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1 # $Id: MedlineArticle.pm,v 1.5 2002/10/22 07:45:11 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Biblio::MedlineArticle
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4 #
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5 # Cared for by Martin Senger <senger@ebi.ac.uk>
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6 # For copyright and disclaimer see below.
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7
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8 # POD documentation - main docs before the code
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9
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10 =head1 NAME
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11
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12 Bio::Biblio::MedlineArticle - Representation of a MEDLINE article
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13
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14 =head1 SYNOPSIS
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15
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16 $obj = new Bio::Biblio::MedlineArticle (-mesh_headings => ...);
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17
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18 # how are Mesh terms stored:
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19 use Data::Dumper;
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20 print Data::Dumper->Dump ( [$obj->mesh_headings], ['MeshHeadings']);
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21
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22 It produces (something like) this:
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23 'MeshHeadings' => [
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24 { 'descriptorName' => 'Adult' },
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25 { 'descriptorName' => 'Cardiovascular Diseases',
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26 'subHeadings' => [ { 'subHeading' => 'etiology' },
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27 { 'majorTopic' => 'Y',
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28 'subHeading' => 'mortality' } ] },
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29 { 'descriptorName' => 'Child Development',
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30 'subHeadings' => [ { 'majorTopic' => 'Y',
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31 'subHeading' => 'physiology' } ] },
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32 { 'descriptorName' => 'Human' },
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33 ]
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34
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35 =head1 DESCRIPTION
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36
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37 A storage object for a MEDLINE article.
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38 See its place in the class hierarchy in
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39 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
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40
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41 =head2 Attributes
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42
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43 The following attributes are specific to this class
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44 (however, you can also set and get all attributes defined in the parent classes):
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45
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46 affiliation
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47 chemicals type: array ref of hashes
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48 citation_owner
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49 comment_ins type: array ref of hashes
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50 comment_ons type: array ref of hashes
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51 date_of_electronic_publication
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52 erratum_fors type: array ref of hashes
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53 erratum_in type: array ref of hashes
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54 gene_symbols
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55 general_notes type: array ref of hashes
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56 grant_list_complete
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57 grants type: array ref of hashes
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58 medline_date
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59 medline_id
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60 medline_page
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61 mesh_headings type: array ref of hashes
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62 number_of_references
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63 original_report_ins type: array ref of hashes
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64 other_abstracts type: array ref of hashes
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65 other_ids type: array ref of hashes
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66 other_languages
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67 pmid
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68 republished_froms type: array ref of hashes
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69 republished_ins type: array ref of hashes
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70 retraction_ins type: array ref of hashes
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71 retraction_ofs type: array ref of hashes
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72 season
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73 status
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74 summary_for_patients_ins type: array ref of hashes
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75 update_ins type: array ref of hashes
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76 update_ofs type: array ref of hashes
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77 vernacular_title
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78
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79 =head1 SEE ALSO
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80
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81 =over
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82
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83 =item *
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84
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85 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
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86
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87 =item *
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88
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89 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
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90
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91 =back
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92
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93 =head1 FEEDBACK
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94
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95 =head2 Mailing Lists
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96
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97 User feedback is an integral part of the evolution of this and other
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98 Bioperl modules. Send your comments and suggestions preferably to
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99 the Bioperl mailing list. Your participation is much appreciated.
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100
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101 bioperl-l@bioperl.org - General discussion
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102 http://bioperl.org/MailList.shtml - About the mailing lists
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103
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104 =head2 Reporting Bugs
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105
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106 Report bugs to the Bioperl bug tracking system to help us keep track
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107 of the bugs and their resolution. Bug reports can be submitted via
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108 email or the web:
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109
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110 bioperl-bugs@bioperl.org
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111 http://bugzilla.bioperl.org/
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112
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113 =head1 AUTHORS
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114
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115 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
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116 Martin Senger (senger@ebi.ac.uk)
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117
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118 =head1 COPYRIGHT
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119
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120 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
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121
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122 This module is free software; you can redistribute it and/or modify
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123 it under the same terms as Perl itself.
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124
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125 =head1 DISCLAIMER
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126
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127 This software is provided "as is" without warranty of any kind.
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128
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129 =cut
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130
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131
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132 # Let the code begin...
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133
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134
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135 package Bio::Biblio::MedlineArticle;
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136 use strict;
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137 use vars qw(@ISA);
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138
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139 use Bio::Biblio::Article;
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140
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141 @ISA = qw(Bio::Biblio::Article);
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142
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143 #
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144 # a closure with a list of allowed attribute names (these names
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145 # correspond with the allowed 'get' and 'set' methods); each name also
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146 # keep what type the attribute should be (use 'undef' if it is a
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147 # simple scalar)
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148 #
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149 {
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150 my %_allowed =
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151 (
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152 _affiliation => undef,
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153 _chemicals => 'ARRAY',
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154 _citation_owner => undef,
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155 _comment_ins => 'ARRAY',
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156 _comment_ons => 'ARRAY',
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157 _date_of_electronic_publication => undef,
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158 _erratum_fors => 'ARRAY',
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159 _erratum_ins => 'ARRAY',
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160 _gene_symbols => undef,
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161 _general_notes => 'ARRAY',
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162 _grant_list_complete => undef,
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163 _grants => 'ARRAY',
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164 _medline_date => undef,
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165 _medline_id => undef,
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166 _medline_page => undef,
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167 _mesh_headings => 'ARRAY',
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168 _number_of_references => undef,
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169 _original_report_ins => 'ARRAY',
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170 _other_abstracts => 'ARRAY',
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171 _other_ids => 'ARRAY',
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172 _other_languages => undef,
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173 _pmid => undef,
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174 _republished_froms => 'ARRAY',
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175 _republished_ins => 'ARRAY',
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176 _retraction_ins => 'ARRAY',
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177 _retraction_ofs => 'ARRAY',
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178 _season => undef,
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179 _status => undef,
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180 _summary_for_patients_ins => 'ARRAY',
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181 _update_ins => 'ARRAY',
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182 _update_ofs => 'ARRAY',
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183 _vernacular_title => undef,
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184 );
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185
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186 # return 1 if $attr is allowed to be set/get in this class
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187 sub _accessible {
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188 my ($self, $attr) = @_;
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189 exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
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190 }
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191
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192 # return an expected type of given $attr
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193 sub _attr_type {
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194 my ($self, $attr) = @_;
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195 if (exists $_allowed{$attr}) {
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196 return $_allowed{$attr};
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197 } else {
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198 return $self->SUPER::_attr_type ($attr);
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199 }
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200 }
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201 }
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202
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203
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204 1;
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205 __END__
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