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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::DBSQL::OntologyTermAdaptor
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24
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25 =head1 SYNOPSIS
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26
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27 my $goa =
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28 $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
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29
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30 my $term = $goa->fetch_by_accession('GO:0010885');
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31
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32 my @children = @{ $goa->fetch_all_by_parent_term($term) };
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33 my @descendants = @{ $goa->fetch_all_by_ancestor_term($term) };
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34
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35 my @parents = @{ $goa->fetch_all_by_child_term($term) };
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36 my @ancestors = @{ $goa->fetch_all_by_descendant_term($term) };
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37
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38 my %ancestor_chart = %{ $goa->_fetch_ancestor_chart($term) };
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39
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40 =head1 DESCRIPTION
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41
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42 An abstract adaptor class for fetching ontology
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43 terms, creates Bio::EnsEMBL::OntologyTerm objects.
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44
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45 =head1 METHODS
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46
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47 =cut
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48
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49 package Bio::EnsEMBL::DBSQL::OntologyTermAdaptor;
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50
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51 use strict;
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52 use warnings;
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53
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54 use DBI qw( :sql_types );
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55
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56 use Bio::EnsEMBL::Utils::Exception qw( throw );
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57 use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
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58
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59 use Bio::EnsEMBL::OntologyTerm;
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60
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61 use base qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
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62
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63 =head2 fetch_all_by_name
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64
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65 Arg [1] : String, name of term, or SQL pattern
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66 Arg [2] : (optional) String, name of ontology
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67
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68 Description : Fetches ontology term(s) given a name, a synonym, or a
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69 SQL pattern like "%splice_site%"
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70
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71 Example :
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72
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73 my ($term) =
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74 @{ $ot_adaptor->fetch_by_name( 'DNA_binding_site', 'SO' ) };
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75
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76 # Will find terms in both SO and GO:
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77 my @terms = @{ $ot_adaptor->fetch_by_name('%splice_site%') };
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78
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79 Return type : listref of Bio::EnsEMBL::OntologyTerm
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80
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81 =cut
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82
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83 sub fetch_all_by_name {
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84 my ( $this, $pattern, $ontology ) = @_;
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85
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86 my $statement = q(
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87 SELECT DISTINCT
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88 term.term_id,
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89 term.accession,
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90 term.name,
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91 term.definition,
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92 term.subsets,
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93 ontology.namespace
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94 FROM ontology
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95 JOIN term USING (ontology_id)
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96 LEFT JOIN synonym USING (term_id)
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97 WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
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98
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99 if ( defined($ontology) ) {
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100 $statement .= " AND ontology.name = ?";
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101 }
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102
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103 my $sth = $this->prepare($statement);
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104 $sth->bind_param( 1, $pattern, SQL_VARCHAR );
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105 $sth->bind_param( 2, $pattern, SQL_VARCHAR );
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106
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107 if ( defined($ontology) ) {
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108 $sth->bind_param( 3, $ontology, SQL_VARCHAR );
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109 }
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110
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111 $sth->execute();
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112
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113 my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
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114 $sth->bind_columns(
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115 \( $dbid, $accession, $name, $definition, $subsets, $namespace ) );
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116
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117 my @terms;
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118
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119 while ( $sth->fetch() ) {
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120 $subsets ||= '';
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121
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122 push @terms,
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123 Bio::EnsEMBL::OntologyTerm->new(
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124 '-dbid' => $dbid,
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125 '-adaptor' => $this,
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126 '-accession' => $accession,
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127 '-namespace' => $namespace,
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128 '-subsets' => [ split( /,/, $subsets ) ],
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129 '-name' => $name,
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130 '-definition' => $definition, );
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131 }
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132
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133 return \@terms;
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134 } ## end sub fetch_all_by_name
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135
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136
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137 =head2 fetch_by_accession
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138
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139 Arg [1] : String
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140
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141 Description : Fetches an ontology term given an accession.
