function ParseEntry($obj, $type)
{
$o = $obj["omim"]["entryList"][0]["entry"];
$omim_id = $o['mimNumber'];
$omim_uri = parent::getNamespace() . $o['mimNumber'];
if (isset($o['version'])) {
parent::setDatasetVersion($o['version']);
}
// add the links
parent::addRDF($this->QQuadO_URL($omim_uri, "rdfs:seeAlso", "http://omim.org/entry/" . $omim_id));
parent::addRDF($this->QQuadO_URL($omim_uri, "owl:sameAs", "http://identifiers.org/omim/" . $omim_id));
// parse titles
$titles = $o['titles'];
parent::addRDF(parent::describeIndividual($omim_uri, $titles['preferredTitle'], parent::getVoc() . str_replace(array(" ", "/"), "-", ucfirst($type))) . parent::describeClass(parent::getVoc() . str_replace(array(" ", "/"), "-", ucfirst($type)), $type));
if (isset($titles['preferredTitle'])) {
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "preferred-title", $titles['preferredTitle']));
}
if (isset($titles['alternativeTitles'])) {
$b = explode(";;", $titles['alternativeTitles']);
foreach ($b as $title) {
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "alternative-title", trim($title)));
}
}
// parse text sections
if (isset($o['textSectionList'])) {
foreach ($o['textSectionList'] as $i => $section) {
if ($section['textSection']['textSectionTitle'] == "Description") {
parent::addRDF(parent::triplifyString($omim_uri, "dc:description", $section['textSection']['textSectionContent']));
} else {
$p = str_replace(" ", "-", strtolower($section['textSection']['textSectionTitle']));
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "{$p}", $section['textSection']['textSectionContent']));
}
// parse the omim references
preg_match_all("/\\{([0-9]{6})\\}/", $section['textSection']['textSectionContent'], $m);
if (isset($m[1][0])) {
foreach ($m[1] as $oid) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "refers-to", "omim:{$oid}"));
}
}
}
}
// allelic variants
if (isset($o['allelicVariantList'])) {
foreach ($o['allelicVariantList'] as $i => $v) {
$v = $v['allelicVariant'];
$uri = parent::getRes() . "{$omim_id}" . "_allele_" . $i;
$label = str_replace("\n", " ", $v['name']);
parent::addRDF(parent::describeIndividual($uri, $label, parent::getVoc() . "Allelic-Variant") . parent::describeClass(parent::getVoc() . "Allelic-Variant", "Allelic Variant"));
if (isset($v['alternativeNames'])) {
$names = explode(";;", $v['alternativeNames']);
foreach ($names as $name) {
$name = str_replace("\n", " ", $name);
parent::addRDF(parent::triplifyString($uri, parent::getVoc() . "alternative-names", $name));
}
}
if (isset($v['text'])) {
parent::addRDF(parent::triplifyString($uri, "dc:description", $v['text']));
}
if (isset($v['mutations'])) {
parent::addRDF(parent::triplifyString($uri, parent::getVoc() . "mutation", $v['mutations']));
}
if (isset($v['dbSnps'])) {
$snps = explode(",", $v['dbSnps']);
foreach ($snps as $snp) {
parent::addRDF(parent::triplify($uri, parent::getVoc() . "x-dbsnp", "dbsnp:" . $snp));
}
}
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "variant", $uri));
}
}
// clinical synopsis
if (isset($o['clinicalSynopsis'])) {
$cs = $o['clinicalSynopsis'];
$cs_uri = parent::getRes() . "" . $omim_id . "_cs";
parent::addRDF(parent::describeIndividual($cs_uri, "Clinical synopsis for omim {$omim_id}", parent::getVoc() . "Clinical-Synopsis") . parent::describeClass(parent::getVoc() . "Clinical-Synopsis", "Clinical Synopsis") . parent::triplify($omim_uri, parent::getVoc() . "clinical-synopsis", $cs_uri));
foreach ($cs as $k => $v) {
if (!strstr($k, "Exists")) {
// ignore the boolean assertion.
