/usr/share/perl5/GO/Handlers/owl.pm is in libgo-perl 0.15-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 | # stag-handle.pl -p GO::Parsers::GoOntParser -m <THIS> function/function.ontology
# $Id: owl.pm,v 1.5 2004/07/08 04:08:42 cmungall Exp $
#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
=head1 NAME
GO::Handlers::owl - writes OWL
=head1 SYNOPSIS
use GO::Parser;
my $p = GO::Parser->new({handler=>'owl'});
$p->parse("function.ontology");
=head1 DESCRIPTION
Consumes an OBO-XML event stream and generates OWL XML
See the file
go-dev/doc/mapping-obo-to-owl.txt
For more details
=head1 COMMAND LINE
go2fmt.pl -w owl function.obo
=cut
package GO::Handlers::owl;
use base qw(Data::Stag::Writer Exporter);
use XML::Writer;
use strict;
sub is_transform { 0 }
sub init {
my $self = shift;
$self->SUPER::init(@_);
my $gen = XML::Writer->new(OUTPUT=>$self->safe_fh);
$self->{writer} = $gen;
$gen->setDataMode(1);
$gen->setDataIndent(4);
}
sub s_obo {
my $self = shift;
$self->{writer}->xmlDecl("UTF-8");
# $self->{writer}->doctype("owl:RDF",
# '-//Gene Ontology//Custom XML/RDF Version 2.0//EN',
# 'http://www.godatabase.org/dtd/go.dtd');
$self->{writer}->startTag('rdf:RDF',
'xmlns:rdf'=>"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
'xmlns:rdfs'=>"http://www.w3.org/2000/01/rdf-schema#",
'xmlns:owl'=>"http://www.w3.org/2002/07/owl#",
'xmlns'=>"http://www.geneontology.org/owl/obo/#",
'xmlns:obo'=>"http://www.geneontology.org/owl/obo/#",
'xml:base'=>"http://www.geneontology.org/owl/obo/",
'xmlns:dc'=>"http://purl.org/dc/elements/1.1/",
);
}
sub e_obo {
my $self = shift;
$self->{writer}->endTag('rdf:RDF');
}
sub w {
shift->{writer}
}
sub e_term {
my ($self, $term) = @_;
my $id = $term->get_id || $self->throw($term->sxpr);
my $w = $self->w;
$id = rdfsafe($id);
my $name_h = $self->{name_h};
my $name = $term->get_name;
$w->startTag('owl:Class', 'rdf:ID'=>$id);
if ($name) {
if (!$name_h) {
$name_h = {};
$self->{name_h} = $name_h;
}
$name_h->{$id} = $name;
$self->cmt("-- $name --\n");
$w->dataElement('rdfs:label', $name);
}
my $def = $term->get_definition;
if ($def) {
$w->dataElement('dc:description',
$def->get_definition_text);
}
my $ont = $term->get_ontology;
# if ($ont) {
# $self->fact('belongs', [$id, $ont]);
# }
my @is_as = $term->get_is_a;
$w->dataElement('rdfs:subClassOf',
'',
'rdf:resource'=>rdfres($_)) foreach @is_as;
my @rels = $term->get_relationship;
foreach (@rels) {
$w->startTag('rdfs:subClassOf');
$w->startTag('owl:Restriction');
$w->dataElement('owl:onProperty', '',
'rdf:resource'=>rdfres($_->get_type));
$w->dataElement('owl:someValuesFrom', '',
'rdf:resource'=>rdfres($_->get_to));
$w->endTag('owl:Restriction');
$w->endTag('rdfs:subClassOf');
}
$w->endTag('owl:Class');
return;
}
sub e_typedef {
my ($self, $typedef) = @_;
my $id = $typedef->get_id || $self->throw($typedef->sxpr);
my $w = $self->w;
$id = rdfsafe($id);
my $name = $typedef->get_name;
$w->startTag('owl:ObjectProperty', 'rdf:ID'=>$id);
if ($name) {
# $w->dataElement('rdfs:label', $name);
}
my $def = $typedef->get_definition;
if ($def) {
$w->dataElement('dc:description',
$def->get_definition_text);
}
my @is_as = $typedef->get_is_a;
$w->dataElement('rdfs:subPropertyOf',
'',
'rdf:resource'=>rdfres($_)) foreach @is_as;
my $domain = $typedef->get_domain;
my $range = $typedef->get_range;
$w->dataElement('rdfs:domain','','rdf:resource'=>rdfres($domain)) if $domain;
$w->dataElement('rdfs:range','','rdf:resource'=>rdfres($range)) if $range;
$w->endTag('owl:ObjectProperty');
return;
}
sub out {
my $self = shift;
print "@_";
}
sub cmt {
my $self = shift;
my $cmt = shift;
# $self->out(" % $cmt") if $cmt;
return;
}
sub rdfres {
my $w = rdfsafe(shift);
return "#$w";
}
sub rdfsafe {
my $w = shift;
$w =~ s/:/_/g;
$w;
}
1;
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