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142
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143 Example :
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144
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145 my $term = $ot_adaptor->fetch_by_accession('GO:0030326');
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146
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147 Return type : Bio::EnsEMBL::OntologyTerm
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148
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149 =cut
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150
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151 sub fetch_by_accession {
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152 my ( $this, $accession ) = @_;
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153
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154 my $statement = q(
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155 SELECT term.term_id,
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156 term.name,
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157 term.definition,
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158 term.subsets,
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159 ontology.name,
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160 ontology.namespace
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161 FROM ontology
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162 JOIN term USING (ontology_id)
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163 WHERE term.accession = ?);
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164
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165 my $sth = $this->prepare($statement);
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166 $sth->bind_param( 1, $accession, SQL_VARCHAR );
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167
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168 $sth->execute();
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169
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170 my ( $dbid, $name, $definition, $subsets, $ontology, $namespace );
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171 $sth->bind_columns(
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172 \( $dbid, $name, $definition, $subsets, $ontology, $namespace ) );
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173
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174 $sth->fetch();
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175 $subsets ||= '';
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176
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177 my $term =
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178 Bio::EnsEMBL::OntologyTerm->new(
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179 '-dbid' => $dbid,
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180 '-adaptor' => $this,
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181 '-accession' => $accession,
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182 '-ontology' => $ontology,
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183 '-namespace' => $namespace,
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184 '-subsets' => [ split( /,/, $subsets ) ],
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185 '-name' => $name,
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186 '-definition' => $definition,
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187 '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
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188 );
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189 $sth->finish();
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190
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191 return $term;
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192 } ## end sub fetch_by_accession
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193
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194 =head2 fetch_all_by_parent_term
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195
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196 Arg [1] : Bio::EnsEMBL::OntologyTerm
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197 The term whose children terms should be fetched.
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198
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199 Description : Given a parent ontology term, returns a list of
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200 its immediate children terms.
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201
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202 Example :
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203
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204 my @children =
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205 @{ $ot_adaptor->fetch_all_by_parent_term($term) };
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206
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207 Return type : listref of Bio::EnsEMBL::OntologyTerm
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208
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209 =cut
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210
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211 sub fetch_all_by_parent_term {
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212 my ( $this, $term ) = @_;
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213
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214 assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
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215
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216 my @terms;
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217
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218 if ( !$term->{'child_terms_fetched'} ) {
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219 my $statement = q(
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220 SELECT child_term.term_id,
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221 child_term.accession,
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222 child_term.name,
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223 child_term.definition,
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224 child_term.subsets,
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225 rt.name
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226 FROM term child_term
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227 JOIN relation ON (relation.child_term_id = child_term.term_id)
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228 JOIN relation_type rt USING (relation_type_id)
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229 WHERE relation.parent_term_id = ?);
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230
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231 my $sth = $this->prepare($statement);
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232 $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
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233
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234 $sth->execute();
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235
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236 my ( $dbid, $accession, $name, $definition, $subsets, $relation );
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237 $sth->bind_columns(
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238 \( $dbid, $accession, $name, $definition, $subsets, $relation ) );
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239
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240 while ( $sth->fetch() ) {
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241 $subsets ||= '';
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242
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243 my $child_term =
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244 Bio::EnsEMBL::OntologyTerm->new(
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245 '-dbid' => $dbid,
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246 '-adaptor' => $this,
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247 '-accession' => $accession,
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248 '-ontology' => $term->{'ontology'},
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249 '-namespace' => $term->{'namespace'},
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250 '-subsets' => [ split( /,/, $subsets ) ],
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251 '-name' => $name,
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252 '-definition' => $definition, );
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253
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254 push( @terms, $child_term );
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255 push( @{ $term->{'children'}{$relation} }, $child_term );
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256 }
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257
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258 $term->{'child_terms_fetched'} = 1;
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259 } else {
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260 foreach my $relation ( values( %{ $term->{'children'} } ) ) {
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261 push( @terms, @{$relation} );
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262 }
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263 }
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264
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265 return \@terms;
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266 } ## end sub fetch_all_by_parent_term
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267
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268 =head2 fetch_all_by_ancestor_term
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269
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270 Arg [1] : Bio::EnsEMBL::OntologyTerm
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271 The term whose descendant terms should be fetched.