// @todo ignore provenance for now
if (in_array($k, array('contributors', 'creationDate', 'editHistory', 'epochCreated', 'dateCreated', 'epochUpdated', 'dateUpdated'))) {
continue;
}
if (!is_array($v)) {
$v = array($k => $v);
}
foreach ($v as $k1 => $v1) {
$phenotypes = explode(";", $v1);
foreach ($phenotypes as $coded_phenotype) {
// parse out the codes
$coded_phenotype = trim($coded_phenotype);
if (!$coded_phenotype) {
continue;
}
$phenotype = preg_replace("/\\{.*\\}/", "", $coded_phenotype);
$phenotype_id = parent::getRes() . "" . md5(strtolower($phenotype));
$entity_id = parent::getRes() . "" . $k1;
parent::addRDF(parent::describeIndividual($phenotype_id, $phenotype, parent::getVoc() . 'Characteristic') . parent::describeClass(parent::getVoc() . 'Characteristic', 'Characteristic') . parent::triplify($cs_uri, parent::getVoc() . "feature", $phenotype_id) . parent::describeIndividual($entity_id, $k1, parent::getVoc() . "Entity") . parent::describeClass(parent::getVoc() . "Entity", "Entity") . parent::triplify($phenotype_id, parent::getVoc() . "characteristic-of", $entity_id));
// parse out the vocab references
preg_match_all("/\\{([0-9A-Za-z \\:\\-\\.]+)\\}|;/", $coded_phenotype, $codes);
//preg_match_all("/((UMLS|HPO HP|SNOMEDCT|ICD10CM|ICD9CM|EOM ID)\:[A-Z0-9]+)/",$coded_phenotype,$m);
if (isset($codes[1][0])) {
foreach ($codes[1] as $entry) {
$entries = explode(" ", trim($entry));
foreach ($entries as $e) {
if ($e == "HPO" || $e == "EOM") {
continue;
}
$this->getRegistry()->parseQName($e, $ns, $id);
if (!isset($ns) || $ns == '') {
$b = explode(".", $id);
$ns = "omim";
$id = $b[0];
} else {
$ns = str_replace(array("hpo", "id", "icd10cm", "icd9cm", "snomedct"), array("hp", "eom", "icd10", "icd9", "snomed"), $ns);
}
parent::addRDF(parent::triplify($phenotype_id, parent::getVoc() . "x-{$ns}", "{$ns}:{$id}"));
}
// foreach
}
// foreach
}
// codes
}
//foreach
}
// foreach
}
// exists
}
}
// clinical synopsis
// genemap
if (isset($o['geneMap'])) {
$map = $o['geneMap'];
if (isset($map['chromosome'])) {
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "chromosome", (string) $map['chromosome']));
}
if (isset($map['cytoLocation'])) {
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "cytolocation", (string) $map['cytoLocation']));
}
if (isset($map['geneSymbols'])) {
$b = preg_split("/[,;\\. ]+/", $map['geneSymbols']);
foreach ($b as $symbol) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "gene-symbol", "symbol:" . trim($symbol)));
}
}
if (isset($map['geneName'])) {
$b = explode(",", $map['geneName']);
foreach ($b as $name) {
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "gene-name", trim($name)));
}
}
if (isset($map['mappingMethod'])) {
$b = explode(",", $map['mappingMethod']);
foreach ($b as $c) {
$mapping_method = trim($c);
$method_uri = $this->get_method_type($mapping_method);
if ($method_uri !== false) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "mapping-method", $method_uri));
}
}
}
if (isset($map['mouseGeneSymbol'])) {
$b = explode(",", $map['mouseGeneSymbol']);
foreach ($b as $c) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "mouse-gene-symbol", "symbol:" . strtoupper($c)));
}
}
if (isset($map['mouseMgiID'])) {
$b = explode(",", $map['mouseMgiID']);
foreach ($b as $c) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "x-mgi", $c));
}
}
if (isset($map['geneInheritance']) && $map['geneInheritance'] != '') {
parent::addRDF(parent::triplifyString($omim_uri, parent::getVoc() . "gene-inheritance", $map['geneInheritance']));
}
}
if (isset($o['phenotypeMapList'])) {
