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1 # $Id: Term.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 Term - 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->each_synonym() ) {
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39 print $synonym, "\n";
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40 }
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41
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42 =head1 DESCRIPTION
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43
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44 This is "dumb" interface for ontology terms providing basic methods
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45 (it provides no functionality related to graphs). It implements the
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46 L<Bio::Ontology::TermI> interface.
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47
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48 This class also implements L<Bio::IdentifiableI> and
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49 L<Bio::DescribableI>.
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50
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51 =head1 FEEDBACK
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52
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53 =head2 Mailing Lists
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54
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55 User feedback is an integral part of the evolution of this and other
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56 Bioperl modules. Send your comments and suggestions preferably to one
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57 of the Bioperl mailing lists. Your participation is much appreciated.
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58
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59 bioperl-l@bioperl.org - General discussion
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60 http://bio.perl.org/MailList.html - About the mailing lists
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61
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62 =head2 Reporting Bugs
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63
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64 Report bugs to the Bioperl bug tracking system to help us keep track
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65 the bugs and their resolution. Bug reports can be submitted via email
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66 or the web:
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67
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68 bioperl-bugs@bio.perl.org
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69 http://bugzilla.bioperl.org/
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70
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71 =head1 AUTHOR
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72
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73 Christian M. Zmasek
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74
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75 Email: czmasek@gnf.org or cmzmasek@yahoo.com
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76
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77 WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
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78
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79 Address:
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80
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81 Genomics Institute of the Novartis Research Foundation
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82 10675 John Jay Hopkins Drive
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83 San Diego, CA 92121
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84
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85 =head1 APPENDIX
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86
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87 The rest of the documentation details each of the object
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88 methods.
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89
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90 =cut
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91
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92
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93 # Let the code begin...
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94
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95 package Bio::Ontology::Term;
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96 use vars qw( @ISA );
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97 use strict;
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98 use Bio::Root::Object;
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99 use Bio::Ontology::TermI;
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100 use Bio::Ontology::Ontology;
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101 use Bio::Ontology::OntologyStore;
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102 use Bio::IdentifiableI;
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103 use Bio::DescribableI;
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104
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105 use constant TRUE => 1;
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106 use constant FALSE => 0;
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107
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108 @ISA = qw( Bio::Root::Root
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109 Bio::Ontology::TermI
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110 Bio::IdentifiableI
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111 Bio::DescribableI
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112 );
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113
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114
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115
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116 =head2 new
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117
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118 Title : new
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119 Usage : $term = Bio::Ontology::Term->new( -identifier => "16847",
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120 -name => "1-aminocyclopropane-1-carboxylate synthase",
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121 -definition => "Catalysis of ...",
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122 -is_obsolete => 0,
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123 -comment => "" );
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124 Function: Creates a new Bio::Ontology::Term.
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125 Returns : A new Bio::Ontology::Term object.
