function genes($file)
{
$xml = new CXML($file);
while ($xml->parse("DisorderList") == TRUE) {
$x = $xml->GetXMLRoot();
foreach ($x->Disorder as $d) {
$orphanet_id = parent::getNamespace() . (string) $d->OrphaNumber;
$disorder_name = (string) $d->Name;
foreach ($d->DisorderGeneAssociationList->DisorderGeneAssociation as $dga) {
// gene
$gene = $dga->Gene;
$gene_id = parent::getNamespace() . (string) $gene->OrphaNumber;
$gene_internal_id = (string) $gene->attributes()->id;
$gene_label = (string) $gene->Name;
$gene_symbol = (string) $gene->Symbol;
parent::addRDF(parent::describeIndividual($gene_id, $gene_label, parent::getVoc() . "Gene") . parent::describeClass(parent::getVoc() . "Gene", "orphanet gene") . parent::triplifyString($gene_id, parent::getVoc() . "symbol", $gene_symbol));
foreach ($gene->SynonymList as $s) {
$synonym = (string) $s->Synonym;
parent::addRDF(parent::triplifyString($gene_id, parent::getVoc() . "synonym", $synonym));
}
foreach ($gene->ExternalReferenceList as $erl) {
$er = $erl->ExternalReference;
$db = (string) $er->Source;
$db = parent::getRegistry()->getPreferredPrefix($db);
$id = (string) $er->Reference;
$xref = "{$db}:{$id}";
parent::addRDF(parent::triplify($gene_id, parent::getVoc() . "x-{$db}", $xref));
}
$dga_id = parent::getRes() . (string) $d->OrphaNumber . "_" . md5($dga->asXML());
$ga = $dga->DisorderGeneAssociationType;
$ga_id = parent::getNamespace() . (string) $ga->attributes()->id;
$ga_label = (string) $ga->Name;
$s = $dga->DisorderGeneAssociationStatus;
$s_id = parent::getNamespace() . (string) $s->attributes()->id;
$s_label = (string) $s->Name;
parent::addRDF(parent::describeIndividual($dga_id, "{$ga_label} {$gene_label} in {$disorder_name} ({$s_label})", $ga_id) . parent::describeClass($ga_id, $ga_label, parent::getVoc() . "Disorder-Gene-Association") . parent::triplify($dga_id, parent::getVoc() . "status", $s_id) . parent::describeClass($s_id, $s_label, parent::getVoc() . "Disorder-Gene-Association-Status") . parent::triplify($dga_id, parent::getVoc() . "disorder", $orphanet_id) . parent::describeIndividual($orphanet_id, $disorder_name, parent::getVoc() . "Disorder") . parent::triplify($dga_id, parent::getVoc() . "gene", $gene_id));
}
parent::writeRDFBufferToWriteFile();
}
}
unset($xml);
}
function parse_drugbank($ldir, $infile)
{
$xml = new CXML($ldir . $infile);
while ($xml->parse("drug") == TRUE) {
if (isset($this->id_list) and count($this->id_list) == 0) {
break;
}
$this->parseDrugEntry($xml);
}
unset($xml);
}
function parse($file)
{
$xml = new CXML($file);
$xml->parse();
$entry = $xml->getXMLRoot();
if (!isset($entry) or !$entry) {
return false;
}
foreach ($entry->children() as $o) {
$rsid = "rs" . $o->attributes()->rsId;
$id = parent::getNamespace() . $rsid;
$type = parent::getVoc() . ucfirst(str_replace(" ", "-", (string) $o->attributes()->snpClass));
$snpclass = parent::getVoc() . (string) $o->attributes()->snpClass;
$moltype = parent::getVoc() . (string) $o->attributes()->molType;
// attributes
parent::addRDF(parent::describeIndividual($id, $rsid, $type) . parent::describeClass($type, ucfirst("" . $o->attributes()->snpClass)) . parent::triplify($id, parent::getVoc() . "mol-type", $moltype) . parent::describeClass($moltype, (string) $o->attributes()->molType, parent::getVoc() . "Moltype") . parent::describeClass(parent::getVoc() . "Moltype", "Moltype") . parent::triplify($id, parent::getVoc() . "taxid", "taxonomy:" . (string) $o->attributes()->taxId));
$genotype = (string) $o->attributes()->genoType;
