<td bgcolor="#AAAAAA"><strong>Total</strong></td>
</tr>
<?php
foreach ($rs as $row) {
$o = $row['ontology_abbrv'];
$settings = getSettings($o);
$classQueryString = "\nPREFIX rdf: <{$settings['ns_rdf']}>\nPREFIX owl: <{$settings['ns_owl']}>\nSELECT count(distinct ?s) as ?cCount\nFROM <{$settings['ns_main']}>\nWHERE\n{\n?s a owl:Class .\nFILTER (isIRI(?s)).\n}\n";
$objectQueryString = "\nPREFIX rdf: <{$settings['ns_rdf']}>\nPREFIX owl: <{$settings['ns_owl']}>\nSELECT count(distinct ?s) as ?oCount\nFROM <{$settings['ns_main']}>\nWHERE\n{\n?s a owl:ObjectProperty .\nFILTER (isIRI(?s)).\n}\n";
$datatypeQueryString = "\nPREFIX rdf: <{$settings['ns_rdf']}>\nPREFIX owl: <{$settings['ns_owl']}>\nSELECT count(distinct ?s) as ?dCount\nFROM <{$settings['ns_main']}>\nWHERE\n{\n?s a owl:DatatypeProperty .\nFILTER (isIRI(?s)).\n}\n";
$annotationQueryString = "\nPREFIX rdf: <{$settings['ns_rdf']}>\nPREFIX owl: <{$settings['ns_owl']}>\nSELECT count(distinct ?s) as ?aCount\nFROM <{$settings['ns_main']}>\nWHERE\n{\n?s a owl:AnnotationProperty .\nFILTER (isIRI(?s)).\n}\n";
$cCountResult = json_query($classQueryString);
$aCountResult = json_query($annotationQueryString);
$dCountResult = json_query($datatypeQueryString);
$oCountResult = json_query($objectQueryString);
$cCount = $cCountResult[0]['cCount'];
$aCount = $aCountResult[0]['aCount'];
$dCount = $dCountResult[0]['dCount'];
$oCount = $oCountResult[0]['oCount'];
$total = $cCount + $aCount + $dCount + $oCount;
?>
<tr align="center" height="25" <?php
if ($index % 2 == 0) {
echo "bgcolor = \"#CCECFB\"";
}
?>
>
<td><strong><?php
echo $index;
?>
function getSubClassAndProperty($ontology_uri, &$results, $tmp_iri)
{
global $ns_rdf, $ns_rdfs, $ns_owl, $num_queries, $processed_iris, $included_iris, $parent_included_iris, $strOutput;
$querystring = "\r\nPREFIX rdf: <{$ns_rdf}>\r\nPREFIX rdfs: <{$ns_rdfs}>\r\nPREFIX owl: <{$ns_owl}>\r\n\r\nSELECT DISTINCT *\r\n\r\nFROM <{$ontology_uri}>\r\n\t\r\nWHERE { \r\n\t{\r\n\t\t?s rdfs:subClassOf <{$tmp_iri}> .\r\n\t\t?s rdfs:label ?o\r\n\t}\r\n\tUNION\r\n\t{\r\n\t\t?s owl:equivalentClass ?s1 .\r\n\t\t?s1 owl:intersectionOf ?s2 .\r\n\t\t?s2 rdf:first <{$tmp_iri}> .\r\n\t\t?s rdfs:label ?o\r\n\t}\r\n}";
$tmp_results = json_query($querystring);
$num_queries++;
if (!empty($tmp_results)) {
foreach ($tmp_results as $tmp_result) {
$tmp_iri0 = $tmp_result['s'];
if (!isset($processed_iris[$tmp_iri0]) && !isset($included_iris[$tmp_iri0]) && !iriImported($tmp_iri0)) {
$strOutput .= "\r\n<rdf:Description rdf:about=\"{$tmp_iri0}\">\r\n\t\t\t<rdfs:subClassOf rdf:resource=\"{$tmp_iri}\"/>\r\n\t\t </rdf:Description>\r\n";
