalars]
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sub add_secondary_id {
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return shift->term->add_secondary_id(@_);
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=head2 remove_secondary_ids
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Title : remove_secondary_ids
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Usage : $term->remove_secondary_ids();
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Function: Deletes (and returns) the secondary identifiers of this Term.
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Returns : The previous list of secondary identifiers [array of [scalars]]
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sub remove_secondary_ids {
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return shift->term->remove_secondary_ids(@_);
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} # remove_secondary_ids
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Bio/Annotation/OntologyTerm.pm
