branch-1-6/Bio/Ontology/OBOterm.pm

   1 # $Id$
   2
   3 =head1 NAME
   4
   5 Bio::Ontology::OBOterm - representation of OBO terms
   6
   7 =head1 SYNOPSIS
   8
   9   $term = Bio::Ontology::OBOterm->new
  10     ( -identifier       => "GO:0005623",
  11       -name        => "Cell",
  12       -definition  => "The basic structural and functional unit ...",
  13       -is_obsolete => 0,
  14       -comment     => "" );
  15
  16   $term->add_reference( @refs );
  17   $term->add_secondary_id( @ids );
  18   $term->add_synonym( @synonym );
  19
  20   # etc.
  21
  22 =head1 DESCRIPTION
  23
  24 This is data holder class for OBO terms. It is currently a dummy class since we anticipate that the
  25 OBO term will become more richer with more features being added to OBO flat-file format.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to one
  33 of the Bioperl mailing lists.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 the bugs and their resolution.  Bug reports can be submitted via the web:
  53
  54   http://bugzilla.open-bio.org/
  55
  56 =head1 AUTHOR
  57
  58 Sohel Merchant
  59
  60 Email: s-merchant@northwestern.edu
  61
  62 Address:
  63
  64   Northwestern University
  65   Center for Genetic Medicine (CGM), dictyBase
  66   Suite 1206,
  67   676 St. Clair st
  68   Chicago IL 60611
  69
  70 =head1 APPENDIX
  71
  72 The rest of the documentation details each of the object
  73 methods.
  74
  75 =cut
  76
  77 # Let the code begin...
  78
  79 package Bio::Ontology::OBOterm;
  80 use strict;
  81
  82 use constant TRUE  => 1;
  83 use constant FALSE => 0;
  84
  85 use base qw(Bio::Ontology::Term);
  86
  87 =head2 new
  88
  89  Title   : new
  90  Usage   :   $term = Bio::Ontology::OBOterm->new
  91      ( -identifier       => "GO:0005623",
  92       -name        => "Cell",
  93       -definition  => "The basic structural and functional unit ...",
  94       -is_obsolete => 0,
  95       -comment     => "" );
  96
  97  Function: Creates a new Bio::Ontology::OBOterm.
  98  Returns : A new Bio::Ontology::OBOterm object.
  99  Args    : -identifier    => the id of this OBO term [GO:nnnnnnn]
 100                              integer of seven digits)
 101            -name          => the name of this OBO term [scalar]
 102            -definition    => the definition of this OBO term [scalar]
 103            -ontology      => the ontology for this term (a
 104                              Bio::Ontology::OntologyI compliant object)
 105            -version       => version information [scalar]
 106            -is_obsolete   => the obsoleteness of this OBO term [0 or 1]
 107            -comment       => a comment [scalar]
 108
 109 =cut
 110
 111 sub new {
 112
 113     my ( $class, @args ) = @_;
 114     my $self = $class->SUPER::new(@args);
 115     return $self;
 116 }    # new
 117
 118
 119
 120 1;