Bio::Ontology
OBOterm
Summary
Bio::Ontology::OBOterm - representation of OBO terms
Package variables
No package variables defined.
Inherit
Synopsis
$term = Bio::Ontology::OBOterm->new
( -identifier => "GO:0005623",
-name => "Cell",
-definition => "The basic structural and functional unit ...",
-is_obsolete => 0,
-comment => "" );
$term->add_reference( @refs );
$term->add_secondary_id( @ids );
$term->add_synonym( @synonym );
# etc.
Description
This is data holder class for OBO terms. It is currently a dummy class since we anticipate that the
OBO term will become more richer with more features being added to OBO flat-file format.
Methods
Methods description
Title : new
Usage : $term = Bio::Ontology::OBOterm->new
( -identifier => "GO:0005623",
-name => "Cell",
-definition => "The basic structural and functional unit ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::OBOterm.
Returns : A new Bio::Ontology::OBOterm object.
Args : -identifier => the id of this OBO term [GO:nnnnnnn]
integer of seven digits)
-name => the name of this OBO term [scalar]
-definition => the definition of this OBO term [scalar]
-ontology => the ontology for this term (a
Bio::Ontology::OntologyI compliant object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this OBO term [0 or 1]
-comment => a comment [scalar] |
Methods code
sub new
{
my ( $class, @args ) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Sohel Merchant
Email:
s-merchant@northwestern.eduAddress:
Northwestern University
Center for Genetic Medicine (CGM), dictyBase
Suite 1206,
676 St. Clair st
Chicago IL 60611
The rest of the documentation details each of the object
methods.