$class_id = "rs" . $rs_id;
$owl .= "Class: " . $class_id . "\n";
// Create subclasses of Polymorphism->(1)rsid; (2)rdfs:label; (3)can_be_tested_with; (4)relevant_for; (5)rdfs:seeAlso; (6)dbsnp_orientation_on_reference_genome;
$owl .= " SubClassOf: polymorphism" . "\n";
$owl .= " Annotations: rsid \"rs" . $rs_id . "\"\n";
$owl .= " Annotations: rdfs:label \"rs" . $rs_id . "\"\n";
if (in_array($class_id, $list_genes_and_snps_in_rules)) {
$rank_pos = array_search($class_id, $list_genes_and_snps_in_rules);
$genotype_rank = $rank_pos + 1;
$owl .= "\tAnnotations: rank \"" . $genotype_rank . "\"\n";
$snp_group_info_rank = $genotype_rank . "\t";
//Add rank element.
} else {
$owl .= "\tAnnotations: rank \"-1\"\n";
}
$owl .= generate_assay_annotations($class_id);
$snp_group_info_listgenomictest = generate_assay_annotations_semicolon_separated($class_id) . "\t";
//Add the listgenomictest element.
$fxn_symbols = null;
foreach ($fxn_sets as $fxn_set) {
if (isset($fxn_set["symbol"])) {
$fxn_symbols[] = make_valid_id($fxn_set["symbol"]);
}
}
if (isset($fxn_symbols)) {
$fxn_symbols = array_unique($fxn_symbols);
foreach ($fxn_symbols as $fxn_symbol) {
$owl .= " Annotations: relevant_for " . $fxn_symbol . "\n";
}
}
$owl .= " Annotations: rdfs:seeAlso <http://bio2rdf.org/dbsnp:rs" . $rs_id . "> \n";
$observed_alleles[$j] = flipOrientationOfStringRepresentation($observed_alleles[$j]);
}
}
sort($observed_alleles, SORT_STRING);
// Create OWL classes for all possible genotype variants
$class_id = "rs" . $rs_id;
$polymorphisms .= "Class: " . $class_id . "\n";
// Create subclasses of Polymorphism->(1)rsid; (2)rdfs:label; (3)can_be_tested_with; (4)relevant_for; (5)rdfs:seeAlso; (6)dbsnp_orientation_on_reference_genome;
$polymorphisms .= " SubClassOf: polymorphism" . "\n";
$polymorphisms .= " Annotations: rsid \"rs" . $rs_id . "\"\n";
$polymorphisms .= " Annotations: rdfs:label \"rs" . $rs_id . "\"\n";
if (rankSNPInGenotype($class_id)) {
$polymorphisms .= "\tAnnotations: rank \"" . $genotype_rank . "\"\n";
$genotype_rank++;
}
$polymorphisms .= generate_assay_annotations($class_id);
$fxn_symbols = null;
foreach ($fxn_sets as $fxn_set) {
if (isset($fxn_set["symbol"])) {
$fxn_symbols[] = make_valid_id($fxn_set["symbol"]);
}
}
if (isset($fxn_symbols)) {
$fxn_symbols = array_unique($fxn_symbols);
foreach ($fxn_symbols as $fxn_symbol) {
$polymorphisms .= " Annotations: relevant_for " . $fxn_symbol . "\n";
}
}
$polymorphisms .= " Annotations: rdfs:seeAlso <http://bio2rdf.org/dbsnp:rs" . $rs_id . "> \n";
$polymorphisms .= " Annotations: dbsnp_orientation_on_reference_genome \"" . $orient . "\" \n\n";
$polymorphism_disjoint_list[] = $class_id;
