Term - 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->each_synonym() ) { print $synonym, "\n"; } This is "dumb" interface for ontology terms providing basic methods (it provides no functionality related to graphs). It implements the Bio::Ontology::TermI interface. This class also implements Bio::IdentifiableI and Bio::DescribableI.

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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.

new
Title : new Usage : $term = Bio::Ontology::Term->new( -identifier => "16847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); Function: Creates a new Bio::Ontology::Term. Returns : A new Bio::Ontology::Term object. Args : -identifier => the identifier of this term [scalar] -name => the name of this term [scalar] -definition => the definition of this term [scalar] -ontology => the ontology this term lives in (a L<Bio::Ontology::OntologyI> object) -version => version information [scalar] -is_obsolete => the obsoleteness of this term [0 or 1] -comment => a comment [scalar] -dblinks => L<Bio::Annotation::DBLink> objects [reference to array] -references => L<Bio::Annotation::Reference> objects [reference to array]

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. Note that with the ontology in hand you can query for all related terms etc. See L<Bio::Ontology::OntologyI>. 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. 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 onto 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_references
Title : get_references Usage : @references = $self->get_references Fuctnion: Returns a list of references Return : A list of objects Args : [none]

add_reference
Title : add_reference Usage : $self->add_reference($reference); $self->add_reference($reference1, $reference2); Fuctnion: Add one or more references Returns : [none]

remove_references
Title : remove_references Usage : $self->remove_references; Function: Deletes (and returns) all references Returns : A list of references Args : [none]

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 :

object_id
Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. This is a synonym for identifier(). Returns : A scalar

authority
Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) This forwards to ontology()->authority(). Note that you cannot set the authority before having set the ontology or the namespace (which will set the ontology). Returns : A scalar Args : on set, the new value (a scalar)

namespace
Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection. This forwards to ontology() (set mode) and ontology()->name() (get mode). I.e., setting the namespace will set the ontology to one matching that name in the ontology store, or to one newly created. Returns : A scalar Args : on set, the new value (a scalar)

display_name
Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user. The definition in L<Bio::DescribableI> states that the string should not contain spaces. As this isn't very sensible for ontology terms, we relax this here. The implementation just forwards to name(). Returns : A scalar Args : on set, the new value (a scalar)

description
Title : description Usage : $string = $obj->description() Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. This forwards to definition(). The caveat is that the text will often be longer for ontology term definitions than the 255 characters stated in the definition in L<Bio::DescribableI>. Returns : A scalar Args : on set, the new value (a scalar) Used for looking up the methods that supercedes them.

category
Title : category Usage : Function: This method is deprecated. Use ontology() instead. Example : Returns : Args :