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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::OntologyTerm
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24
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25 =head1 DESCRIPTION
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26
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27 An ontology term object, (most often) created by
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28 Bio::EnsEMBL::DBSQL::GOTermAdaptor and used in querying for
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29 transcripts, genes, and translations using the relevant adaptors and
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30 methods.
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31
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32 =head1 METHODS
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33
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34 =cut
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35
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36 package Bio::EnsEMBL::OntologyTerm;
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37
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38 use strict;
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39 use warnings;
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40
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41 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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42
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43 use base qw( Bio::EnsEMBL::Storable );
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44
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45 =head2 new
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46
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47 Arg [-ACCESSION] : String
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48 The accession of the ontology term.
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49
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50 Arg [-ONTOLOGY] : String
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51 The ontology that the term belongs to.
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52
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53 Arg [-NAMESPACE] : String
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54 The namespace of the ontology term.
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55
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56 Arg [-NAME] : String
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57 The name of the ontology term.
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58
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59 Arg [-SUBSETS] : (optional) Listref of strings
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60 The subsets within the ontology to which this
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61 term belongs.
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62
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63 Arg [-DEFINITION] : (optional) String
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64 The definition of the ontology term.
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65
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66 Arg [-SYNONYMS] : (optional) Listref of strings
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67 The synonyms of this term.
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68
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69 Arg : Further arguments required for parent class
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70 Bio::EnsEMBL::Storable.
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71
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72 Description : Creates an ontology term object.
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73
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74 Example :
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75
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76 my $term = Bio::EnsEMBL::OntologyTerm->new(
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77 '-accession' => 'GO:0021785',
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78 '-ontology' => 'GO',
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79 '-namespace' => 'biological_process',
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80 '-name' => 'branchiomotor neuron axon guidance',
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81 '-definition' => 'The process in which a branchiomotor '
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82 . 'neuron growth cone is directed to a specific target site. '
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83 . 'Branchiomotor neurons are located in the hindbrain and '
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84 . 'innervate branchial arch-derived muscles that control jaw '
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85 . 'movements, facial expression, the larynx, and the pharynx.',
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86 '-synonyms' => [ 'BMN axon guidance',
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87 'branchial motor axon guidance',
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88 'special visceral motor neuron axon guidance' ]
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89
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90 # ... other arguments required by Bio::EnsEMBL::Storable.
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91 );
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92
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93 Return type : Bio::EnsEMBL::OntologyTerm
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94
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95 =cut
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96
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97 sub new {
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98 my $proto = shift(@_);
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99
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100 my $this = $proto->SUPER::new(@_);
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101
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102 my ( $accession, $ontology, $namespace, $name, $definition, $subsets )
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103 = rearrange( [ 'ACCESSION', 'ONTOLOGY', 'NAMESPACE', 'NAME',
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104 'DEFINITION', 'SUBSETS' ],
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105 @_ );
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106
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107 $this->{'accession'} = $accession;
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108 $this->{'ontology'} = $ontology;
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109 $this->{'namespace'} = $namespace;
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110 $this->{'name'} = $name;
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111 $this->{'definition'} = $definition;
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112 $this->{'subsets'} = [ @{$subsets} ];
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113
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114 $this->{'child_terms_fetched'} = 0;
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115 $this->{'parent_terms_fetched'} = 0;
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116
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117 return $this;
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118 }
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119
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120 =head2 accession
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121
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122 Arg : None
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123
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124 Description : Returns the accession for the ontology term in question.
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125
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126 Example : my $accession = $term->accession();
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127
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128 Return type : String
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129
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130 =cut
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131
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132 sub accession {
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133 my ($this) = @_;
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134 return $this->{'accession'};
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135 }
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136
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137 =head2 ontology
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138
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139 Arg : None
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140
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141 Description : Returns the ontology for the ontology term in question.
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142
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143 Example : my $ontology = $term->ontology();
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144
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145 Return type : String
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146
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147 =cut
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148
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149 sub ontology {
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150 my ($this) = @_;
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151 return $this->{'ontology'};
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152 }
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153
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154 =head2 namespace
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155
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156 Arg : None
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157
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158 Description : Returns the namespace for the ontology term in question.
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159
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160 Example : my $acc = $term->namespace();
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161
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162 Return type : String
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163
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164 =cut
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165
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166 sub namespace {
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167 my ($this) = @_;
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168 return $this->{'namespace'};
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169 }
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170
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171 =head2 name
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172
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173 Arg : None
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174
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175 Description : Returns the name for the ontology term in question.