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272
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273 Description : Given a parent ontology term, returns a list of
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274 all its descendant terms, down to and including
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275 any leaf terms. Relations of the type 'is_a' and
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276 'part_of' are followed.
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277
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278 Example :
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279
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280 my @descendants =
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281 @{ $ot_adaptor->fetch_all_by_ancestor_term($term) };
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282
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283 Return type : listref of Bio::EnsEMBL::OntologyTerm
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284
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285 =cut
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286
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287 sub fetch_all_by_ancestor_term {
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288 my ( $this, $term ) = @_;
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289
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290 assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
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291
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292 my $statement = q(
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293 SELECT DISTINCT
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294 child_term.term_id,
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295 child_term.accession,
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296 child_term.name,
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297 child_term.definition,
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298 child_term.subsets
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299 FROM term child_term
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300 JOIN closure ON (closure.child_term_id = child_term.term_id)
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301 WHERE closure.parent_term_id = ?
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302 AND closure.distance > 0
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303 ORDER BY closure.distance, child_term.accession);
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304
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305 my $sth = $this->prepare($statement);
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306 $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
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307
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308 $sth->execute();
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309
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310 my ( $dbid, $accession, $name, $definition, $subsets );
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311 $sth->bind_columns(
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312 \( $dbid, $accession, $name, $definition, $subsets ) );
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313
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314 my @terms;
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315
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316 while ( $sth->fetch() ) {
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317 $subsets ||= '';
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318
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319 push( @terms,
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320 Bio::EnsEMBL::OntologyTerm->new(
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321 '-dbid' => $dbid,
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322 '-adaptor' => $this,
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323 '-accession' => $accession,
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324 '-ontology' => $term->{'ontology'},
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325 '-namespace' => $term->{'namespace'},
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326 '-subsets' => [ split( /,/, $subsets ) ],
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327 '-name' => $name,
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328 '-definition' => $definition, ) );
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329 }
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330
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331 return \@terms;
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332 } ## end sub fetch_all_by_ancestor_term
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333
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334 =head2 fetch_all_by_child_term
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335
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336 Arg [1] : Bio::EnsEMBL::OntologyTerm
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337 The term whose parent terms should be fetched.
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338
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339 Description : Given a child ontology term, returns a list of
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340 its immediate parent terms.
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341
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342 Example :
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343
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344 my @parents = @{ $ot_adaptor->fetch_all_by_child_term($term) };
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345
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346 Return type : listref of Bio::EnsEMBL::OntologyTerm
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347
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348 =cut
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349
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350 sub fetch_all_by_child_term {
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351 my ( $this, $term ) = @_;
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352
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353 assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
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354
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355 my @terms;
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356
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357 if ( !$term->{'parent_terms_fetched'} ) {
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358 my $statement = q(
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359 SELECT parent_term.term_id,
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360 parent_term.accession,
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361 parent_term.name,
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362 parent_term.definition,
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363 parent_term.subsets,
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364 rt.name
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365 FROM term parent_term
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366 JOIN relation ON (relation.parent_term_id = parent_term.term_id)
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367 JOIN relation_type rt USING (relation_type_id)
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368 WHERE relation.child_term_id = ?);
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369
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370 my $sth = $this->prepare($statement);
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371 $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
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372
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373 $sth->execute();
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374
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375 my ( $dbid, $accession, $name, $definition, $subsets, $relation );
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376 $sth->bind_columns(
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377 \( $dbid, $accession, $name, $definition, $subsets, $relation ) );
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378
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379 while ( $sth->fetch() ) {
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380 $subsets ||= '';
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381
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382 my $parent_term =
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383 Bio::EnsEMBL::OntologyTerm->new(
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384 '-dbid' => $dbid,
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385 '-adaptor' => $this,
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386 '-accession' => $accession,
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387 '-ontology' => $term->{'ontology'},
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388 '-namespace' => $term->{'namespace'},
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389 '-subsets' => [ split( /,/, $subsets ) ],
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390 '-name' => $name,
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391 '-definition' => $definition, );
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392
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393 push( @terms, $parent_term );
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394 push( @{ $term->{'parents'}{$relation} }, $parent_term );
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395 }
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396
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397 $term->{'parent_terms_fetched'} = 1;
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398 } else {
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399 foreach my $relation ( values( %{ $term->{'parents'} } ) ) {
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400 push( @terms, @{$relation} );
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401 }
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402 }
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403
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404 return \@terms;
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405 } ## end sub fetch_all_by_child_term
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406
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407 =head2 fetch_all_by_descendant_term
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408
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409 Arg [1] : Bio::EnsEMBL::OntologyTerm
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410 The term whose ancestor terms should be fetched.