if ($genotype) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "genotype", parent::getVoc() . $genotype, "xsd:bool"));
}
// frequency
// create/update
/* if(!isset($o->Update)) $a = $o->Create;
else $a = $o->Update;
parent::addRDF(parent::triplifyString($id,parent::getVoc()."build",(string) $a->attributes()->build));
*/
//validation
$a = $o->Validation;
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "validation-by-cluster", (string) $a->attributes()->byCluster) . parent::triplifyString($id, parent::getVoc() . "validation-by-frequency", (string) $a->attributes()->byFrequency) . parent::triplifyString($id, parent::getVoc() . "validation-by-2hit2allele", (string) $a->attributes()->by2Hit2Allele) . parent::triplifyString($id, parent::getVoc() . "validation-by-1000G", (string) $a->attributes()->by1000G));
//hgvs names
foreach ($o->hgvs as $name) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "hgvs-name", (string) $name));
}
// assembly
$assembly = $o->Assembly;
if ($assembly and $assembly->attributes()->reference == "true") {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "dbsnp-build", (string) $assembly->attributes()->dbSnpBuild) . parent::triplifyString($id, parent::getVoc() . "genome-build", (string) $assembly->attributes()->genomeBuild));
$component = $assembly->Component;
if ($component) {
parent::addRDF(parent::triplify($id, parent::getVoc() . "contig-accession", "genbank:" . (string) $component->attributes()->accession) . parent::triplify($id, parent::getVoc() . "contig-gi", "gi:" . (string) $component->attributes()->gi) . parent::triplifyString($id, parent::getVoc() . "chromosome", (string) $component->attributes()->chromosome));
$maploc = $component->MapLoc;
if ($maploc) {
foreach ($maploc->children() as $fxnset) {
$fxnset_id = parent::getRes() . md5($fxnset->asXML());
parent::addRDF(parent::triplify($id, parent::getVoc() . "maps-to", $fxnset_id) . parent::triplify($fxnset_id, "rdf:type", parent::getVoc() . "Fxnset") . parent::describeClass(parent::getVoc() . "Fxnset", "Fxnset"));
if (isset($fxnset->attributes()->geneId)) {
parent::addRDF(parent::triplify($fxnset_id, parent::getVoc() . "gene", "ncbigene:" . (string) $fxnset->attributes()->geneId));
}
if (isset($fxnset->attributes()->symbol)) {
parent::addRDF(parent::triplifyString($fxnset_id, parent::getVoc() . "gene-symbol", (string) $fxnset->attributes()->symbol));
}
if (isset($fxnset->attributes()->mrnaAcc)) {
parent::addRDF(parent::triplify($fxnset_id, parent::getVoc() . "mrna", "refseq:" . (string) $fxnset->attributes()->mrnaAcc));
}
if (isset($fxnset->attributes()->protAcc)) {
parent::addRDF(parent::triplify($fxnset_id, parent::getVoc() . "protein", "refseq:" . (string) $fxnset->attributes()->protAcc));
}
if (isset($fxnset->attributes()->fxnClass)) {
parent::addRDF(parent::triplifyString($fxnset_id, parent::getVoc() . "fxn-class", (string) $fxnset->attributes()->fxnClass));
}
if (isset($fxnset->attributes()->allele)) {
parent::addRDF(parent::triplifyString($fxnset_id, parent::getVoc() . "allele", (string) $fxnset->attributes()->allele));
}
if (isset($fxnset->attributes()->residue)) {
parent::addRDF(parent::triplifyString($fxnset_id, parent::getVoc() . "residue", (string) $fxnset->attributes()->residue));
}
if (isset($fxnset->attributes()->readingFrame)) {
parent::addRDF(parent::triplifyString($fxnset_id, parent::getVoc() . "reading-frame", (string) $fxnset->attributes()->readingFrame));
}
if (isset($fxnset->attributes()->aaPosition)) {
parent::addRDF(parent::triplifyString($fxnset_id, parent::getVoc() . "position", (string) $fxnset->attributes()->aaPosition));
}
}
}
}
}
}
unset($xml);
}