foreach ($o['phenotypeMapList'] as $i => $phenotypeMap) {
$phenotypeMap = $phenotypeMap['phenotypeMap'];
$pm_uri = parent::getRes() . $omim_id . "_pm_" . ($i + 1);
parent::addRDF(parent::describeIndividual($pm_uri, "phenotype mapping for {$omim_id}", parent::getVoc() . "Phenotype-Map") . parent::describeClass(parent::getVoc() . "Phenotype-Map", "OMIM Phenotype-Map") . parent::triplify($omim_uri, parent::getVoc() . "phenotype-map", $pm_uri));
foreach (array_keys($phenotypeMap) as $k) {
if (in_array($k, array("mimNumber", "phenotypeMimNumber", "phenotypicSeriesMimNumber"))) {
parent::addRDF(parent::triplify($pm_uri, parent::getVoc() . $k, "omim:" . $phenotypeMap[$k]));
} else {
if ($k == "geneSymbols") {
$l = explode(", ", $phenotypeMap[$k]);
foreach ($l as $gene) {
parent::addRDF(parent::triplify($pm_uri, parent::getVoc() . "gene-symbol", "hgnc.symbol:" . $gene));
}
} else {
if ($k == "phenotypeMappingKey") {
$l = $this->get_phenotype_mapping_method_type($phenotypeMap[$k]);
parent::addRDF(parent::triplify($pm_uri, parent::getVoc() . "mapping-method", $l));
} else {
parent::addRDF(parent::triplifyString($pm_uri, parent::getVoc() . $k, $phenotypeMap[$k]));
}
}
}
}
}
}
// references
if (isset($o['referenceList'])) {
foreach ($o['referenceList'] as $i => $r) {
$r = $r['reference'];
if (isset($r['pubmedID'])) {
$pubmed_uri = "pubmed:" . $r['pubmedID'];
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "article", $pubmed_uri));
$title = 'article';
if (isset($r['title'])) {
$title = $r['title'];
}
parent::addRDF(parent::describe($pubmed_uri, addslashes($r['title'])));
if (isset($r['articleUrl'])) {
parent::addRDF($this->QQuadO_URL($pubmed_uri, "rdfs:seeAlso", htmlentities($r['articleUrl'])));
}
}
}
}
// external ids
if (isset($o['externalLinks'])) {
foreach ($o['externalLinks'] as $k => $id) {
if ($id === false) {
continue;
}
$ns = '';
switch ($k) {
case 'approvedGeneSymbols':
$ns = 'symbol';
break;
case 'geneIDs':
$ns = 'ncbigene';
break;
case 'ncbiReferenceSequences':
$ns = 'gi';
break;
case 'genbankNucleotideSequences':
$ns = 'gi';
break;
case 'proteinSequences':
$ns = 'gi';
break;
case 'uniGenes':
$ns = 'unigene';
break;
case 'ensemblIDs':
$ns = 'ensembl';
break;
case 'swissProtIDs':
$ns = 'uniprot';
break;
case 'mgiIDs':
$ns = 'mgi';
$b = explode(":", $id);
$id = $b[1];
break;
case 'flybaseIDs':
$ns = 'flybase';
break;
case 'zfinIDs':
$ns = 'zfin';
break;
case 'hprdIDs':
$ns = 'hprd';
break;
case 'orphanetDiseases':
$ns = 'orphanet';
break;
case 'refSeqAccessionIDs':
$ns = 'refseq';
break;
case 'ordrDiseases':
$ns = 'ordr';
$b = explode(";;", $id);
$id = $b[0];
break;
case 'snomedctIDs':
$ns = 'snomed';
break;
case 'icd10cmIDs':
$ns = 'icd10';
break;
case 'icd9cmIDs':
$ns = 'icd9';
break;
case 'umlsIDs':
$ns = 'umls';
break;
case 'wormbaseIDs':
$ns = 'wormbase';
break;
case 'diseaseOntologyIDs':
$ns = 'do';
break;
// specifically ignorning
// specifically ignorning
case 'geneTests':
case 'cmgGene':
case 'geneticAllianceIDs':
// #
// #
case 'nextGxDx':
case 'nbkIDs':
// NBK1207;;Alport Syndrome and Thin Basement Membrane Nephropathy
// NBK1207;;Alport Syndrome and Thin Basement Membrane Nephropathy
case 'newbornScreeningUrls':
case 'decipherUrls':
case 'geneReviewShortNames':
case 'locusSpecificDBs':
case 'geneticsHomeReferenceIDs':
case 'omiaIDs':
case 'coriellDiseases':
case 'clinicalDiseaseIDs':
case 'possumSyndromes':
case 'keggPathways':
case 'gtr':
case 'gwasCatalog':
case 'mgiHumanDisease':
case 'wormbaseDO':
case 'dermAtlas':
// true/false
break;
default:
