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Bio::Ontology::GOterm.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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    :