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411
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412 Arg [2] : (optional) String
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413 The subset within the ontolgy to which the query
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414 should be restricted. The subset may be specified as
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415 a SQL pattern, e.g., "%goslim%" (but "goslim%" might
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416 not do what you expect), or as a specific subset name,
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417 e.g., "goslim_generic".
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418
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419 Arg [3] : (optional) Boolean
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420 If true (non-zero), only return the closest
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421 term(s). If this argument is true, and the
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422 previous argument is left undefined, this method
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423 will return the parent(s) of the given term.
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424
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425 Arg [4] : (optional) Boolean
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426 If true we will allow the retrieval of terms whose distance
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427 to the current term is 0. If false then we will only return
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428 those which are above the current term in the ontology
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429
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430 Description : Given a child ontology term, returns a list of
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431 all its ancestor terms, up to and including any
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432 root term. Relations of the type 'is_a' and
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433 'part_of' are followed. Optionally, only terms in
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434 a given subset of the ontology may be returned,
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435 and additionally one may ask to only get the
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436 closest term(s) to the given child term.
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437
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438 Example :
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439
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440 my @ancestors =
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441 @{ $ot_adaptor->fetch_all_by_descendant_term($term) };
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442
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443 Return type : listref of Bio::EnsEMBL::OntologyTerm
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444
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445 =cut
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446
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447 sub fetch_all_by_descendant_term {
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448 my ( $this, $term, $subset, $closest_only, $allow_zero_distance ) = @_;
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449
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450 assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
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451
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452 $closest_only ||= 0;
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453
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454 my $statement = q(
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455 SELECT DISTINCT
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456 parent_term.term_id,
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457 parent_term.accession,
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458 parent_term.name,
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459 parent_term.definition,
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460 parent_term.subsets,
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461 closure.distance
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462 FROM term parent_term
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463 JOIN closure ON (closure.parent_term_id = parent_term.term_id)
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464 WHERE closure.child_term_id = ?
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465 AND closure.distance > ?);
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466
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467 if ( defined($subset) ) {
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468 if ( index( $subset, '%' ) != -1 ) {
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469 $statement .= q(
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470 AND parent_term.subsets LIKE ?);
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471 } else {
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472 $statement .= q(