echo "unhandled external link {$k} {$id}" . PHP_EOL;
}
$ids = explode(",", $id);
foreach ($ids as $id) {
if ($ns) {
if (strstr($id, ";;") === FALSE) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "x-{$ns}", $ns . ':' . $id));
} else {
$b = explode(";;", $id);
// multiple ids//names
foreach ($b as $c) {
preg_match("/([a-z])/", $c, $m);
if (!isset($m[1])) {
parent::addRDF(parent::triplify($omim_uri, parent::getVoc() . "x-{$ns}", $ns . ':' . $c));
}
}
}
}
}
}
}
//external links
}
function Parse($file)
{
parent::getReadFile()->read();
// skip the first comment line
$line = 1;
$first = true;
while ($l = parent::getReadFile()->read(500000)) {
if ($l[0] == "#") {
// dataset attributes
$a = explode('=', trim($l));
$r = $this->getVoc() . substr($a[0], 2);
if (isset($a[1])) {
$v = $a[1];
if ($r == "affymetrix_vocabulary:genome-version-create_date") {
$x = explode("-", $a[1]);
if ($x[2] == "00") {
$x[2] = "01";
}
$v = implode("-", $x);
}
parent::addRDF(parent::triplifyString(parent::getDatasetURI(), $r, $v) . parent::describe($r, "{$r}"));
}
continue;
}
if ($first == true) {
$first = false;
// header
$header = explode(",", str_replace('"', '', trim($l)));
// print_r($header);exit;
$n = count($header);
if ($n != 41) {
trigger_error("Expecting 41 columns, found {$n} in header on line {$line}!", E_USER_ERROR);
exit;
}
continue;
}
$a = explode('","', substr($l, 1, -2));
$n = count($a);
if ($n != 41) {
trigger_error("Expecting 41 columns, found {$n} on line {$line}!", E_USER_ERROR);
exit;
}
parent::writeRDFBufferToWriteFile();
$id = $a[0];
$qname = "affymetrix:{$id}";
$label = "probeset {$a['0']} on GeneChip {$a['1']} ({$a['2']})";
parent::addRDF(parent::describeIndividual($qname, $label, $this->getVoc() . "Probeset") . parent::describeClass($this->getVoc() . "Probeset", "Affymetrix probeset"));
trigger_error($id, E_USER_NOTICE);
// now process the entries
foreach ($a as $k => $v) {
if (trim($v) == '---') {
continue;
}
// multi-valued entries are separated by ////
$b = explode(" /// ", $v);
$r = $this->Map($k);
if (isset($r)) {
foreach ($b as $c) {
$d = explode(" // ", $c);
if ($r == 'symbol') {
$d[0] = str_replace(" ", "-", $d[0]);
}
$s = $this->getRegistry()->getPreferredPrefix($r);
if ($s == "ec") {
$e = explode(":", $d[0]);
$d[0] = $e[1];
}
$this->addRDF(parent::triplify($qname, $this->getVoc() . "x-{$s}", "{$s}:" . $d[0]) . parent::describeProperty($this->getVoc() . "x-{$s}", "a relation to {$s}"));
}
} else {
// we handle manually
unset($rel);
$label = $header[$k];
switch ($label) {
case 'GeneChip Array':
$array_id = parent::getRes() . str_replace(" ", "-", $v);
parent::addRDF(parent::triplify($qname, $this->getVoc() . "genechip-array", $array_id) . parent::describeIndividual($array_id, "Affymetrix {$v} GeneChip array", $this->getVoc() . "Genechip-Array") . parent::describeClass($this->getVoc() . "Genechip-Array", "Affymetrix GeneChip array"));
break;
case 'Gene Ontology Biological Process':
if (!isset($rel)) {
$rel = 'go-process';
$prefix = "go";
}
case 'Gene Ontology Cellular Component':
if (!isset($rel)) {
$rel = 'go-location';
$prefix = "go";
}
case 'Gene Ontology Molecular Function':
if (!isset($rel)) {
$rel = 'go-function';
$prefix = "go";
}
$b = explode(" /// ", $v);
foreach ($b as $c) {
$d = explode(" // ", $c);
parent::addRDF($this->triplify($qname, $this->getVoc() . $rel, "{$prefix}:" . $d[0]) . $this->describeProperty($this->getVoc() . $rel, "{$rel}"));
}
break;
case 'Transcript Assignments':
$b = explode(" /// ", $v);
foreach ($b as $c) {
$d = explode(" // ", $c);
$id = $d[0];