$results[$tmp_iri0] = $tmp_result['o'];
getSubClassAndProperty($ontology_uri, $results, $tmp_iri0);
}
}
}
$querystring = "\r\nPREFIX rdf: <{$ns_rdf}>\r\nPREFIX rdfs: <{$ns_rdfs}>\r\nPREFIX owl: <{$ns_owl}>\r\n\r\nSELECT DISTINCT *\r\n\r\nFROM <{$ontology_uri}>\r\n\t\r\nWHERE { \r\n\t{\r\n\t\t?s rdfs:subPropertyOf <{$tmp_iri}> .\r\n\t\t?s rdfs:label ?o\r\n\t}\r\n\tUNION\r\n\t{\r\n\t\t?s owl:equivalentProperty ?s1 .\r\n\t\t?s1 owl:intersectionOf ?s2 .\r\n\t\t?s2 rdf:first <{$tmp_iri}> .\r\n\t\t?s rdfs:label ?o\r\n\t}\r\n}";
$tmp_results = json_query($querystring);
$num_queries++;
if (!empty($tmp_results)) {
foreach ($tmp_results as $tmp_result) {
$tmp_iri0 = $tmp_result['s'];
if (!isset($processed_iris[$tmp_iri0]) && !isset($included_iris[$tmp_iri0]) && !iriImported($tmp_iri0)) {
$strOutput .= "\r\n<rdf:Description rdf:about=\"{$tmp_iri0}\">\r\n\t\t\t<rdfs:subPropertyOf rdf:resource=\"{$tmp_iri}\"/>\r\n\t\t </rdf:Description>\r\n";
$results[$tmp_iri0] = $tmp_result['o'];
getSubClassAndProperty($ontology_uri, $results, $tmp_iri0);
}
}
}
}
</br>
<p>Total #: <strong><?php
echo $index;
?>
</strong></p>
<?php
} elseif ($prefix == "total" && $type == "totalCount") {
$classQueryString = "\nSELECT ?s as ?class ?l as ?label\nFROM <{$domain}>\nWHERE\n{\n?s a owl:Class .\n\nOPTIONAL\n{\n?s rdfs:label ?l.\n}\n\nFILTER (isIRI(?s)).\n\n}\n";
$objectQueryString = "\nSELECT ?s as ?object ?l as ?label\nFROM <{$domain}>\nWHERE\n{\n?s a owl:ObjectProperty .\n\nOPTIONAL\n{\n?s rdfs:label ?l.\n}\n\nFILTER (isIRI(?s)).\n\n}\n";
$datatypeQueryString = "\nSELECT ?s as ?datatype ?l as ?label\nFROM <{$domain}>\nWHERE\n{\n?s a owl:DatatypeProperty .\n\nOPTIONAL\n{\n?s rdfs:label ?l.\n}\n\nFILTER (isIRI(?s)).\n\n}\n";
$annotationQueryString = "\nSELECT ?s as ?annotation ?l as ?label\nFROM <{$domain}>\nWHERE\n{\n?s a owl:AnnotationProperty .\n\nOPTIONAL\n{\n?s rdfs:label ?l.\n}\nFILTER (isIRI(?s)).\n\n}\n";
$classQueryResult = json_query($classQueryString);
$objectQueryResult = json_query($objectQueryString);
$datatypeQueryResult = json_query($datatypeQueryString);
$annotationQueryResult = json_query($annotationQueryString);
$index = 0;
?>
</br>
</br>
<table align="center" width="800">
<tr height="25" align="center">
<td bgcolor="#AAAAAA" ><strong>IRI</strong></td>
<td bgcolor="#AAAAAA"><strong>label</strong></td>
</tr>
<?php
if (sizeof($classQueryResult) != 0) {
foreach ($classQueryResult as $result) {
?>
<tr height="25" <?php
$first_letter_filter = '.
