Bio::Ontology::OBOterm(3) representation of OBO terms


$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.


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.


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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 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 the web:


Sohel Merchant

Email: [email protected]


  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.


 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]