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126 Args : -identifier => the identifier of this term [scalar]
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127 -name => the name of this term [scalar]
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128 -definition => the definition of this term [scalar]
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129 -ontology => the ontology this term lives in
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130 (a L<Bio::Ontology::OntologyI> object)
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131 -version => version information [scalar]
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132 -is_obsolete => the obsoleteness of this term [0 or 1]
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133 -comment => a comment [scalar]
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134
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135 =cut
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136
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137 sub new {
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138
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139 my( $class,@args ) = @_;
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140
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141 my $self = $class->SUPER::new( @args );
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142
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143 my ( $identifier,
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144 $name,
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145 $definition,
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146 $category,
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147 $ont,
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148 $version,
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149 $is_obsolete,
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150 $comment,
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151 $dblinks)
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152 = $self->_rearrange( [ qw( IDENTIFIER
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153 NAME
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154 DEFINITION
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155 CATEGORY
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156 ONTOLOGY
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157 VERSION
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158 IS_OBSOLETE
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159 COMMENT
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160 DBLINKS
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161 ) ], @args );
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162
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163 $self->init();
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164
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165 $identifier && $self->identifier( $identifier );
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166 $name && $self->name( $name );
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167 $definition && $self->definition( $definition );
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168 $category && $self->category( $category );
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169 $ont && $self->ontology( $ont );
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170 defined($version) && $self->version( $version );
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171 defined($is_obsolete) && $self->is_obsolete( $is_obsolete );
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172 $comment && $self->comment( $comment );
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173 ref($dblinks) && $self->add_dblink(@$dblinks);
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174
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175 return $self;
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176
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177 } # new
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178
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179
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180
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181 sub init {
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182
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183 my $self = shift;
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184
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185 $self->identifier(undef);
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186 $self->name(undef);
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187 $self->comment(undef);
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188 $self->definition(undef);
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189 $self->ontology(undef);
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190 $self->is_obsolete(0);
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191 $self->remove_synonyms();
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192 $self->remove_dblinks();
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193 $self->remove_secondary_ids();
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194
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195 } # init
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196
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197
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198
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199 =head2 identifier
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200
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201 Title : identifier
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202 Usage : $term->identifier( "0003947" );
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203 or
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204 print $term->identifier();
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205 Function: Set/get for the identifier of this Term.
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206 Returns : The identifier [scalar].
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207 Args : The identifier [scalar] (optional).
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208
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209 =cut
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210
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211 sub identifier {
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212 my $self = shift;
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213
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214 return $self->{'identifier'} = shift if @_;
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215 return $self->{'identifier'};
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216 } # identifier
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217
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218
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219
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220
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221 =head2 name
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222
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223 Title : name
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224 Usage : $term->name( "N-acetylgalactosaminyltransferase" );
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225 or
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226 print $term->name();
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227 Function: Set/get for the name of this Term.
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228 Returns : The name [scalar].
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229 Args : The name [scalar] (optional).
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230
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231 =cut
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232
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233 sub name {
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234 my $self = shift;
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235
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236 return $self->{'name'} = shift if @_;
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237 return $self->{'name'};
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238 } # name
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239
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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 definition
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245
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246 Title : definition
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247 Usage : $term->definition( "Catalysis of ..." );
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248 or
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249 print $term->definition();
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250 Function: Set/get for the definition of this Term.
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251 Returns : The definition [scalar].
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252 Args : The definition [scalar] (optional).
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253
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254 =cut
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255
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256 sub definition {
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257 my $self = shift;
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258
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259 return $self->{'definition'} = shift if @_;
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260 return $self->{'definition'};
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261 } # definition
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262
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263
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264 =head2 ontology
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265
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266 Title : ontology
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267 Usage : $ont = $term->ontology();
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268 or
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269 $term->ontology( $ont );
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270 Function: Get the ontology this term is in.
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271
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272 Note that with the ontology in hand you can query for all
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273 related terms etc. See L<Bio::Ontology::OntologyI>.
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274
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275 Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI>
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276 implementing object.
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277 Args : On set, the ontology of this Term as a L<Bio::Ontology::OntologyI>
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278 implementing object or a string representing its name.
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279
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280 =cut
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281
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282 sub ontology {
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283 my $self = shift;
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284 my $ont;
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285
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286 if(@_) {
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287 $ont = shift;
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288 if($ont) {
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289 $ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont);
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290 if(! $ont->isa("Bio::Ontology::OntologyI")) {
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291 $self->throw(ref($ont)." does not implement ".
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292 "Bio::Ontology::OntologyI. Bummer.");
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293 }
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294 }
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295 return $self->{"_ontology"} = $ont;
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296 }
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297 return $self->{"_ontology"};
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298 } # ontology
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299
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300
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301 =head2 version
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302
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303 Title : version
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304 Usage : $term->version( "1.00" );
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305 or
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306 print $term->version();
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307 Function: Set/get for version information.
