Bio/Ontology/RelationshipI.pm

   1 #
   2 # BioPerl module for RelationshipI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Peter Dimitrov <dimitrov@gnf.org>
   7 #
   8 # (c) Peter Dimitrov
   9 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
  10 #
  11 # You may distribute this module under the same terms as perl itself.
  12 # Refer to the Perl Artistic License (see the license accompanying this
  13 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  14 # for the terms under which you may use, modify, and redistribute this module.
  15 #
  16 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  17 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  18 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  19 #
  20 # You may distribute this module under the same terms as perl itself
  21
  22 # POD documentation - main docs before the code
  23
  24 =head1 NAME
  25
  26 Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms
  27
  28 =head1 SYNOPSIS
  29
  30     # see documentation of methods and an implementation, e.g.,
  31     # Bio::Ontology::Relationship
  32
  33 =head1 DESCRIPTION
  34
  35 This is the minimal interface for a relationship between two terms in
  36 an ontology. Ontology engines will use this.
  37
  38 The terminology we use here is the one commonly used for ontologies,
  39 namely the triple of (subject, predicate, object), which in addition
  40 is scoped in a namespace (ontology). It is called triple because it is
  41 a tuple of three ontology terms.
  42
  43 There are other terminologies in use for expressing relationships. For
  44 those who it helps to better understand the concept, the triple of
  45 (child, relationship type, parent) would be equivalent to the
  46 terminology chosen here, disregarding the question whether the notion
  47 of parent and child is sensible in the context of the relationship
  48 type or not. Especially in the case of ontologies with a wide variety
  49 of predicates the parent/child terminology and similar ones can
  50 quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A
  51 binds B), or even conflicting (e.g., A is-parent-of B), and are
  52 therefore strongly discouraged.
  53
  54 =head1 FEEDBACK
  55
  56 =head2 Mailing Lists
  57
  58 User feedback is an integral part of the evolution of this and other
  59 Bioperl modules. Send your comments and suggestions preferably to
  60 the Bioperl mailing list.  Your participation is much appreciated.
  61
  62   bioperl-l@bioperl.org                  - General discussion
  63   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  64
  65 =head2 Support
  66
  67 Please direct usage questions or support issues to the mailing list:
  68
  69 I<bioperl-l@bioperl.org>
  70
  71 rather than to the module maintainer directly. Many experienced and
  72 reponsive experts will be able look at the problem and quickly
  73 address it. Please include a thorough description of the problem
  74 with code and data examples if at all possible.
  75
  76 =head2 Reporting Bugs
  77
  78 Report bugs to the Bioperl bug tracking system to help us keep track
  79 of the bugs and their resolution. Bug reports can be submitted via
  80 the web:
  81
  82   https://github.com/bioperl/bioperl-live/issues
  83
  84 =head1 AUTHOR - Peter Dimitrov
  85
  86 Email dimitrov@gnf.org
  87
  88 =head1 CONTRIBUTORS
  89
  90  Hilmar Lapp, email: hlapp at gmx.net
  91
  92 =head1 APPENDIX
  93
  94 The rest of the documentation details each of the object methods.
  95 Internal methods are usually preceded with a _
  96
  97 =cut
  98
  99
 100 # Let the code begin...
 101
 102
 103 package Bio::Ontology::RelationshipI;
 104 use strict;
 105
 106 use base qw(Bio::Root::RootI);
 107
 108 =head2 identifier
 109
 110  Title   : identifier
 111  Usage   : print $rel->identifier();
 112  Function: Set/get for the identifier of this Relationship.
 113
 114            Note that this may not necessarily be used by a particular
 115            ontology.
 116
 117  Returns : The identifier [scalar].
 118  Args    :
 119
 120 =cut
 121
 122 sub identifier{
 123     shift->throw_not_implemented();
 124 }
 125
 126 =head2 subject_term
 127
 128  Title   : subject_term
 129  Usage   : $subj = $rel->subject_term();
 130  Function: Set/get for the subject term of this Relationship.
 131
 132            The common convention for ontologies is to express
 133            relationships between terms as triples (subject, predicate,
 134            object).
 135
 136  Returns : The subject term [Bio::Ontology::TermI].
 137  Args    :
 138
 139 =cut
 140
 141 sub subject_term{
 142     shift->throw_not_implemented();
 143 }
 144
 145 =head2 object_term
 146
 147  Title   : object_term
 148  Usage   : $object = $rel->object_term();
 149  Function: Set/get for the object term of this Relationship.
 150
 151            The common convention for ontologies is to express
 152            relationships between terms as triples (subject, predicate,
 153            object).
 154
 155  Returns : The object term [Bio::Ontology::TermI].
 156  Args    :
 157
 158 =cut
 159
 160 sub object_term{
 161     shift->throw_not_implemented();
 162 }
 163
 164 =head2 predicate_term
 165
 166  Title   : predicate_term
 167  Usage   : $type = $rel->predicate_term();
 168  Function: Set/get for the relationship type of this relationship.
 169
 170            The common convention for ontologies is to express
 171            relationships between terms as triples (subject, predicate,
 172            object).
 173
 174  Returns : The relationship type [Bio::Ontology::TermI].
 175  Args    :
 176
 177 =cut
 178
 179 sub predicate_term{
 180     shift->throw_not_implemented();
 181 }
 182
 183 =head2 ontology
 184
 185  Title   : ontology
 186  Usage   : $ont = $obj->ontology()
 187  Function: Get the ontology that defined (is the scope for) this
 188            relationship.
 189  Example :
 190  Returns : an object implementing Bio::Ontology::OntologyI
 191  Args    :
 192
 193 See L<Bio::Ontology::OntologyI>.
 194
 195 =cut
 196
 197 sub ontology{
 198     shift->throw_not_implemented();
 199 }
 200
 201 1;