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1 # $Id: RelationshipI.pm,v 1.2.2.2 2003/03/27 10:07:56 lapp Exp $
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2 #
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3 # BioPerl module for RelationshipI
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4 #
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5 # Cared for by Peter Dimitrov <dimitrov@gnf.org>
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6 #
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7 # (c) Peter Dimitrov
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8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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9 #
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10 # You may distribute this module under the same terms as perl itself.
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11 # Refer to the Perl Artistic License (see the license accompanying this
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12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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13 # for the terms under which you may use, modify, and redistribute this module.
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14 #
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15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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18 #
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19 # You may distribute this module under the same terms as perl itself
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20
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21 # POD documentation - main docs before the code
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22
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23 =head1 NAME
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24
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25 RelationshipI - Interface for a relationship between ontology terms
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26
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27 =head1 SYNOPSIS
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28
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29 # see documentation of methods and an implementation, e.g.,
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30 # Bio::Ontology::Relationship
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31
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32 =head1 DESCRIPTION
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33
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34 This is the minimal interface for a relationship between two terms in
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35 an ontology. Ontology engines will use this.
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36
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37 The terminology we use here is the one commonly used for ontologies,
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38 namely the triple of (subject, predicate, object), which in addition
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39 is scoped in a namespace (ontology). It is called triple because it is
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40 a tuple of three ontology terms.
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41
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42 There are other terminologies in use for expressing relationships. For
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43 those who it helps to better understand the concept, the triple of
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44 (child, relationship type, parent) would be equivalent to the
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45 terminology chosen here, disregarding the question whether the notion
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46 of parent and child is sensible in the context of the relationship
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47 type or not. Especially in the case of ontologies with a wide variety
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48 of predicates the parent/child terminology and similar ones can
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49 quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A
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50 binds B), or even conflicting (e.g., A is-parent-of B), and are
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51 therefore strongly discouraged.
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52
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53 =head1 FEEDBACK
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54
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55 =head2 Mailing Lists
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56
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57 User feedback is an integral part of the evolution of this and other
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58 Bioperl modules. Send your comments and suggestions preferably to
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59 the Bioperl mailing list. Your participation is much appreciated.
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60
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61 bioperl-l@bioperl.org - General discussion
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62 http://bioperl.org/MailList.shtml - About the mailing lists
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63
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64 =head2 Reporting Bugs
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65
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66 Report bugs to the Bioperl bug tracking system to help us keep track
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67 of the bugs and their resolution. Bug reports can be submitted via
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68 email or the web:
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69
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70 bioperl-bugs@bioperl.org
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71 http://bugzilla.bioperl.org/
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72
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73 =head1 AUTHOR - Peter Dimitrov
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74
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75 Email dimitrov@gnf.org
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76
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77 =head1 CONTRIBUTORS
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78
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79 Hilmar Lapp, email: hlapp at gmx.net
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80
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81 =head1 APPENDIX
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82
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83 The rest of the documentation details each of the object methods.
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84 Internal methods are usually preceded with a _
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85
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86 =cut
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87
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88
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89 # Let the code begin...
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90
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91
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92 package Bio::Ontology::RelationshipI;
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93 use vars qw(@ISA);
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94 use strict;
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95 use Bio::Root::RootI;
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96
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97 @ISA = qw( Bio::Root::RootI );
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98
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99 =head2 identifier
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100
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101 Title : identifier
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102 Usage : print $rel->identifier();
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103 Function: Set/get for the identifier of this Relationship.
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104
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105 Note that this may not necessarily be used by a particular
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106 ontology.
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107
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108 Returns : The identifier [scalar].
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109 Args :
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110
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111 =cut
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112
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113 sub identifier{
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114 shift->throw_not_implemented();
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115 }
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116
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117 =head2 subject_term
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118
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119 Title : subject_term
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120 Usage : $subj = $rel->subject_term();
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121 Function: Set/get for the subject term of this Relationship.
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122
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123 The common convention for ontologies is to express
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124 relationships between terms as triples (subject, predicate,
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125 object).
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126
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127 Returns : The subject term [Bio::Ontology::TermI].
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128 Args :
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129
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130 =cut
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131
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132 sub subject_term{
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133 shift->throw_not_implemented();
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134 }
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135
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136 =head2 object_term
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137
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138 Title : object_term
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139 Usage : $object = $rel->object_term();
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140 Function: Set/get for the object term of this Relationship.
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141
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142 The common convention for ontologies is to express
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143 relationships between terms as triples (subject, predicate,
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144 object).
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145
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146 Returns : The object term [Bio::Ontology::TermI].
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147 Args :
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148
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149 =cut
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150
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151 sub object_term{
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152 shift->throw_not_implemented();
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153 }
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154
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155 =head2 predicate_term
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156
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157 Title : predicate_term
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158 Usage : $type = $rel->predicate_term();
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159 Function: Set/get for the relationship type of this relationship.
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160
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161 The common convention for ontologies is to express
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162 relationships between terms as triples (subject, predicate,
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163 object).
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164
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165 Returns : The relationship type [Bio::Ontology::TermI].
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166 Args :
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167
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168 =cut
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169
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170 sub predicate_term{
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171 shift->throw_not_implemented();
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172 }
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173
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174 =head2 ontology
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175
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176 Title : ontology
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177 Usage : $ont = $obj->ontology()
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178 Function: Get the ontology that defined (is the scope for) this
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179 relationship.
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180 Example :
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181 Returns : an object implementing L<Bio::Ontology::OntologyI>
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182 Args :
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183
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184
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185 =cut
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186
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187 sub ontology{
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188 shift->throw_not_implemented();
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189 }
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190
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191 1;
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