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1 # $Id: TermI.pm,v 1.8.2.3 2003/05/27 22:00:52 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Ontology::Term
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4 #
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5 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
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6 #
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7 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
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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
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24 =head1 NAME
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25
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26 TermI - interface for ontology terms
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27
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28 =head1 SYNOPSIS
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29
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30 #get Bio::Ontology::TermI somehow.
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31
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32 print $term->identifier(), "\n";
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33 print $term->name(), "\n";
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34 print $term->definition(), "\n";
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35 print $term->is_obsolete(), "\n";
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36 print $term->comment(), "\n";
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37
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38 foreach my $synonym ( $term->get_synonyms() ) {
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39 print $synonym, "\n";
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40 }
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41
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42
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43 =head1 DESCRIPTION
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44
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45 This is "dumb" interface for ontology terms providing basic methods
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46 (it provides no functionality related to graphs).
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47
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48 =head1 FEEDBACK
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49
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50 =head2 Mailing Lists
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51
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52 User feedback is an integral part of the evolution of this and other
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53 Bioperl modules. Send your comments and suggestions preferably to one
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54 of the Bioperl mailing lists. Your participation is much appreciated.
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55
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56 bioperl-l@bioperl.org - General discussion
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57 http://bio.perl.org/MailList.html - About the mailing lists
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58
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59 =head2 Reporting Bugs
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60
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61 Report bugs to the Bioperl bug tracking system to help us keep track
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62 the bugs and their resolution. Bug reports can be submitted via email
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63 or the web:
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64
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65 bioperl-bugs@bio.perl.org
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66 http://bugzilla.bioperl.org/
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67
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68 =head1 AUTHOR
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69
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70 Christian M. Zmasek
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71
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72 Email: czmasek@gnf.org or cmzmasek@yahoo.com
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73
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74 WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
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75
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76 Address:
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77
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78 Genomics Institute of the Novartis Research Foundation
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79 10675 John Jay Hopkins Drive
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80 San Diego, CA 92121
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81
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82 =head1 APPENDIX
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83
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84 The rest of the documentation details each of the object
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85 methods.
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86
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87 =cut
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88
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89
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90 # Let the code begin...
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91
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92 package Bio::Ontology::TermI;
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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
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100
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101 =head2 identifier
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102
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103 Title : identifier
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104 Usage : $term->identifier( "0003947" );
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105 or
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106 print $term->identifier();
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107 Function: Set/get for the identifier of this Term.
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108 Returns : The identifier [scalar].
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109 Args : The identifier [scalar] (optional).
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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 } # identifier
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116
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117
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118
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119
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120 =head2 name
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121
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122 Title : name
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123 Usage : $term->name( "N-acetylgalactosaminyltransferase" );
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124 or
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125 print $term->name();
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126 Function: Set/get for the name of this Term.
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127 Returns : The name [scalar].
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128 Args : The name [scalar] (optional).
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129
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130 =cut
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131
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132 sub name {
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133 shift->throw_not_implemented();
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134 } # name
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135
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136
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137
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138
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139
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140 =head2 definition
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141
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142 Title : definition
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143 Usage : $term->definition( "Catalysis of ..." );
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144 or
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145 print $term->definition();
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146 Function: Set/get for the definition of this Term.
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147 Returns : The definition [scalar].
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148 Args : The definition [scalar] (optional).
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149
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150 =cut
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151
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152 sub definition {
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153 shift->throw_not_implemented();
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154 } # definition
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155
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156
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157
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158 =head2 ontology
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159
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160 Title : ontology
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161 Usage : $ont = $term->ontology();
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162 or
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163 $term->ontology( $ont );
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164 Function: Get the ontology this term is in.
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165
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166 An implementation may not permit the value of this
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167 attribute to be changed once it is set, since that may have
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168 serious consequences (note that with the ontology in hand
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169 you can query for all related terms etc).
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170
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171 Note for implementors: you will almost certainly have to
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172 take special precaution in order not to create cyclical
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173 references in memory.
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174
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175 Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI>
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176 implementing object.
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177 Args : On set, the ontology of this Term as a L<Bio::Ontology::OntologyI>
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178 implementing object or a string representing its name.
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179
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180 =cut
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181
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182 sub ontology {
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183 shift->throw_not_implemented();
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184 } # ontology
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185
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186
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187
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188 =head2 version
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189
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190 Title : version
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191 Usage : $term->version( "1.00" );
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192 or
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193 print $term->version();
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194 Function: Set/get for version information.
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195 Returns : The version [scalar].
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196 Args : The version [scalar] (optional).
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197
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198 =cut
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199
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200 sub version {
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201 shift->throw_not_implemented();
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202 } # version
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203
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204
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205
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206
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207 =head2 is_obsolete
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208
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209 Title : is_obsolete
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210 Usage : $term->is_obsolete( 1 );
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211 or
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212 if ( $term->is_obsolete() )
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213 Function: Set/get for the obsoleteness of this Term.
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214 Returns : the obsoleteness [0 or 1].
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215 Args : the obsoleteness [0 or 1] (optional).
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216
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217 =cut
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218
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219 sub is_obsolete {
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220 shift->throw_not_implemented();
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221 } # is_obsolete
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222
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223
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224
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225 =head2 comment
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226
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227 Title : comment
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228 Usage : $term->comment( "Consider the term ..." );
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229 or
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230 print $term->comment();
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231 Function: Set/get for an arbitrary comment about this Term.
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232 Returns : A comment.
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233 Args : A comment (optional).
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234
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235 =cut
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236
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237 sub comment {
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238 shift->throw_not_implemented();
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239 } # comment
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240
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241
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242
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243
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244 =head2 get_synonyms
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245
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246 Title : get_synonyms
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247 Usage : @aliases = $term->get_synonyms();
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248 Function: Returns a list of aliases of this Term.
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249
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250 If an implementor of this interface permits modification of
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251 this array property, the class should define at least
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252 methods add_synonym() and remove_synonyms(), with obvious
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253 functionality.
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254
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255 Returns : A list of aliases [array of [scalar]].
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256 Args :
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257
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258 =cut
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259
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260 sub get_synonyms {
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261 shift->throw_not_implemented();
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262 } # get_synonyms
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263
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264 =head2 get_dblinks
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265
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266 Title : get_dblinks()
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267 Usage : @ds = $term->get_dblinks();
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268 Function: Returns a list of each dblink of this term.
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269
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270 If an implementor of this interface permits modification of
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271 this array property, the class should define at least
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272 methods add_dblink() and remove_dblinks(), with obvious
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273 functionality.
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274
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275 Returns : A list of dblinks [array of [scalars]].
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276 Args :
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277
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278 =cut
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279
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280 sub get_dblinks {
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281 shift->throw_not_implemented();
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282 } # get_dblinks
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283
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284 =head2 get_secondary_ids
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285
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286 Title : get_secondary_ids
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287 Usage : @ids = $term->get_secondary_ids();
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288 Function: Returns a list of secondary identifiers of this Term.
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289
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290 Secondary identifiers mostly originate from merging terms,
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291 or possibly also from splitting terms.
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292
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293 If an implementor of this interface permits modification of
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294 this array property, the class should define at least
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295 methods add_secondary_id() and remove_secondary_ids(), with
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296 obvious functionality.
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297
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298 Returns : A list of secondary identifiers [array of [scalar]]
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299 Args :
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300
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301 =cut
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302
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303 sub get_secondary_ids {
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304 shift->throw_not_implemented();
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305 } # get_secondary_ids
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306
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307
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308 1;
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