$prefix = $d[2];
if ($prefix == '---' || $id == '---') {
continue;
} else {
if ($prefix == 'gb' || $prefix == 'gb_htc') {
$prefix = 'genbank';
} else {
if ($prefix == 'ncbibacterial') {
$prefix = 'gi';
} else {
if ($prefix == 'ncbi_bacterial') {
$prefix = 'gi';
} else {
if ($prefix == 'ens') {
$prefix = 'ensembl';
} else {
if ($prefix == 'ncbi_mito' || $prefix == 'ncbi_organelle' || $prefix == 'organelle') {
$prefix = 'refseq';
} else {
if ($prefix == 'affx' || $prefix == 'unknown' || $prefix == "prop") {
$prefix = 'affymetrix';
} else {
if ($prefix == 'tigr_2004_08') {
$prefix = 'tigr';
} else {
if ($prefix == 'tigr-plantta') {
$prefix = 'genbank';
} else {
if ($prefix == 'newrs.gi') {
$prefix = 'gi';
} else {
if ($prefix == 'newRS.gi') {
$prefix = 'gi';
} else {
if ($prefix == 'primate_viral') {
$prefix = 'genbank';
} else {
if ($prefix == 'jgi-bacterial') {
$prefix = 'ncbigene';
} else {
if ($prefix == 'tb') {
$prefix = 'tuberculist';
} else {
if ($prefix == 'pa') {
$prefix = 'pseudomonas';
} else {
if ($prefix == 'gi|53267') {
$prefix = 'gi';
$id = '53267';
} else {
if ($prefix == 'broad-tcup') {
$e = explode("-", $id);
$id = $e[0];
} else {
if ($prefix == 'organelle') {
$e = explode("-", $id);
$prefix = 'genbank';
$id = $e[0];
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
parent::addRDF(parent::triplify($qname, $this->getVoc() . "transcript-assignment", "{$prefix}:{$id}") . parent::describeProperty($this->getVoc() . "transcript-assignment", "transcript assignment"));
}
break;
case 'Annotation Transcript Cluster':
/*
$id = substr($v,0,strpos($v,"("));
$rel = str_replace(" ","-",strtolower($label));
$this->AddRDF($this->triplify($qname,parent::getVoc()."$rel", "refseq:$id"));
*/
break;
case 'Annotation Date':
// Jun 9, 2011
$rel = "annotation-date";
preg_match("/^([A-Za-z]+) ([0-9]+), ([0-9]{4})\$/", $v, $m);
if (count($m) == 4) {
array_shift($m);
list($m, $day, $year) = $m;
$month = $this->getMonth($m);
if (!$day || $day == "0") {
$day = "01";
}
$date = $year . "-" . $month . "-" . str_pad($day, 2, "0", STR_PAD_LEFT) . "T00:00:00Z";
parent::addRDF(parent::triplifyString($qname, $this->getVoc() . $rel, $date, "xsd:dateTime") . parent::describeProperty($this->getVoc() . $rel, "{$rel}"));
} else {
trigger_error("could not match date from {$v}", E_USER_ERROR);
}
break;
case 'Species Scientific Name':
break;
case 'Transcript ID(Array Design)':
if (!isset($rel)) {
$rel = 'transcript';
}
case 'Sequence type':
default:
if (!isset($rel)) {
$rel = str_replace(" ", "-", strtolower($label));
}
$b = explode(" /// ", $v);
foreach ($b as $c) {
parent::addRDF(parent::triplifyString($qname, $this->getVoc() . $rel, stripslashes($c)) . parent::describeProperty($this->getVoc() . $rel, "{$rel}"));
}
break;
}
// switch
}
// else
}
$this->WriteRDFBufferToWriteFile();
}
}
function parseDrugEntry(&$xml)
{
$declared = null;
// a list of all the entities declared
$counter = 1;
$x = $xml->GetXMLRoot();
$dbid = (string) $x->{"drugbank-id"};
$did = "drugbank:" . $dbid;
$name = (string) $x->name;
$type = ucfirst((string) str_replace(" ", "-", $x->attributes()->type));
$type_label = ucfirst($x->attributes()->type);
$description = null;
if (isset($this->id_list)) {
if (!isset($this->id_list[$dbid])) {
return;
}
unset($this->id_list[$dbid]);
}
echo "Processing {$dbid}" . PHP_EOL;
if (isset($x->description) && $x->description != '') {
$description = trim((string) $x->description);
}
