NAME

       Bio::Ontology::GOterm - representation of GO terms

SYNOPSIS

         $term = Bio::Ontology::GOterm->new
           ( -go_id       => "GO:0016847",
             -name        => "1-aminocyclopropane-1-carboxylate synthase",
             -definition  => "Catalysis of ...",
             -is_obsolete => 0,
             -comment     => "" );

         $term->add_definition_references( @refs );
         $term->add_secondary_GO_ids( @ids );
         $term->add_aliases( @aliases );

         foreach my $dr ( $term->each_definition_reference() ) {
             print $dr, "\n";
         }

         # etc.

DESCRIPTION

       This is "dumb" class for GO terms (it provides no functionality related to graphs).
       Implements Bio::Ontology::TermI.

FEEDBACK

   Mailing Lists
       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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Christian M. Zmasek

       Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com

       WWW:   http://monochrome-effect.net/

       Address:

         Genomics Institute of the Novartis Research Foundation
         10675 John Jay Hopkins Drive
         San Diego, CA 92121

APPENDIX

       The rest of the documentation details each of the object methods.

   new
        Title   : new
        Usage   : $term = Bio::Ontology::GOterm->new(
              -go_id       => "GO:0016847",
              -name        => "1-aminocyclopropane-1-carboxylate synthase",
              -definition  => "Catalysis of ...",
              -is_obsolete => 0,
              -comment     => "" );
        Function: Creates a new Bio::Ontology::GOterm.
        Returns : A new Bio::Ontology::GOterm object.
        Args    : -go_id         => the goid of this GO term [GO:nnnnnnn]
                                    or [nnnnnnn] (nnnnnnn is a zero-padded
                                    integer of seven digits)
                  -name          => the name of this GO term [scalar]
                  -definition    => the definition of this GO term [scalar]
                  -ontology      => the ontology for this term (a
                                    Bio::Ontology::OntologyI compliant object)
                  -version       => version information [scalar]
                  -is_obsolete   => the obsoleteness of this GO term [0 or 1]
                  -comment       => a comment [scalar]

   init
        Title   : init()
        Usage   : $term->init();
        Function: Initializes this GOterm to all "" and empty lists.
        Returns :
        Args    :

   GO_id
        Title   : GO_id
        Usage   : $term->GO_id( "GO:0003947" );
                  or
                  print $term->GO_id();
        Function: Set/get for the goid of this GO term.

                  This is essentially an alias to identifier(), with added
                  format checking.

        Returns : The goid [GO:nnnnnnn].
        Args    : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a
                  zero-padded integer of seven digits) (optional).

   get_secondary_GO_ids
        Title   : get_secondary_GO_ids
        Usage   : @ids = $term->get_secondary_GO_ids();
        Function: Returns a list of secondary goids of this Term.

                  This is aliased to remove_secondary_ids().

        Returns : A list of secondary goids [array of [GO:nnnnnnn]]
                  (nnnnnnn is a zero-padded integer of seven digits).
        Args    :

   add_secondary_GO_id
        Title   : add_secondary_GO_id
        Usage   : $term->add_secondary_GO_id( @ids );
                  or
                  $term->add_secondary_GO_id( $id );
        Function: Pushes one or more secondary goids into
                  the list of secondary goids.

                  This is aliased to remove_secondary_ids().

        Returns :
        Args    : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list
                  of secondary goids [array of [GO:nnnnnnn or nnnnnnn]]
                  (nnnnnnn is a zero-padded integer of seven digits).

   remove_secondary_GO_ids
        Title   : remove_secondary_GO_ids()
        Usage   : $term->remove_secondary_GO_ids();
        Function: Deletes (and returns) the secondary goids of this Term.

                  This is aliased to remove_secondary_ids().

        Returns : A list of secondary goids [array of [GO:nnnnnnn]]
                  (nnnnnnn is a zero-padded integer of seven digits).
        Args    :

   to_string
        Title   : to_string()
        Usage   : print $term->to_string();
        Function: to_string method for GO terms.
        Returns : A string representation of this GOterm.
        Args    :