Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI 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); Ontology term annotation object

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Reporting Bugs
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/ Email bioperl-l@bio.perl.org Email hlapp at gmx.net The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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.

as_text
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

hash_tree
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

tagname
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)

term
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)

identifier
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).

name
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).

definition
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).

ontology
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).

is_obsolete
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).

comment
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).

get_synonyms
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 :

add_synonym
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]].

remove_synonyms
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 :

get_dblinks
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 :

add_dblink
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]].

remove_dblinks
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 :

get_secondary_ids
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 :

add_secondary_id
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]

remove_secondary_ids
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 :