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1 # $Id: OntologyTerm.pm,v 1.4.2.2 2003/04/04 15:53:20 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Annotation::OntologyTerm
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4 #
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5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 #
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12 # (c) Hilmar Lapp, hlapp at gmx.net, 2002.
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13 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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14 #
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15 # You may distribute this module under the same terms as perl itself.
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16 # Refer to the Perl Artistic License (see the license accompanying this
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17 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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18 # for the terms under which you may use, modify, and redistribute this module.
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19 #
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20 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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21 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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22 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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23 #
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24
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25 # POD documentation - main docs before the code
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26
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27 =head1 NAME
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28
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29 Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
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30
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31 =head1 SYNOPSIS
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32
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33 use Bio::Annotation::OntologyTerm;
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34 use Bio::Annotation::Collection;
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35 use Bio::Ontology::Term;
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36
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37 my $coll = new Bio::Annotation::Collection;
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38
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39 # this also implements a tag/value pair, where tag _and_ value are treated
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40 # as ontology terms
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41 my $annterm = new Bio::Annotation::OntologyTerm(-label => 'ABC1',
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42 -tagname => 'Gene Name');
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43 # ontology terms can be added directly - they implicitly have a tag
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44 $coll->add_Annotation($annterm);
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45
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46 # implementation is by composition - you can get/set the term object
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47 # e.g.
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48 my $term = $annterm->term(); # term is-a Bio::Ontology::TermI
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49 print "ontology term ",$term->name()," (ID ",$term->identifier(),
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50 "), ontology ",$term->ontology()->name(),"\n";
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51 $term = Bio::Ontology::Term->new(-name => 'ABC2', -ontology => 'Gene Name');
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52 $annterm->term($term);
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53
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54 =head1 DESCRIPTION
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55
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56 Ontology term annotation object
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57
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58 =head1 FEEDBACK
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59
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60 =head2 Mailing Lists
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61
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62 User feedback is an integral part of the evolution of this and other
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63 Bioperl modules. Send your comments and suggestions preferably to one
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64 of the Bioperl mailing lists. Your participation is much appreciated.
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65
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66 bioperl-l@bioperl.org - General discussion
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67 http://bio.perl.org/MailList.html - About the mailing lists
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68
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69 =head2 Reporting Bugs
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70
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71 Report bugs to the Bioperl bug tracking system to help us keep track
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72 the bugs and their resolution. Bug reports can be submitted via email
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73 or the web:
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74
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75 bioperl-bugs@bioperl.org
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76 http://bugzilla.bioperl.org/
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77
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78 =head1 AUTHOR - Hilmar Lapp
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79
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80 Email bioperl-l@bio.perl.org
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81 Email hlapp at gmx.net
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82
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83
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84 =head1 APPENDIX
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85
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86 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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87
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88 =cut
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89
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90
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91 # Let the code begin...
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92
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93
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94 package Bio::Annotation::OntologyTerm;
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95 use vars qw(@ISA);
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96 use strict;
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97
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98 # Object preamble - inherits from Bio::Root::Root
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99
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100 use Bio::AnnotationI;
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101 use Bio::Ontology::TermI;
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102 use Bio::Ontology::Term;
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103 use Bio::Root::Root;
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104
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105 @ISA = qw(Bio::Root::Root Bio::AnnotationI Bio::Ontology::TermI);
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106
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107 =head2 new
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108
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109 Title : new
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110 Usage : my $sv = new Bio::Annotation::OntologyTerm;
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111 Function: Instantiate a new OntologyTerm object
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112 Returns : Bio::Annotation::OntologyTerm object
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113 Args : -term => $term to initialize the term data field [optional]
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114 Most named arguments that Bio::Ontology::Term accepts will work
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115 here too. -label is a synonym for -name, -tagname is a synonym for
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116 -ontology.
