Bio::Ontology TermFactory
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Ontology::TermFactory - Instantiates a new
Bio::Ontology::TermI (or derived class) through a factory
Package variables
No package variables defined.
Included modules
    use Bio::Ontology::TermFactory;
# the default type is Bio::Ontology::Term my $factory = Bio::Ontology::TermFactory->new( -type => 'Bio::Ontology::GOterm'); my $term = $factory->create_object(-name => 'peroxisome', -ontology => 'Gene Ontology', -identifier => 'GO:0005777');
This object will build Bio::Ontology::TermI objects generically.
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Ontology::TermFactory->new();
Function: Builds a new Bio::Ontology::TermFactory object
Returns : Bio::Ontology::TermFactory
Args : -type => string, name of a Bio::Ontology::TermI derived class.
The default is Bio::Ontology::Term.
See Bio::Ontology::TermI, Bio::Ontology::Term.
Methods code
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    # make sure this matches our requirements
$self->interface("Bio::Ontology::TermI"); $self->type($self->type() || "Bio::Ontology::Term"); return $self;
General documentation
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User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.                  - General discussion - About the mailing lists
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Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
AUTHOR - Hilmar LappTop
Email hlapp at
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
 Title   : create_object
Usage : my $term = $factory->create_object(<named parameters>);
Function: Instantiates new Bio::Ontology::TermI (or one of its child classes)
This object allows us to genericize the instantiation of Term objects. Returns : Bio::Ontology::TermI compliant object The return type is configurable using new(-type =>"..."). Args : initialization parameters specific to the type of term object we want. Typically -name => $name -identifier => identifier for the term -ontology => ontology for the term
See Bio::Ontology::TermI.