Bio/Ontology/OBOterm.pm

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