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117
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118 =cut
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119
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120 sub new{
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121 my ($class,@args) = @_;
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122
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123 my $self = $class->SUPER::new(@args);
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124
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125 my ($term,$name,$label,$identifier,$definition,$ont,$tag) =
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126 $self->_rearrange([qw(TERM
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127 NAME
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128 LABEL
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129 IDENTIFIER
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130 DEFINITION
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131 ONTOLOGY
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132 TAGNAME)],
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133 @args);
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134 if($term) {
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135 $self->term($term);
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136 } else {
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137 $self->name($name || $label) if $name || $label;
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138 $self->identifier($identifier) if $identifier;
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139 $self->definition($definition) if $definition;
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140 }
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141 $self->ontology($ont || $tag) if $ont || $tag;
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142
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143 return $self;
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144 }
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145
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146
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147 =head1 AnnotationI implementing functions
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148
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149 =cut
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150
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151 =head2 as_text
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152
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153 Title : as_text
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154 Usage : my $text = $obj->as_text
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155 Function: return the string "Name: $v" where $v is the name of the term
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156 Returns : string
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157 Args : none
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158
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159
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160 =cut
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161
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162 sub as_text{
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163 my ($self) = @_;
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164
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165 return $self->tagname()."|".$self->name()."|".$self->identifier();
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166 }
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167
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168 =head2 hash_tree
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169
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170 Title : hash_tree
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171 Usage : my $hashtree = $value->hash_tree
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172 Function: For supporting the AnnotationI interface just returns the value
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173 as a hashref with the key 'value' pointing to the value
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174 Returns : hashrf
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175 Args : none
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176
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177
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178 =cut
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179
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180 sub hash_tree{
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181 my ($self) = @_;
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182
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183 my $h = {};
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184 $h->{'name'} = $self->name();
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185 $h->{'identifier'} = $self->identifier();
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186 $h->{'definition'} = $self->definition();
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187 $h->{'synonyms'} = [$self->each_synonym()];
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188 }
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189
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190
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191 =head2 tagname
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192
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193 Title : tagname
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194 Usage : $obj->tagname($newval)
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195 Function: Get/set the tagname for this annotation value.
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196
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197 Setting this is optional. If set, it obviates the need to provide
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198 a tag to AnnotationCollection when adding this object.
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199
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200 This is aliased to ontology() here.
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201 Example :
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202 Returns : value of tagname (a scalar)
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203 Args : new value (a scalar, optional)
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204
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205
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206 =cut
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207
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208 sub tagname{
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209 my $self = shift;
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210
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211 return $self->ontology(@_) if @_;
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212 # if in get mode we need to get the name from the ontology
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213 my $ont = $self->ontology();
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214 return ref($ont) ? $ont->name() : $ont;
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215 }
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216
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217 =head1 Methods for Bio::Ontology::TermI compliance
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218
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219 =cut
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220
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221 =head2 term
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222
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223 Title : term
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224 Usage : $obj->term($newval)
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225 Function: Get/set the Bio::Ontology::TermI implementing object.
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226
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227 We implement TermI by composition, and this method sets/gets the
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228 object we delegate to.
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229 Example :
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230 Returns : value of term (a Bio::Ontology::TermI compliant object)
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231 Args : new value (a Bio::Ontology::TermI compliant object, optional)
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232
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233
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234 =cut
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235
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236 sub term{
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237 my ($self,$value) = @_;
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238 if( defined $value) {
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239 $self->{'term'} = $value;
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240 }
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241 if(! exists($self->{'term'})) {
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242 $self->{'term'} = Bio::Ontology::Term->new();
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243 }
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244 return $self->{'term'};
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245 }
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246
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247 =head2 identifier
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248
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249 Title : identifier
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250 Usage : $term->identifier( "0003947" );
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251 or
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252 print $term->identifier();
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253 Function: Set/get for the identifier of this Term.
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254 Returns : The identifier [scalar].
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255 Args : The identifier [scalar] (optional).
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256
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257 =cut
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258
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259 sub identifier {
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260 return shift->term()->identifier(@_);
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261 } # identifier
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262
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263 =head2 name
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264
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265 Title : name
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266 Usage : $term->name( "N-acetylgalactosaminyltransferase" );
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267 or
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268 print $term->name();
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269 Function: Set/get for the name of this Term.
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270 Returns : The name [scalar].
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271 Args : The name [scalar] (optional).
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272
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273 =cut
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274
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275 sub name {
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276 return shift->term()->name(@_);
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277 } # name
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278
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279
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280 =head2 definition
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281
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282 Title : definition
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283 Usage : $term->definition( "Catalysis of ..." );
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284 or
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285 print $term->definition();
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286 Function: Set/get for the definition of this Term.
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287 Returns : The definition [scalar].
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288 Args : The definition [scalar] (optional).
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289
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290 =cut
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291
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292 sub definition {
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293 return shift->term()->definition(@_);
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294 } # definition
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295
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296 =head2 ontology
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297
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298 Title : ontology
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299 Usage : $term->ontology( $top );
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300 or
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301 $top = $term->ontology();
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302 Function: Set/get for a relationship between this Term and
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303 another Term (e.g. the top level of the ontology).
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304 Returns : The ontology of this Term [TermI].
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305 Args : The ontology of this Term [TermI or scalar -- which
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306 becomes the name of the catagory term] (optional).
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307
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308 =cut
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309
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310 sub ontology {
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311 return shift->term()->ontology(@_);
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312 }
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313
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314 =head2 is_obsolete
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315
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316 Title : is_obsolete
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317 Usage : $term->is_obsolete( 1 );
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318 or
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319 if ( $term->is_obsolete() )
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320 Function: Set/get for the obsoleteness of this Term.
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321 Returns : the obsoleteness [0 or 1].
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322 Args : the obsoleteness [0 or 1] (optional).