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473 AND FIND_IN_SET(?, parent_term.subsets) > 0);
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474 }
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475 }
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476
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477 $statement .= q(
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478 ORDER BY closure.distance, parent_term.accession);
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479
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480 my $sth = $this->prepare($statement);
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481 $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
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482 my $query_distance = ($allow_zero_distance) ? -1 : 0;
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483 $sth->bind_param( 2, $query_distance, SQL_INTEGER );
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484
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485 if ( defined($subset) ) {
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486 $sth->bind_param( 3, $subset, SQL_VARCHAR );
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487 }
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488
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489 $sth->execute();
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490
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491 my ( $dbid, $accession, $name, $definition, $subsets, $distance );
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492 $sth->bind_columns(
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493 \( $dbid, $accession, $name, $definition, $subsets, $distance ) );
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494
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495 my @terms;
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496 my $min_distance;
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497
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498 while ( $sth->fetch() ) {
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499 $subsets ||= '';
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|
500 $min_distance ||= $distance;
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501
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|
|
502 if ( !$closest_only || $distance == $min_distance ) {
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|
503 push( @terms,
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|
504 Bio::EnsEMBL::OntologyTerm->new(
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505 '-dbid' => $dbid,
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506 '-adaptor' => $this,
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507 '-accession' => $accession,
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508 '-ontology' => $term->{'ontology'},
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509 '-namespace' => $term->{'namespace'},
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|
510 '-subsets' => [ split( /,/, $subsets ) ],
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|
511 '-name' => $name,
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|
512 '-definition' => $definition, ) );
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|
513 } else {
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|
514 $sth->finish();
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|
515 last;
|
|
|
516 }
|
|
|
517 }
|
|
|
518
|
|
|
519 return \@terms;
|
|
|
520 } ## end sub fetch_all_by_descendant_term
|
|
|
521
|
|
|
522 sub _fetch_synonyms_by_dbID {
|
|
|
523 my ( $this, $dbID ) = @_;
|
|
|
524
|
|
|
525 my $statement = q(
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|
|
526 SELECT synonym.name
|
|
|
527 FROM synonym
|
|
|
528 WHERE synonym.term_id = ?);
|
|
|
529
|
|
|
530 my $sth = $this->prepare($statement);
|
|
|
531 $sth->bind_param( 1, $dbID, SQL_INTEGER );
|
|
|
532
|
|
|
533 $sth->execute();
|
|
|
534
|
|
|
535 my $synonym;
|
|
|
536 $sth->bind_col( 1, \$synonym );
|
|
|
537
|
|
|
538 my @synonyms;
|
|
|
539 while ( $sth->fetch() ) {
|
|
|
540 push( @synonyms, $synonym );
|
|
|
541 }
|
|
|
542
|
|
|
543 return \@synonyms;
|
|
|
544 }
|
|
|
545
|
|
|
546
|
|
|
547
|
|
|
548 =head2 _fetch_ancestor_chart
|
|
|
549
|
|
|
550 Arg [1] : Bio::EnsEMBL::OntologyTerm
|
|
|
551 The term whose ancestor terms should be fetched.
|
|
|
552
|
|
|
553 Description : Given a child ontology term, returns a hash
|
|
|
554 structure containing its ancestor terms, up to and
|
|
|
555 including any root term. Relations of the type
|
|
|
556 'is_a' and 'part_of' are included.
|
|
|
557
|
|
|
558 Example :
|
|
|
559
|
|
|
560 my %chart = %{ $ot_adaptor->_fetch_ancestor_chart($term) };
|
|
|
561
|
|
|
562 Return type : A reference to a hash structure like this:
|
|
|
563
|
|
|
564 {
|
|
|
565 'GO:XXXXXXX' => {
|
|
|
566 'term' => # ref to Bio::EnsEMBL::OntologyTerm object
|
|
|
567 'is_a' => [...], # listref of Bio::EnsEMBL::OntologyTerm
|
|
|
568 'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
|
|
|
569 },
|
|
|
570 'GO:YYYYYYY' => {
|
|
|
571 # Similarly for all ancestors,
|
|
|
572 # and including the query term itself.
|
|
|
573 }
|
|
|
574 }
|
|
|
575
|
|
|
576 =cut
|
|
|
577
|
|
|
578 sub _fetch_ancestor_chart {
|
|
|
579 my ( $this, $term ) = @_;