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176
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177 Example : my $name = $term->name();
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178
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179 Return type : String
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180
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181 =cut
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182
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183 sub name {
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184 my ($this) = @_;
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185 return $this->{'name'};
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186 }
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187
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188 =head2 definition
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189
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190 Arg : None
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191
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192 Description : Returns the definition for the ontology term in question.
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193
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194 Example : my $definition = $term->definition();
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195
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196 Return type : String
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197
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198 =cut
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199
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200 sub definition {
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201 my ($this) = @_;
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202 return $this->{'definition'};
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203 }
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204
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205 =head2 synonyms
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206
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207 Arg : None
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208
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209 Description : Returns the list of synonyms defined for this term
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210 (if any).
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211
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212 Example : my @synonyms = @{ $term->synonyms() };
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213
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214 Return type : Listref of strings
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215
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216 =cut
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217
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218 sub synonyms {
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219 my ($this) = @_;
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220
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221 if ( !exists( $this->{'synonyms'} ) ) {
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222 $this->{'synonyms'} =
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223 $this->adaptor()->_fetch_synonyms_by_dbID( $this->dbID() );
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224 }
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225
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226 return $this->{'synonyms'};
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227 }
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228
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229 =head2 subsets
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230
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231 Arg : None
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232
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233 Description : Returns a list of subsets that this term is part
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234 of. The list might be empty.
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235
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236 Example : my @subsets = @{ $term->subsets() };
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237
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238 Return type : listref of strings
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239
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240 =cut
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241
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242 sub subsets {
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243 my ($this) = @_;
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244 return $this->{'subsets'};
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245 }
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246
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247 =head2 children
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248
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249 Arg : (optional) List of strings
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250 The type of relations to retrieve children for.
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251
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252 Description : Returns the children terms of this ontology term.
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253
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254 Example : my @children =
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255 @{ $term->children( 'is_a', 'part_of' ) };
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256
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257 Return type : listref of Bio::EnsEMBL::OntologyTerm
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258
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259 =cut
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260
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261 sub children {
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262 my ( $this, @relations ) = @_;
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263
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264 my @terms = @{ $this->adaptor()->fetch_all_by_parent_term($this) };
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265
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266 if (@relations) {
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267 @terms = ();
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268 foreach my $relation (@relations) {
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269 if ( exists( $this->{'children'}{$relation} ) ) {
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270 push( @terms, @{ $this->{'children'}{$relation} } );
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271 }
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272 }
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273 }
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274
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275 return \@terms;
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276 }
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277
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278 =head2 descendants
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279
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280 Arg : None
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281
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282 Description : Returns the complete set of 'is_a' and 'part_of'
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283 descendant terms of this ontology term, down to
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284 and including any leaf terms.
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285
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286 Example : my @descendants = @{ $term->descendants() };
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287
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288 Return type : listref of Bio::EnsEMBL::OntologyTerm
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289
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290 =cut
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291
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292 sub descendants {
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293 my ($this) = @_;
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294 return $this->adaptor()->fetch_all_by_ancestor_term($this);
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295 }
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296
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297 =head2 parents
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298
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299 Arg : (optional) List of strings
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300 The type of relations to retrieve parents for.
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301
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302 Description : Returns the parent terms of this ontology term.
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303
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304 Example : my @parents =
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305 @{ $term->parents( 'is_a', 'part_of' ) };
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306
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307 Return type : listref of Bio::EnsEMBL::OntologyTerm
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308
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309 =cut
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310
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311 sub parents {
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312 my ( $this, @relations ) = @_;
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313
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314 my @terms = @{ $this->adaptor()->fetch_all_by_child_term($this) };
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315
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316 if (@relations) {
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317 @terms = ();
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318 foreach my $relation (@relations) {
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319 if ( exists( $this->{'parents'}{$relation} ) ) {
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320 push( @terms, @{ $this->{'parents'}{$relation} } );
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321 }
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322 }
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323 }
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324
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325 return \@terms;
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326 }
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327
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328 =head2 ancestors
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329
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330 Arg : None
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331
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332 Description : Returns the complete set of 'is_a' and 'part_of'
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333 ancestor terms of this ontology term, up to and
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334 including the root term.
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335
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336 Example : my @ancestors = @{ $term->ancestors() };
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337
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338 Return type : listref of Bio::EnsEMBL::OntologyTerm
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339
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340 =cut
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341
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342 sub ancestors {
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343 my ($this) = @_;
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344 return $this->adaptor()->fetch_all_by_descendant_term($this);
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345 }
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346
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347 1;
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