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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::OntologyXref
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24
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25 =head1 DESCRIPTION
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26
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27 This class extends the DBEntry in order to associate Evidence Tags
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28 to the relationship between EnsEMBL objects and ontology accessions
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29 (primarily GO accessions).
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30
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31 The relationship to GO that is stored in the database is actually
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32 derived through the relationship of EnsEMBL peptides to SwissProt
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33 peptides, i.e. the relationship is derived like this:
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34
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35 ENSP -> SWISSPROT -> GO
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36
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37 And the evidence tag describes the relationship between the SwissProt
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38 Peptide and the GO entry.
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39
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40 In reality, however, we store this in the database like this:
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41
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42 ENSP -> SWISSPROT
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43 ENSP -> GO
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44
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45 and the evidence tag hangs off of the relationship between the ENSP and
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46 the GO identifier. Some ENSPs are associated with multiple closely
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47 related Swissprot entries which may both be associated with the same GO
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48 identifier but with different evidence tags. For this reason a single
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49 'OntologyXref' can have multiple evidence tags.
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50
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51 =head1 SYNOPSIS
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52
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53 my $ontology_xref = Bio::EnsEMBL::OntologyXref->new();
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54 $ontology_xref->add_linkage_type('IEA');
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55
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56 foreach my $evtag ( @{ $ontology_xref->get_all_linkage_types() } ) {
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57 print "$evtag\n";
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58 }
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59
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60 =head1 METHODS
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61
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62 =cut
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63
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64 package Bio::EnsEMBL::OntologyXref;
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65
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66 use strict;
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67
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68 use base qw( Bio::EnsEMBL::DBEntry );
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69
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70 =head2 add_linkage_type
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71
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72 Arg [1] : string $value
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73 allowed values:
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74 'IC', 'IDA', 'IEA', 'IEP', 'IGI', 'IMP', 'IPI',
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75 'ISS', NAS', 'ND', 'TAS', 'NR', 'RCA'
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76 Arg [2] : (optional) Bio::EnsEMBL::DBEntry $source
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77 Example : $ontology_xref->add_linkage_type('IGI');
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78 Description: Associates a linkage type and source DBEntry with
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79 this ontology_xref
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80 Returntype : integer; number of linkages
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81 Exceptions : thrown if $linkage_type argument not supplied or
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82 the optional DBEntry is not a DBEntry object.
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83 Caller : DBEntryAdaptor
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84 Status : Experimantal
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85
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86 =cut
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87
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88 sub add_linkage_type {
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89 my ( $self, $lt, $source_dbentry ) = @_;
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90
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91 if ( !defined($lt) ) {
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92 $self->throw("linkage type argument required");
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93 }
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94
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95 if ( defined($source_dbentry)
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96 && !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
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97 {
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98 $self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
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99 }
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100
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101 $self->{'linkage_types'} ||= [];
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102
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103 push @{ $self->{'linkage_types'} },
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104 [ $lt, ( $source_dbentry || () ) ];
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105 }
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106
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107
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108 =head2 get_all_linkage_info
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109
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110 Arg [1] : none
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111 Example :
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112
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113 foreach ( @{ $ontology_xref->get_all_linkage_info() } ) {
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114 print "evidence: $_->[0] via $_->[1]->display_id";
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115 }
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116
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117 Description: Retrieves a list of evidence-tag/source-DBEntry pairs
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118 associated with this ontology_xref
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119 Returntype : listref of listrefs
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120 Exceptions : none
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121 Caller : geneview? general.
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122 Status : Experimental
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123
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124 =cut
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125
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126 sub get_all_linkage_info {
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127 my ($self) = @_;
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128
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129 return $self->{'linkage_types'} || [];
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130 }
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131
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132
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133 =head2 get_all_linkage_types
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134
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135 Arg [1] : none
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136 Example :
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137
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138 print( join( ' ', @{ $ontology_xref->get_all_linkage_types() } ),
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139 "\n" );
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140
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141 Description: Retrieves a unique list of evidence tags associated with
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142 this ontology_xref
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143 Returntype : none
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144 Exceptions : none
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145 Caller : geneview? general
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146 Status : Stable
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147
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148 =cut
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149
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150 sub get_all_linkage_types {
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151 my ($self) = @_;
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152
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153 my %seen;
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154 return [ grep { !$seen{$_}++ }
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155 map { $_->[0] } @{ $self->{'linkage_types'} } ];
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156
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157 #return [ map{ $_->[0]} @{ $self->{'linkage_types'} || [] } ];
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158 }
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159
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160
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161 =head2 flush_linkage_types
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162
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163 Arg [1] : none
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164 Example : $ontology_xref->flush_linkage_types();
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165 Description: Removes any associated evidence tags
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166 Returntype : none
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167 Exceptions : none
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168 Caller : general
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169 Status : Stable
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170
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171 =cut
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172
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173 sub flush_linkage_types {
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174 my ($self) = @_;
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175
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176 $self->{'linkage_types'} = [];
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177 }
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178
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179 1;
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