}
$nrules = $nrules + 1;
$textualtriggeringrule = "Class: " . make_valid_id($phenotype_label) . "\n";
$textualtriggeringrule .= "\tSubClassOf: phenotype_rule " . "\n";
$textualtriggeringrule .= "\tAnnotations: rdfs:comment \"" . preg_replace('/\\s+/', ' ', trim($phenotype_logical_statements)) . "\"\n";
$textualtriggeringrule .= "\tAnnotations: rdfs:label \"" . $phenotype_label . "\"\n";
$humantriggeringrule = "Class: human_with_" . make_valid_id($phenotype_label) . "\n";
$humantriggeringrule .= " SubClassOf: human_triggering_phenotype_inference_rule" . "\n";
$humantriggeringrule .= " Annotations: rdfs:label \"human with " . $phenotype_label . "\"\n";
if (strlen($phenotype_logical_statements) != 0) {
$humantriggeringrule .= "\tEquivalentTo: human and (" . preg_replace('/\\s+/', ' ', trim($phenotype_logical_statements)) . ")\n";
}
$textualtriggeringrule .= " Annotations: source \"" . $phenotype_source . "\"\n";
$humantriggeringrule .= " Annotations: source \"" . $phenotype_source . "\"\n";
$textualtriggeringrule .= parse_multiple_URLs($phenotype_URL);
$humantriggeringrule .= parse_multiple_URLs($phenotype_URL);
if (isset($date_of_evidence) && $date_of_evidence != "") {
$textualtriggeringrule .= " Annotations: date_of_evidence \"" . $date_of_evidence . "\"\n";
$humantriggeringrule .= " Annotations: date_of_evidence \"" . $date_of_evidence . "\"\n";
}
if (isset($date_of_addition) && $date_of_addition != "") {
$textualtriggeringrule .= " Annotations: date_of_addition \"" . $date_of_addition . "\"\n";
$humantriggeringrule .= " Annotations: date_of_addition \"" . $date_of_addition . "\"\n";
}
if (isset($date_last_validation) && $date_last_validation != "") {
$textualtriggeringrule .= " Annotations: date_last_validation \"" . $date_last_validation . "\"\n";
$humantriggeringrule .= " Annotations: date_last_validation \"" . $date_last_validation . "\"\n";
}
if (isset($author_last_validation) && $author_last_validation != "") {
$textualtriggeringrule .= " Annotations: author_last_validation \"" . $author_last_validation . "\"\n";
$humantriggeringrule .= " Annotations: author_last_validation \"" . $author_last_validation . "\"\n";
$row_array = array();
// Skip first row
if ($row->getRowIndex() == 1) {
continue;
}
// Processing of other rows (except the first) from here on
$cellIterator = $row->getCellIterator();
foreach ($cellIterator as $cell) {
$row_array[$cell->getColumn()] = $cell->getCalculatedValue();
}
$entity_label = $row_array["A"];
$comment = $row_array["B"];
$external_URL = $row_array["C"];
$owl .= "Class: " . make_valid_id($entity_label) . "\n";
$owl .= " Annotations: rdfs:label \"" . $entity_label . "\"\n";
$owl .= parse_multiple_URLs($external_URL);
$owl .= " Annotations: rdfs:comment \"" . $comment . "\"\n\n";
}
/********************************************************************
******** Sort rank of the elements in a genotype profile **********
********************************************************************/
$list_genes = array();
$list_snps = array();
foreach ($list_genes_and_snps_in_rules as $value) {
if (strpos($value, "rs") === 0) {
$list_snps[] = $value;
} else {
$list_genes[] = $value;
}
}
sort($list_snps);
if (isset($row_array["J"])) {
$author_last_validation = $row_array['J'];
} else {
$author_last_validation = "";
}
if (isset($row_array["K"])) {
$author_addition = $row_array['K'];
} else {
$author_addition = "";
}
$owl .= "Class: " . make_valid_id($phenotype_label) . "\n";
$owl .= "\tSubClassOf: human_triggering_phenotype_inference_rule " . "\n";
$owl .= "\tEquivalentTo: " . preg_replace('/\\s+/', ' ', trim($phenotype_logical_statements)) . "\n";
$owl .= "\tAnnotations: rdfs:label \"" . $phenotype_label . "\"\n";
$owl .= "\tAnnotations: source \"" . $phenotype_source . "\"\n";
$owl .= parse_multiple_URLs($phenotype_URL);
if (isset($date_of_evidence) && $date_of_evidence == "") {
$owl .= " Annotations: date_of_evidence \"" . $date_of_evidence . "\"\n";
}
if (isset($date_of_addition) && $date_of_addition == "") {
$owl .= " Annotations: date_of_addition \"" . $date_of_addition . "\"\n";
}
if (isset($date_last_validation) && $date_last_validation == "") {
$owl .= " Annotations: date_last_validation \"" . $date_last_validation . "\"\n";
}
if (isset($author_last_validation) && $author_last_validation == "") {
$owl .= " Annotations: author_last_validation \"" . $author_last_validation . "\"\n";
}
if (isset($author_addition) && $author_addition == "") {
$owl .= " Annotations: author_addition \"" . $author_addition . "\"\n";
}