parent::addRDF(parent::describeIndividual($did, $name, parent::getVoc() . "Drug", $name, $description) . parent::describeClass(parent::getVoc() . "Drug", "Drug") . parent::triplify($did, "owl:sameAs", "http://identifiers.org/drugbank/" . $dbid) . parent::triplify($did, "rdfs:seeAlso", "http://www.drugbank.ca/drugs/" . $dbid) . parent::triplify($did, "rdf:type", parent::getVoc() . $type) . parent::describeClass(parent::getVoc() . $type, $type_label));
foreach ($x->{'drugbank-id'} as $id) {
parent::addRDF(parent::triplifyString($did, parent::getVoc() . "drugbank-id", $id));
}
if (isset($x->{'cas-number'})) {
parent::addRDF(parent::triplify($did, parent::getVoc() . "x-cas", "cas:" . $x->{'cas-number'}));
}
$literals = array("indication", "pharmacodynamics", "mechanism-of-action", "toxicity", "biotransformation", "absorption", "half-life", "protein-binding", "route-of-elimination", "volume-of-distribution", "clearance");
foreach ($literals as $l) {
if (isset($x->{$l}) and $x->{$l} != '') {
$lid = parent::getRes() . md5($l . $x->{$l});
parent::addRDF(parent::describeIndividual($lid, "{$l} for {$did}", parent::getVoc() . ucfirst($l), "{$l} for {$did}", $x->{$l}) . parent::describeClass(parent::getVoc() . ucfirst($l), ucfirst(str_replace("-", " ", $l))) . parent::triplify($did, parent::getVoc() . $l, $lid));
}
}
// TODO:: Replace the next two lines
$this->AddList($x, $did, "groups", "group", parent::getVoc() . "group");
$this->AddList($x, $did, "categories", "category", parent::getVoc() . "category");
if (isset($x->classification)) {
foreach ($x->classification->children() as $k => $v) {
$cid = parent::getRes() . md5($v);
parent::addRDF(parent::describeIndividual($cid, $v, parent::getVoc() . "Drug-Classification-Category") . parent::describeClass(parent::getVoc() . "Drug-Classification-Category", "Drug Classification Category") . parent::triplify($did, parent::getVoc() . "drug-classification-category", $cid));
}
}
$this->addLinkedResource($x, $did, 'atc-codes', 'atc-code', 'atc');
$this->addLinkedResource($x, $did, 'ahfs-codes', 'ahfs-code', 'ahfs');
// taxonomy
$this->AddText($x, $did, "taxonomy", "kingdom", parent::getVoc() . "kingdom");
// substructures
$this->AddText($x, $did, "taxonomy", "substructures", parent::getVoc() . "substructure", "substructure");
// synonyms
$this->AddCategory($x, $did, "synonyms", "synonym", parent::getVoc() . "synonym");
// brand names
$this->AddCategory($x, $did, "international-brands", "international-brand", parent::getVoc() . "brand");
// salt
if (isset($x->salts->salt)) {
foreach ($x->salts->salt as $s) {
$sid = parent::getPrefix() . ':' . $s->{'drugbank-id'};
parent::addRDF(parent::describeIndividual($sid, $s->name, parent::getVoc() . "Salt") . parent::describeClass(parent::getVoc() . "Salt", "Salt") . parent::triplify($did, parent::getVoc() . "salt", $sid) . parent::triplify($sid, parent::getVoc() . "x-cas", "cas:" . $s->{'cas-number'}) . parent::triplify($sid, parent::getVoc() . "x-inchikey", "inchikey:" . $s->{'inchikey'}));
}
}
// mixtures
// <mixtures><mixture><name>Cauterex</name><ingredients>dornase alfa + fibrinolysin + gentamicin sulfate</ingredients></mixture>
if (isset($x->mixtures)) {
$id = 0;
foreach ($x->mixtures->mixture as $item) {
if (isset($item)) {
$o = $item;
$mid = parent::getRes() . str_replace(" ", "-", $o->name[0]);
parent::addRDF(parent::triplify($did, parent::getVoc() . "mixture", $mid) . parent::describeIndividual($mid, $o->name[0], parent::getVoc() . "Mixture") . parent::describeClass(parent::getVoc() . "Mixture", "mixture") . parent::triplifyString($mid, $this->getVoc() . "ingredients", "" . $o->ingredients[0]));
$a = explode(" + ", $o->ingredients[0]);
