TermI - interface for ontology terms #get Bio::Ontology::TermI somehow. print $term->identifier(), "\n"; print $term->name(), "\n"; print $term->definition(), "\n"; print $term->is_obsolete(), "\n"; print $term->comment(), "\n"; foreach my $synonym ( $term->get_synonyms() ) { print $synonym, "\n"; } This is "dumb" interface for ontology terms providing basic methods (it provides no functionality related to graphs).

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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@bio.perl.org http://bugzilla.bioperl.org/ Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 The rest of the documentation details each of the object methods.

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 : $ont = $term->ontology(); or $term->ontology( $ont ); Function: Get the ontology this term is in. An implementation may not permit the value of this attribute to be changed once it is set, since that may have serious consequences (note that with the ontology in hand you can query for all related terms etc). Note for implementors: you will almost certainly have to take special precaution in order not to create cyclical references in memory. Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI> implementing object. Args : On set, the ontology of this Term as a L<Bio::Ontology::OntologyI> implementing object or a string representing its name.

version
Title : version Usage : $term->version( "1.00" ); or print $term->version(); Function: Set/get for version information. Returns : The version [scalar]. Args : The version [scalar] (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. If an implementor of this interface permits modification of this array property, the class should define at least methods add_synonym() and remove_synonyms(), with obvious functionality. Returns : A list of aliases [array of [scalar]]. Args :

get_dblinks
Title : get_dblinks() Usage : @ds = $term->get_dblinks(); Function: Returns a list of each dblink of this term. If an implementor of this interface permits modification of this array property, the class should define at least methods add_dblink() and remove_dblinks(), with obvious functionality. Returns : A list of dblinks [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. If an implementor of this interface permits modification of this array property, the class should define at least methods add_secondary_id() and remove_secondary_ids(), with obvious functionality. Returns : A list of secondary identifiers [array of [scalar]] Args :