|
|
|
580
|
|
|
581 assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
|
|
|
582
|
|
|
583 my $statement = q(
|
|
|
584 SELECT subparent_term.term_id,
|
|
|
585 parent_term.term_id,
|
|
|
586 relation_type.name
|
|
|
587 FROM closure
|
|
|
588 JOIN relation
|
|
|
589 ON (relation.parent_term_id = closure.parent_term_id
|
|
|
590 AND relation.child_term_id = closure.subparent_term_id)
|
|
|
591 JOIN relation_type USING (relation_type_id)
|
|
|
592 JOIN term subparent_term
|
|
|
593 ON (subparent_term.term_id = closure.subparent_term_id)
|
|
|
594 JOIN term parent_term ON (parent_term.term_id = closure.parent_term_id)
|
|
|
595 WHERE closure.child_term_id = ?
|
|
|
596 ORDER BY closure.distance);
|
|
|
597
|
|
|
598 my $sth = $this->prepare($statement);
|
|
|
599 $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
|
|
|
600
|
|
|
601 $sth->execute();
|
|
|
602
|
|
|
603 my ( $subparent_id, $parent_id, $relation );
|
|
|
604 $sth->bind_columns( \( $subparent_id, $parent_id, $relation ) );
|
|
|
605
|
|
|
606 my %id_chart;
|
|
|
607 my %acc_chart;
|
|
|
608
|
|
|
609 while ( $sth->fetch() ) {
|
|
|
610 if ( !exists( $id_chart{$parent_id} ) ) {
|
|
|
611 $id_chart{$parent_id} = {};
|
|
|
612 }
|
|
|
613 push( @{ $id_chart{$subparent_id}{$relation} }, $parent_id );
|
|
|
614 }
|
|
|
615
|
|
|
616 my @terms = @{ $this->fetch_all_by_dbID_list( [ keys(%id_chart) ] ) };
|
|
|
617
|
|
|
618 foreach my $term (@terms) {
|
|
|
619 $id_chart{ $term->dbID() }{'term'} = $term;
|
|
|
620 $acc_chart{ $term->accession() }{'term'} = $term;
|
|
|
621 }
|
|
|
622
|
|
|
623 foreach my $term (@terms) {
|
|
|
624 my $accession = $term->accession();
|
|
|
625 my $dbID = $term->dbID();
|
|
|
626
|
|
|
627 foreach my $relation ( keys( %{ $id_chart{$dbID} } ) ) {
|
|
|
628 if ( $relation eq 'term' ) { next }
|
|
|
629
|
|
|
630 foreach my $id ( @{ $id_chart{$dbID}{$relation} } ) {
|
|
|
631 push( @{ $acc_chart{$accession}{$relation} },
|
|
|
632 $id_chart{$id}{'term'} );
|
|
|
633 }
|
|
|
634 }
|
|
|
635 }
|
|
|
636
|
|
|
637 return \%acc_chart;
|
|
|
638 } ## end sub _fetch_ancestor_chart
|
|
|
639
|
|
|
640 #-----------------------------------------------------------------------
|
|
|
641 # Useful public methods that implement functionality not properly
|
|
|
642 # provided by the parent class Bio::EnsEMBL::DBSQL::BaseAdaptor.
|
|
|
643
|
|
|
644 sub fetch_by_dbID {
|
|
|
645 my ( $this, $dbid ) = @_;
|
|
|
646
|
|
|
647 my $statement = q(
|
|
|
648 SELECT term.accession,
|
|
|
649 term.name,
|
|
|
650 term.definition,
|
|
|
651 term.subsets,
|
|
|
652 ontology.name,
|
|
|
653 ontology.namespace
|
|
|
654 FROM ontology
|
|
|
655 JOIN term USING (ontology_id)
|
|
|
656 WHERE term.term_id = ?);
|
|
|
657
|
|
|
658 my $sth = $this->prepare($statement);
|
|
|
659 $sth->bind_param( 1, $dbid, SQL_INTEGER );
|
|
|
660
|
|
|
661 $sth->execute();
|
|
|
662
|
|
|
663 my ( $accession, $name, $definition, $subsets, $ontology,
|
|
|
664 $namespace );
|
|
|
665 $sth->bind_columns(
|
|
|
666 \( $accession, $name, $definition, $subsets, $ontology, $namespace
|
|
|
667 ) );
|
|
|
668
|
|
|
669 $sth->fetch();
|
|
|
670 $subsets ||= '';
|
|
|
671
|
|
|
672 my $term =
|
|
|
673 Bio::EnsEMBL::OntologyTerm->new(
|
|
|