foreach ($a as $b) {
$b = trim($b);
$iid = parent::getRes() . str_replace(" ", "-", $b);
parent::addRDF(parent::describeClass($iid, $b, parent::getVoc() . "Ingredient") . parent::describeClass(parent::getVoc() . "Ingredient", "Ingredient") . parent::triplify($mid, parent::getVoc() . "ingredient", $iid));
}
}
}
}
// packagers
// <packagers><packager><name>Cardinal Health</name><url>http://www.cardinal.com</url></packager>
if (isset($x->packagers)) {
foreach ($x->packagers as $items) {
if (isset($items->packager)) {
foreach ($items->packager as $item) {
$pid = parent::getRes() . md5($item->name);
parent::addRDF(parent::triplify($did, parent::getVoc() . "packager", $pid));
if (!isset($defined[$pid])) {
$defined[$pid] = '';
parent::addRDF(parent::describe($pid, "" . $item->name[0]));
if (strstr($item->url, "http://") && $item->url != "http://BASF Corp.") {
parent::addRDF($this->triplify($pid, "rdfs:seeAlso", "" . $item->url[0]));
}
}
}
}
}
}
// manufacturers
$this->AddText($x, $did, "manufacturers", "manufacturer", parent::getVoc() . "manufacturer");
// @TODO RESOURCE
// prices
if (isset($x->prices->price)) {
foreach ($x->prices->price as $product) {
$pid = parent::getRes() . md5($product->description);
parent::addRDF(parent::describeIndividual($pid, $product->description, parent::getVoc() . "Pharmaceutical", $product->description) . parent::describeClass(parent::getVoc() . "Pharmaceutical", "pharmaceutical") . parent::triplifyString($pid, parent::getVoc() . "price", "" . $product->cost, "xsd:float") . parent::triplify($did, parent::getVoc() . "product", $pid));
$uid = parent::getVoc() . md5($product->unit);
parent::addRDF(parent::describeIndividual($uid, $product->unit, parent::getVoc() . "Unit", $product->unit) . parent::describeClass(parent::getVoc() . "Unit", "unit") . parent::triplify($pid, parent::getVoc() . "form", $uid));
}
}
// dosages <dosages><dosage><form>Powder, for solution</form><route>Intravenous</route><strength></strength></dosage>
if (isset($x->dosages->dosage)) {
foreach ($x->dosages->dosage as $dosage) {
$id = parent::getRes() . md5($dosage->strength . $dosage->form . $dosage->route);
$label = ($dosage->strength != '' ? $dosage->strength . " " : "") . $dosage->form . " form with " . $dosage->route . " route";
parent::addRDF(parent::describeIndividual($id, $label, parent::getVoc() . "Dosage") . parent::describeClass(parent::getVoc() . "Dosage", "Dosage") . parent::triplify($did, parent::getVoc() . "dosage", $id));
$rid = parent::getVoc() . md5($dosage->route);
$this->typify($id, $rid, "Route", "" . $dosage->route);
$fid = parent::getVoc() . md5($dosage->form);
$this->typify($id, $fid, "Form", "" . $dosage->form);
if ($dosage->strength != '') {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "strength", $dosage->strength));
}
}
}
// experimental-properties
$props = array("experimental-properties", "calculated-properties");
foreach ($props as $prop) {
$subtype = substr($prop, 0, strpos("-", $prop));
if (isset($x->{$prop})) {
foreach ($x->{$prop} as $properties) {
foreach ($properties as $property) {
$type = (string) $property->kind;
$value = (string) $property->value;
$type_uri = parent::getVoc() . ucfirst(str_replace(" ", "-", $type));
$id = parent::getRes() . $prop . "-" . $dbid . "-" . $counter++;
$label = $property->kind . ": {$value}" . ($property->source == '' ? '' : " from " . $property->source);