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308 Returns : The version [scalar].
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309 Args : The version [scalar] (optional).
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310
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311 =cut
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312
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313 sub version {
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314 my $self = shift;
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315
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316 return $self->{'version'} = shift if @_;
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317 return $self->{'version'};
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318 } # version
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319
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320
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321
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322 =head2 is_obsolete
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323
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324 Title : is_obsolete
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325 Usage : $term->is_obsolete( 1 );
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326 or
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327 if ( $term->is_obsolete() )
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328 Function: Set/get for the obsoleteness of this Term.
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329 Returns : the obsoleteness [0 or 1].
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330 Args : the obsoleteness [0 or 1] (optional).
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331
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332 =cut
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333
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334 sub is_obsolete{
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335 my $self = shift;
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336
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337 return $self->{'is_obsolete'} = shift if @_;
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338 return $self->{'is_obsolete'};
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339 } # is_obsolete
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340
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341
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342
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343
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344
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345 =head2 comment
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346
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347 Title : comment
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348 Usage : $term->comment( "Consider the term ..." );
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349 or
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350 print $term->comment();
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351 Function: Set/get for an arbitrary comment about this Term.
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352 Returns : A comment.
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353 Args : A comment (optional).
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354
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355 =cut
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356
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357 sub comment{
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358 my $self = shift;
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359
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360 return $self->{'comment'} = shift if @_;
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361 return $self->{'comment'};
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362 } # comment
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363
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364
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365
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366
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367 =head2 get_synonyms
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368
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369 Title : get_synonyms
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370 Usage : @aliases = $term->get_synonyms;
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371 Function: Returns a list of aliases of this Term.
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372 Returns : A list of aliases [array of [scalar]].
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373 Args :
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374
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375 =cut
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376
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377 sub get_synonyms {
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378 my $self = shift;
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379
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380 return @{ $self->{ "_synonyms" } } if exists($self->{ "_synonyms" });
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381 return ();
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382 } # get_synonyms
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383
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384
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385 =head2 add_synonym
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386
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387 Title : add_synonym
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388 Usage : $term->add_synonym( @asynonyms );
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389 or
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390 $term->add_synonym( $synonym );
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391 Function: Pushes one or more synonyms into the list of synonyms.
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392 Returns :
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393 Args : One synonym [scalar] or a list of synonyms [array of [scalar]].
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394
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395 =cut
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396
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397 sub add_synonym {
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398 my ( $self, @values ) = @_;
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399
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400 return unless( @values );
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401
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402 # avoid duplicates
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403 foreach my $syn (@values) {
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404 next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }};
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405 push( @{ $self->{ "_synonyms" } }, $syn );
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406 }
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407
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408 } # add_synonym
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409
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410
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411 =head2 remove_synonyms
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412
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413 Title : remove_synonyms()
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414 Usage : $term->remove_synonyms();
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415 Function: Deletes (and returns) the synonyms of this Term.
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416 Returns : A list of synonyms [array of [scalar]].
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417 Args :
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418
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419 =cut
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420
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421 sub remove_synonyms {
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422 my ( $self ) = @_;
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423
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424 my @a = $self->get_synonyms();
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425 $self->{ "_synonyms" } = [];
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426 return @a;
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427
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428 } # remove_synonyms
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429
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430 =head2 get_dblinks
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431
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432 Title : get_dblinks()
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433 Usage : @ds = $term->get_dblinks();
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434 Function: Returns a list of each dblinks of this GO term.
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435 Returns : A list of dblinks [array of [scalars]].
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436 Args :
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437
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438 =cut
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439
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440 sub get_dblinks {
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441 my $self = shift;
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442
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443 return @{$self->{ "_dblinks" }} if exists($self->{ "_dblinks" });
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444 return ();
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445 } # get_dblinks
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446
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447
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448 =head2 add_dblink
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449
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450 Title : add_dblink
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451 Usage : $term->add_dblink( @dbls );
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452 or
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453 $term->add_dblink( $dbl );
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454 Function: Pushes one or more dblinks onto the list of dblinks.