FILTER regex(?o, "^[^A-Z]")';
}
$querystring = "\nPREFIX rdf: <{$settings['ns_rdf']}>\nSELECT distinct ?s ?o\n";
if ($graph != '') {
$querystring .= "\nFROM <{$graph}>\n";
} else {
$querystring .= "\nFROM <{$settings['ns_main']}>\n";
}
$querystring .= "\nWHERE {\n\t{ ?s rdf:type <{$iri}> .\n\tFILTER (isIRI(?s)).\n\tOPTIONAL { ?s rdfs:label ?o } \n\t}\n";
if ($iri == $settings['ns_owl'] . 'ObjectProperty') {
$querystring .= "\n\tUNION {?s rdf:type owl:TransitiveProperty.\n\tFILTER (isIRI(?s)).\n\tOPTIONAL { ?s rdfs:label ?o } \n\t} \n\tUNION {?s rdf:type owl:SymmetricProperty.\n\tFILTER (isIRI(?s)).\n\tOPTIONAL { ?s rdfs:label ?o } \n\t}\n";
}
$querystring .= "\n\n}\n\nLIMIT 10000\n";
// print($querystring);
$results = json_query($querystring);
$final_results = array();
if (!empty($results)) {
foreach ($results as $result) {
$sub = $result['s'];
$obj = isset($result['o']) ? $result['o'] : '';
$final_results[$sub] = $obj != '' ? $obj : getShortTerm($sub);
if ($final_results[$sub] == '') {
$final_results[$sub] = 'NA';
}
}
} else {
}
asort($final_results);
if (!empty($final_results)) {
$numOfRecords = sizeof($final_results);
$rs = $db->Execute($strSql);
if (!$rs->EOF) {
$filename = $ontology;
// print(filemtime("userfiles/$filename.xls") - time());
if (!file_exists("userfiles/{$filename}.xls") || time() - filemtime("userfiles/{$filename}.xls") > 60 * 60 * 8) {
$end_point = $rs->Fields('end_point');
$graph_url = $rs->Fields('ontology_graph_url');
$querystring = "\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\n\nSELECT *\n\nFROM <{$graph_url}>\n\nWHERE\n{\n\t?s rdf:type owl:Class .\n\t?s rdfs:label ?l .\n\tFILTER (isIRI(?s)).\n\tOPTIONAL {?s <http://purl.obolibrary.org/obo/IAO_0000118> ?alt_names}.\n\tOPTIONAL {?s <http://purl.obolibrary.org/obo/IAO_0000115> ?definition}.\n\tOPTIONAL {?s rdfs:subClassOf ?pTerm.\n\t\tFILTER (isIRI(?pTerm)).\n\t\t?pTerm rdfs:label ?pLabel}.\n\t\n}\n\nlimit 10000\n";
//print($querystring);
$tmp_results = json_query($querystring, $end_point);
$terms = array();
foreach ($tmp_results as $result) {
$terms[$result['s']] = $result;
}
$querystring = "\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\n\nSELECT *\n\nFROM <{$graph_url}>\n\nWHERE\n{\n\t?s rdf:type ?o .\n\t?s rdfs:label ?l .\n\tFILTER (?o in(<" . join('>, <', $a_signature_term_type) . ">)).\n\tFILTER (isIRI(?s)).\n\tOPTIONAL {?s <http://purl.obolibrary.org/obo/IAO_0000118> ?alt_names}.\n\tOPTIONAL {?s <http://purl.obolibrary.org/obo/IAO_0000115> ?definition}.\n\tOPTIONAL {?s rdfs:subPropertyOf ?pTerm.\n\t\tFILTER (isIRI(?pTerm)).\n\t\t?pTerm rdfs:label ?pLabel}.\n\t\n}\n\nlimit 10000\n";
$tmp_results = json_query($querystring, $end_point);
foreach ($tmp_results as $result) {
$terms[$result['s']] = $result;
}
/** PHPExcel */
require_once 'inc/PHPExcel.php';
/** PHPExcel_Cell_AdvancedValueBinder */
require_once 'inc/PHPExcel/Cell/AdvancedValueBinder.php';