parent::addRDF(parent::describeIndividual($id, $label, $type_uri) . parent::describeClass($type_uri, $type, parent::getVoc() . ucfirst($prop)) . parent::describeClass(parent::getVoc() . ucfirst($prop), str_replace("-", " ", $prop)) . parent::triplifyString($id, $this->getVoc() . "value", $value) . parent::triplify($did, $this->getVoc() . $prop, $id));
// Source
if (isset($property->source)) {
foreach ($property->source as $source) {
$s = (string) $source;
if ($s == '') {
continue;
}
$sid = parent::getRes() . md5($s);
parent::addRDF(parent::describeIndividual($sid, $s, parent::getVoc() . "Source") . parent::describeClass(parent::getVoc() . "Source", "Source") . parent::triplify($id, parent::getVoc() . "source", $sid));
}
}
}
}
}
}
// identifiers
// <patents><patent><number>RE40183</number><country>United States</country><approved>1996-04-09</approved> <expires>2016-04-09</expires>
if (isset($x->patents->patent)) {
foreach ($x->patents->patent as $patent) {
$id = "uspto:" . $patent->number;
parent::addRDF(parent::triplify($did, $this->getVoc() . "patent", $id) . parent::describeIndividual($id, $patent->country . " patent " . $patent->number, $this->getVoc() . "Patent") . parent::describeClass(parent::getVoc() . "Patent", "patent") . parent::triplifyString($id, $this->getVoc() . "approved", "" . $patent->approved) . parent::triplifyString($id, $this->getVoc() . "expires", "" . $patent->expires));
$cid = parent::getRes() . md5($patent->country);
$this->typify($id, $cid, "Country", "" . $patent->country);
}
}
// partners
$partners = array('target', 'enzyme', 'transporter', 'carrier');
foreach ($partners as $partner) {
$plural = $partner . 's';
if (isset($x->{$plural})) {
foreach ($x->{$plural} as $list) {
foreach ($list->{$partner} as $item) {
$this->parsePartnerRelation($did, $item, $partner);
parent::writeRDFBufferToWriteFile();
}
}
}
}
// drug-interactions
$y = (int) substr($dbid, 2);
if (isset($x->{"drug-interactions"})) {
foreach ($x->{"drug-interactions"} as $ddis) {
foreach ($ddis->{"drug-interaction"} as $ddi) {
$dbid2 = $ddi->{'drugbank-id'};
if ($dbid < $dbid2) {
// don't repeat
$ddi_id = parent::getRes() . $dbid . "_" . $dbid2;
parent::addRDF(parent::triplify("drugbank:" . $dbid, parent::getVoc() . "ddi-interactor-in", "" . $ddi_id) . parent::triplify("drugbank:" . $dbid2, parent::getVoc() . "ddi-interactor-in", "" . $ddi_id) . parent::describeIndividual($ddi_id, "DDI between {$name} and " . $ddi->name . " - " . $ddi->description, parent::getVoc() . "Drug-Drug-Interaction") . parent::describeClass(parent::getVoc() . "Drug-Drug-Interaction", "drug-drug interaction"));
}
}
}
}
// food-interactions
$this->AddText($x, $did, "food-interactions", "food-interaction", parent::getVoc() . "food-interaction");
// affected-organisms
$this->AddCategory($x, $did, "affected-organisms", "affected-organism", parent::getVoc() . "affected-organism");
// <external-identifiers>
if (isset($x->{"external-identifiers"})) {
foreach ($x->{"external-identifiers"} as $objs) {
foreach ($objs as $obj) {
$ns = $this->NSMap($obj->resource);
$id = $obj->identifier;
if ($ns == "genecards") {
$id = str_replace(array(" "), array("_"), $id);
}
parent::addRDF(parent::triplify($did, parent::getVoc() . "x-{$ns}", "{$ns}:{$id}"));
if ($ns == "pubchemcompound") {
parent::addRDF(parent::triplify("{$ns}:{$id}", "skos:exactMatch", "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/{$id}"));
}
}
}
}
// <external-links>
if (isset($x->{"external-links"})) {
foreach ($x->{"external-links"}->{'external-link'} as $el) {
if (strpos($el->url, 'http') !== false) {
parent::addRDF(parent::triplify($did, "rdfs:seeAlso", "" . $el->url));
}
}
}
parent::writeRDFBufferToWriteFile();
}