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455 Returns :
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456 Args : One dblink [scalar] or a list of
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457 dblinks [array of [scalars]].
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458
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459 =cut
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460
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461 sub add_dblink {
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462 my ( $self, @values ) = @_;
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463
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464 return unless( @values );
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465
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466 # avoid duplicates
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467 foreach my $dbl (@values) {
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468 next if grep { $_ eq $dbl; } @{$self->{ "_dblinks" }};
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|
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469 push( @{ $self->{ "_dblinks" } }, $dbl );
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470 }
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471
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472 } # add_dblink
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|
|
473
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474
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475 =head2 remove_dblinks
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476
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|
|
477 Title : remove_dblinks()
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478 Usage : $term->remove_dblinks();
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479 Function: Deletes (and returns) the definition references of this GO term.
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480 Returns : A list of definition references [array of [scalars]].
|
|
|
481 Args :
|
|
|
482
|
|
|
483 =cut
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484
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485 sub remove_dblinks {
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486 my ( $self ) = @_;
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|
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487
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|
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488 my @a = $self->get_dblinks();
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489 $self->{ "_dblinks" } = [];
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490 return @a;
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491
|
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|
492 } # remove_dblinks
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|
|
493
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|
494 =head2 get_secondary_ids
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495
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496 Title : get_secondary_ids
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|
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497 Usage : @ids = $term->get_secondary_ids();
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498 Function: Returns a list of secondary identifiers of this Term.
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|
|
499
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|
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500 Secondary identifiers mostly originate from merging terms,
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501 or possibly also from splitting terms.
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|
|
502
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|
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503 Returns : A list of secondary identifiers [array of [scalar]]
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504 Args :
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505
|
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506 =cut
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507
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508 sub get_secondary_ids {
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509 my $self = shift;
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510
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511 return @{$self->{"_secondary_ids"}} if exists($self->{"_secondary_ids"});
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512 return ();
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|
513 } # get_secondary_ids
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514
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515
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|
516 =head2 add_secondary_id
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|
|
517
|
|
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518 Title : add_secondary_id
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|
|
519 Usage : $term->add_secondary_id( @ids );
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520 or
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521 $term->add_secondary_id( $id );
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522 Function: Adds one or more secondary identifiers to this term.
|
|
|
523 Returns :
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|
524 Args : One or more secondary identifiers [scalars]
|
|
|
525
|
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|
526 =cut
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|
|
527
|
|
|
528 sub add_secondary_id {
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|
529 my $self = shift;
|
|
|
530
|
|
|
531 return unless @_;
|
|
|
532
|
|
|
533 # avoid duplicates
|
|
|
534 foreach my $id (@_) {
|
|
|
535 next if grep { $_ eq $id; } @{$self->{ "_secondary_ids" }};
|
|
|
536 push( @{ $self->{ "_secondary_ids" } }, $id );
|
|
|
537 }
|
|
|
538
|
|
|
539 } # add_secondary_id
|
|
|
540
|
|
|
541
|
|
|
542 =head2 remove_secondary_ids
|
|
|
543
|
|
|
544 Title : remove_secondary_ids
|
|
|
545 Usage : $term->remove_secondary_ids();
|
|
|
546 Function: Deletes (and returns) the secondary identifiers of this Term.
|
|
|
547 Returns : The previous list of secondary identifiers [array of [scalars]]
|
|
|
548 Args :
|
|
|
549
|
|
|
550 =cut
|
|
|
551
|
|
|
552 sub remove_secondary_ids {
|
|
|
553 my $self = shift;
|
|
|
554
|
|
|
555 my @a = $self->get_secondary_ids();
|
|
|
556 $self->{ "_secondary_ids" } = [];
|
|
|
557 return @a;
|
|
|
558
|
|
|
559 } # remove_secondary_ids
|
|
|
560
|
|
|
561
|
|
|
562 # Title :_is_true_or_false
|
|
|
563 # Function: Checks whether the argument is TRUE or FALSE.