/** PHPExcel_IOFactory */
require_once 'inc/PHPExcel/IOFactory.php';
// Set value binder
PHPExcel_Cell::setValueBinder(new PHPExcel_Cell_AdvancedValueBinder());
// Create new PHPExcel object
$objPHPExcel = new PHPExcel();
$objPHPExcel->getActiveSheet()->getColumnDimension('A')->setWidth(45);
$objPHPExcel->getActiveSheet()->getColumnDimension('B')->setWidth(45);
} else {
$annotationPrefixArray[$prefix] = 1;
}
} elseif (preg_match('/\\/([a-z]+)_[0-9]+/', $property['annotation'], $match)) {
$prefix = $match[1];
if (array_key_exists($prefix, $annotationPrefixArray)) {
$annotationPrefixArray[$prefix] += 1;
} else {
$annotationPrefixArray[$prefix] = 1;
}
} else {
$annotationNoPrefixCount++;
}
}
}
$dpropertyResult = json_query($DatatypePropertyQueryString);
$datatypePrefixArray = array();
$datatypeNoPrefixCount = 0;
if (count($dpropertyResult) != 0) {
foreach ($dpropertyResult as $property) {
if (preg_match('/\\/([A-Za-z\\.\\-_]+)#[a-zA-Z_0-9]+/', $property['datatype'], $match)) {
$prefix = $match[1];
if (array_key_exists($prefix, $datatypePrefixArray)) {
$datatypePrefixArray[$prefix] += 1;
} else {
$datatypePrefixArray[$prefix] = 1;
}
} elseif (preg_match('/\\/([A-Z][A-Za-z]+)_[-a-zA-Z_0-9]+/', $property['datatype'], $match)) {
$prefix = $match[1];
if (array_key_exists($prefix, $datatypePrefixArray)) {
$datatypePrefixArray[$prefix] += 1;
if (preg_match('/[a-zA-Z]+[:_]\\d{7,}/', $keywords)) {
$search_term_url = 'http://purl.obolibrary.org/obo/' . preg_replace('/:/', '_', $keywords);
$querystring = "SELECT distinct ?s ?o\nfrom <{$settings['ns_main']}>\nWHERE{\n?s ?p ?o .\nfilter (?p in (<" . join('>,<', $array_property) . ">)).\nfilter (?s in (<{$search_term_url}>)).\n}\nlimit 5000\n";
} else {
$querystring = "SELECT distinct ?s ?o\nfrom <{$settings['ns_main']}>\nWHERE{\n?s ?p ?o .\nfilter (?p in (<" . join('>,<', $array_property) . ">)).\nFILTER (isIRI(?s)).\n?o bif:contains \"'{$keywords}*'\".\n}\nlimit 5000\n";
}
} else {
if (preg_match('/[a-zA-Z]+[:_]\\d{7,}/', $keywords)) {
$search_term_url = 'http://purl.obolibrary.org/obo/' . preg_replace('/:/', '_', $keywords);
$querystring = "SELECT distinct ?g ?s ?o\nWHERE{\ngraph ?g \n{\n?s ?p ?o .\nfilter (?p in (<" . join('>,<', $array_property) . ">)).\nfilter (?s in (<{$search_term_url}>)).\n}\n}\nlimit 5000\n";
} else {
$querystring = "SELECT distinct ?g ?s ?o\nWHERE{\ngraph ?g \n{\n?s ?p ?o .\nfilter (?p in (<" . join('>,<', $array_property) . ">)).\nFILTER (isIRI(?s)).\n?o bif:contains \"'{$keywords}*'\".\n}\n}\nlimit 5000\n";
}
}
// print ($querystring);
$results = json_query($querystring, $default_end_point);
if (!empty($results)) {
$tkeywords = preg_replace('/\\W/', ' ', $keywords);
?>
<p>
Terms with '<?php
echo $keywords;
?>
' included in their label:
<ol>
<?php
$results2 = array();
foreach ($results as $result) {
if (strtolower($result['o']) == strtolower($keywords)) {
if (isset($result['g'])) {