674 '-dbid' => $dbid,
|
|
|
675 '-adaptor' => $this,
|
|
|
676 '-accession' => $accession,
|
|
|
677 '-ontology' => $ontology,
|
|
|
678 '-namespace' => $namespace,
|
|
|
679 '-subsets' => [ split( /,/, $subsets ) ],
|
|
|
680 '-name' => $name,
|
|
|
681 '-definition' => $definition,
|
|
|
682 '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
|
|
|
683 );
|
|
|
684 $sth->finish();
|
|
|
685
|
|
|
686 return $term;
|
|
|
687 } ## end sub fetch_by_dbID
|
|
|
688
|
|
|
689 sub fetch_all_by_dbID_list {
|
|
|
690 my ( $this, $dbids ) = @_;
|
|
|
691
|
|
|
692 if ( !@{$dbids} ) { return [] }
|
|
|
693
|
|
|
694 my $stmt = q(
|
|
|
695 SELECT term.term_id,
|
|
|
696 term.accession,
|
|
|
697 term.name,
|
|
|
698 term.definition,
|
|
|
699 term.subsets,
|
|
|
700 ontology.name,
|
|
|
701 ontology.namespace
|
|
|
702 FROM ontology
|
|
|
703 JOIN term USING (ontology_id)
|
|
|
704 WHERE term.term_id IN (%s));
|
|
|
705
|
|
|
706 my $statement = sprintf(
|
|
|
707 $stmt,
|
|
|
708 join(
|
|
|
709 ',',
|
|
|
710 map {
|
|
|
711 $this->dbc()->db_handle()->quote( $_, SQL_INTEGER )
|
|
|
712 } @{$dbids} ) );
|
|
|
713
|
|
|
714 my $sth = $this->prepare($statement);
|
|
|
715
|
|
|
716 $sth->execute();
|
|
|
717
|
|
|
718 my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
|
|
|
719 $namespace );
|
|
|
720 $sth->bind_columns( \( $dbid, $accession, $name, $definition,
|
|
|
721 $subsets, $ontology, $namespace ) );
|
|
|
722
|
|
|
723 my @terms;
|
|
|
724
|
|
|
725 while ( $sth->fetch() ) {
|
|
|
726 $subsets ||= '';
|
|
|
727
|
|
|
728 push( @terms,
|
|
|
729 Bio::EnsEMBL::OntologyTerm->new(
|
|
|
730 '-dbid' => $dbid,
|
|
|
731 '-adaptor' => $this,
|
|
|
732 '-accession' => $accession,
|
|
|
733 '-ontology' => $ontology,
|
|
|
734 '-namespace' => $namespace,
|
|
|
735 '-subsets' => [ split( /,/, $subsets ) ],
|
|
|
736 '-name' => $name,
|
|
|
737 '-definition' => $definition, ) );
|
|
|
738 }
|
|
|
739
|
|
|
740 return \@terms;
|
|
|
741 } ## end sub fetch_all_by_dbID_list
|
|
|
742
|
|
|
743 sub fetch_all {
|
|
|
744 my ($this) = @_;
|
|
|
745
|
|
|
746 my $statement = q(
|
|
|
747 SELECT term.term_id,
|
|
|
748 term.accession,
|
|
|
749 term.name,
|
|
|
750 term.definition,
|
|
|
751 term.subsets,
|
|
|
752 ontology.name,
|
|
|
753 ontology.namespace
|
|
|
754 FROM ontology
|
|
|
755 JOIN term USING (ontology_id));
|
|
|
756
|
|
|
757 my $sth = $this->prepare($statement);
|
|
|
758 $sth->execute();
|
|
|
759
|
|
|
760 my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
|
|
|
761 $namespace );
|
|
|
762 $sth->bind_columns( \( $dbid, $accession, $name, $definition,
|
|
|
763 $subsets, $ontology, $namespace ) );
|
|
|
764
|
|
|
765 my @terms;
|
|
|
766
|
|
|
767 while ( $sth->fetch() ) {
|
|
|
768 $subsets ||= '';
|
|
|
769
|
|
|
770 push( @terms,
|
|
|
771 Bio::EnsEMBL::OntologyTerm->new(
|
|
|
772 '-dbid' => $dbid,
|
|
|
773 '-adaptor' => $this,
|
|
|
774 '-accession' => $accession,
|
|
|
775 '-ontology' => $ontology,
|
|
|
776 '-namespace' => $namespace,
|
|
|
777 '-subsets' => [ split( /,/, $subsets ) ],
|
|
|
778 '-name' => $name,
|
|
|
779 '-definition' => $definition ) );
|
|
|
780 }
|
|
|
781
|
|
|
782 return \@terms;
|
|
|
783 } ## end sub fetch_all
|
|
|
784
|
|
|
785 1;
|