|
|
|
564 # Returns :
|
|
|
565 # Args : The value to be checked.
|
|
|
566 sub _is_true_or_false {
|
|
|
567 my ( $self, $value ) = @_;
|
|
|
568 unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
|
|
|
569 $self->throw( "Found [" . $value
|
|
|
570 . "] where " . TRUE . " or " . FALSE . " expected" );
|
|
|
571 }
|
|
|
572 } # _is_true_or_false
|
|
|
573
|
|
|
574 =head1 Methods implementing L<Bio::IdentifiableI> and L<Bio::DescribableI>
|
|
|
575
|
|
|
576 =cut
|
|
|
577
|
|
|
578 =head2 object_id
|
|
|
579
|
|
|
580 Title : object_id
|
|
|
581 Usage : $string = $obj->object_id()
|
|
|
582 Function: a string which represents the stable primary identifier
|
|
|
583 in this namespace of this object.
|
|
|
584
|
|
|
585 This is a synonym for identifier().
|
|
|
586
|
|
|
587 Returns : A scalar
|
|
|
588
|
|
|
589 =cut
|
|
|
590
|
|
|
591 sub object_id {
|
|
|
592 return shift->identifier(@_);
|
|
|
593 }
|
|
|
594
|
|
|
595 =head2 authority
|
|
|
596
|
|
|
597 Title : authority
|
|
|
598 Usage : $authority = $obj->authority()
|
|
|
599 Function: a string which represents the organisation which
|
|
|
600 granted the namespace, written as the DNS name for
|
|
|
601 organisation (eg, wormbase.org)
|
|
|
602
|
|
|
603 This forwards to ontology()->authority(). Note that you
|
|
|
604 cannot set the authority before having set the ontology or
|
|
|
605 the namespace (which will set the ontology).
|
|
|
606
|
|
|
607 Returns : A scalar
|
|
|
608 Args : on set, the new value (a scalar)
|
|
|
609
|
|
|
610 =cut
|
|
|
611
|
|
|
612 sub authority {
|
|
|
613 my $self = shift;
|
|
|
614 my $ont = $self->ontology();
|
|
|
615
|
|
|
616 return $ont->authority(@_) if $ont;
|
|
|
617 $self->throw("cannot manipulate authority prior to ".
|
|
|
618 "setting the namespace or ontology") if @_;
|
|
|
619 return undef;
|
|
|
620 }
|
|
|
621
|
|
|
622
|
|
|
623 =head2 namespace
|
|
|
624
|
|
|
625 Title : namespace
|
|
|
626 Usage : $string = $obj->namespace()
|
|
|
627 Function: A string representing the name space this identifier
|
|
|
628 is valid in, often the database name or the name
|
|
|
629 describing the collection.
|
|
|
630
|
|
|
631 This forwards to ontology() (set mode) and
|
|
|
632 ontology()->name() (get mode). I.e., setting the namespace
|
|
|
633 will set the ontology to one matching that name in the
|
|
|
634 ontology store, or to one newly created.
|
|
|
635
|
|
|
636 Returns : A scalar
|
|
|
637 Args : on set, the new value (a scalar)
|
|
|
638
|
|
|
639 =cut
|
|
|
640
|
|
|
641 sub namespace {
|
|
|
642 my $self = shift;
|
|
|
643
|
|
|
644 $self->ontology(@_) if(@_);
|
|
|
645 my $ont = $self->ontology();
|
|
|
646 return defined($ont) ? $ont->name() : undef;
|
|
|
647 }
|
|
|
648
|
|
|
649 =head2 display_name
|
|
|
650
|
|
|
651 Title : display_name
|
|
|
652 Usage : $string = $obj->display_name()
|
|
|
653 Function: A string which is what should be displayed to the user.
|
|
|
654
|
|
|
655 The definition in L<Bio::DescribableI> states that the
|
|
|
656 string should not contain spaces. As this isn't very
|
|
|
657 sensible for ontology terms, we relax this here. The
|
|
|
658 implementation just forwards to name().