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323
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324 =cut
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325
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326 sub is_obsolete {
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327 return shift->term()->is_obsolete(@_);
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328 } # is_obsolete
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329
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330 =head2 comment
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331
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332 Title : comment
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333 Usage : $term->comment( "Consider the term ..." );
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334 or
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335 print $term->comment();
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336 Function: Set/get for an arbitrary comment about this Term.
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337 Returns : A comment.
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338 Args : A comment (optional).
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339
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340 =cut
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341
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342 sub comment {
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343 return shift->term()->comment(@_);
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344 } # comment
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345
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346 =head2 get_synonyms
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347
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348 Title : get_synonyms()
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349 Usage : @aliases = $term->get_synonyms();
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350 Function: Returns a list of aliases of this Term.
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351 Returns : A list of aliases [array of [scalar]].
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352 Args :
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353
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354 =cut
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355
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356 sub get_synonyms {
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357 return shift->term()->get_synonyms(@_);
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358 } # get_synonyms
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359
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360 =head2 add_synonym
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361
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362 Title : add_synonym
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363 Usage : $term->add_synonym( @asynonyms );
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364 or
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365 $term->add_synonym( $synonym );
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366 Function: Pushes one or more synonyms into the list of synonyms.
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367 Returns :
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368 Args : One synonym [scalar] or a list of synonyms [array of [scalar]].
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369
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370 =cut
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371
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372 sub add_synonym {
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373 return shift->term()->add_synonym(@_);
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374 } # add_synonym
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375
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376
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377 =head2 remove_synonyms
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378
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379 Title : remove_synonyms()
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380 Usage : $term->remove_synonyms();
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381 Function: Deletes (and returns) the synonyms of this Term.
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382 Returns : A list of synonyms [array of [scalar]].
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383 Args :
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384
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385 =cut
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386
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387 sub remove_synonyms {
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388 return shift->term()->remove_synonyms(@_);
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389 } # remove_synonyms
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390
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391 =head2 get_dblinks
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392
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393 Title : get_dblinks()
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394 Usage : @ds = $term->get_dblinks();
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395 Function: Returns a list of each dblinks of this GO term.
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396 Returns : A list of dblinks [array of [scalars]].
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397 Args :
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398
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399 =cut
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400
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401 sub get_dblinks {
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402 return shift->term->get_dblinks(@_);
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403 } # get_dblinks
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404
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405
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406 =head2 add_dblink
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407
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408 Title : add_dblink
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409 Usage : $term->add_dblink( @dbls );
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410 or
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411 $term->add_dblink( $dbl );
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412 Function: Pushes one or more dblinks
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413 into the list of dblinks.
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414 Returns :
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415 Args : One dblink [scalar] or a list of
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416 dblinks [array of [scalars]].
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417
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418 =cut
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419
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420 sub add_dblink {
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421 return shift->term->add_dblink(@_);
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422 } # add_dblink
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423
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424
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425 =head2 remove_dblinks
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426
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427 Title : remove_dblinks()
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428 Usage : $term->remove_dblinks();
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429 Function: Deletes (and returns) the definition references of this GO term.
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430 Returns : A list of definition references [array of [scalars]].
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431 Args :
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432
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433 =cut
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434
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435 sub remove_dblinks {
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436 return shift->term->remove_dblinks(@_);
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437 } # remove_dblinks
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438
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439 =head2 get_secondary_ids
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440
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441 Title : get_secondary_ids
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442 Usage : @ids = $term->get_secondary_ids();
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443 Function: Returns a list of secondary identifiers of this Term.
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444
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445 Secondary identifiers mostly originate from merging terms,
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446 or possibly also from splitting terms.
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447
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448 Returns : A list of secondary identifiers [array of [scalar]]
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449 Args :
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450
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451 =cut
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452
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453 sub get_secondary_ids {
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454 return shift->term->get_secondary_ids(@_);
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455 } # get_secondary_ids
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456
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457
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458 =head2 add_secondary_id
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459
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460 Title : add_secondary_id
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461 Usage : $term->add_secondary_id( @ids );
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462 or
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463 $term->add_secondary_id( $id );
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464 Function: Adds one or more secondary identifiers to this term.
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465 Returns :
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466 Args : One or more secondary identifiers [scalars]
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467
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468 =cut
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469
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470 sub add_secondary_id {
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471 return shift->term->add_secondary_id(@_);
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472 } # add_secondary_id
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473
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474
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475 =head2 remove_secondary_ids
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476
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477 Title : remove_secondary_ids
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478 Usage : $term->remove_secondary_ids();
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479 Function: Deletes (and returns) the secondary identifiers of this Term.
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480 Returns : The previous list of secondary identifiers [array of [scalars]]
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481 Args :
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482
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483 =cut
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484
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485 sub remove_secondary_ids {
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486 return shift->term->remove_secondary_ids(@_);
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487 } # remove_secondary_ids
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488
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489
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490 1;
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