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://github.com/bioperl/bioperl-live/issues

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    :