|
|
|
659
|
|
|
660 Returns : A scalar
|
|
|
661 Args : on set, the new value (a scalar)
|
|
|
662
|
|
|
663 =cut
|
|
|
664
|
|
|
665 sub display_name {
|
|
|
666 return shift->name(@_);
|
|
|
667 }
|
|
|
668
|
|
|
669
|
|
|
670 =head2 description
|
|
|
671
|
|
|
672 Title : description
|
|
|
673 Usage : $string = $obj->description()
|
|
|
674 Function: A text string suitable for displaying to the user a
|
|
|
675 description. This string is likely to have spaces, but
|
|
|
676 should not have any newlines or formatting - just plain
|
|
|
677 text.
|
|
|
678
|
|
|
679 This forwards to definition(). The caveat is that the text
|
|
|
680 will often be longer for ontology term definitions than the
|
|
|
681 255 characters stated in the definition in
|
|
|
682 L<Bio::DescribableI>.
|
|
|
683
|
|
|
684 Returns : A scalar
|
|
|
685 Args : on set, the new value (a scalar)
|
|
|
686
|
|
|
687 =cut
|
|
|
688
|
|
|
689 sub description {
|
|
|
690 return shift->definition(@_);
|
|
|
691 }
|
|
|
692
|
|
|
693 #################################################################
|
|
|
694 # aliases or forwards to maintain backward compatibility
|
|
|
695 #################################################################
|
|
|
696
|
|
|
697 =head1 Deprecated methods
|
|
|
698
|
|
|
699 Used for looking up the methods that supercedes them.
|
|
|
700
|
|
|
701 =cut
|
|
|
702
|
|
|
703 =head2 category
|
|
|
704
|
|
|
705 Title : category
|
|
|
706 Usage :
|
|
|
707 Function: This method is deprecated. Use ontology() instead.
|
|
|
708 Example :
|
|
|
709 Returns :
|
|
|
710 Args :
|
|
|
711
|
|
|
712
|
|
|
713 =cut
|
|
|
714
|
|
|
715 sub category {
|
|
|
716 my $self = shift;
|
|
|
717
|
|
|
718 $self->warn("TermI::category is deprecated and being phased out. ".
|
|
|
719 "Use TermI::ontology instead.");
|
|
|
720
|
|
|
721 # called in set mode?
|
|
|
722 if(@_) {
|
|
|
723 # yes; what is incompatible with ontology() is if we were given
|
|
|
724 # a TermI object
|
|
|
725 my $arg = shift;
|
|
|
726 $arg = $arg->name() if ref($arg) && $arg->isa("Bio::Ontology::TermI");
|
|
|
727 return $self->ontology($arg,@_);
|
|
|
728 } else {
|
|
|
729 # No, called in get mode. This is always incompatible with ontology()
|
|
|
730 # since category is supposed to return a TermI.
|
|
|
731 my $ont = $self->ontology();
|
|
|
732 my $term;
|
|
|
733 if(defined($ont)) {
|
|
|
734 $term = Bio::Ontology::Term->new(-name => $ont->name(),
|
|
|
735 -identifier =>$ont->identifier());
|
|
|
736 }
|
|
|
737 return $term;
|
|
|
738 }
|
|
|
739 } # category
|
|
|
740
|
|
|
741 *each_synonym = \&get_synonyms;
|
|
|
742 *add_synonyms = \&add_synonym;
|
|
|
743 *each_dblink = \&get_dblinks;
|
|
|
744 *add_dblinks = \&add_dblink;
|
|
|
745
|
|
|
746 1;
|
