function addDate($id, $field, $dateobj)
{
if ($dateobj == null) {
return FALSE;
}
$year = $dateobj->Year;
$month = $dateobj->Month;
$day = $dateobj->Day;
parent::addRDF(parent::triplifyString($id, parent::getVoc() . $field, "{$year}-{$month}-{$day}", "xsd:date"));
}
public function makeDescription($title, $type)
{
if (!$title) {
return null;
}
$uri = parent::getRes() . md5($title);
$type_uri = parent::getVoc() . str_replace(" ", "-", $type);
parent::addRDF(parent::describeIndividual($uri, $title, $type_uri) . parent::describeClass($type_uri, $type));
return $uri;
}
function parseItem($item)
{
$id = $item['@attributes']['id'];
$label = $item['name'];
parent::addRDF(parent::describeIndividual($id, $item['name'], parent::getVoc() . "Entry") . parent::describeClass(parent::getVoc() . "Entry", "MIRIAM database entry") . parent::triplifyString($id, parent::getVoc() . "namespace", $item['namespace']));
if (isset($item['@attributes'])) {
foreach ($item['@attributes'] as $k => $v) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . $k, $v));
}
}
if (isset($item['comment'])) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "comment", $item['comment']));
}
if (isset($item['definition'])) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "definition", $item['definition']));
}
if (isset($item['synonyms'])) {
$mylist = null;
if (is_array($item['synonyms']['synonym'])) {
$mylist = $item['synonyms']['synonym'];
} else {
$mylist[] = $item['synonyms']['synonym'];
}
foreach ($mylist as $myitem) {
parent::addRDF(parent::triplifyString($id, "skos:altLabel", $myitem));
}
}
if (isset($item['uris'])) {
foreach ($item['uris']['uri'] as $uri) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "uri", $uri));
}
}
if (isset($item['resources'])) {
$mylist = null;
if (!isset($item['resources']['resource']['dataEntry'])) {
$mylist = $item['resources']['resource'];
} else {
$mylist[] = $item['resources']['resource'];
}
foreach ($mylist as $myitem) {
$rid = $myitem['@attributes']['id'];
parent::addRDF(parent::describeIndividual($rid, $myitem['dataInfo'], parent::getVoc() . "Resource") . parent::describeClass(parent::getVoc() . "Resource", "MIRIAM Resource") . parent::triplify($rid, parent::getVoc() . "url", $myitem['dataResource']) . parent::triplifyString($rid, parent::getVoc() . "urlTemplate", $myitem['dataEntry']) . parent::triplifyString($rid, parent::getVoc() . "organization", is_array($myitem['dataInstitution']) ? "" : $myitem['dataInstitution']) . parent::triplifyString($rid, parent::getVoc() . "location", is_array($myitem['dataLocation']) ? "" : $myitem['dataLocation']) . parent::triplify($id, parent::getVoc() . "resource", $rid));
}
}
if (isset($item['tags'])) {
$i = $item['tags']['tag'];
$mylist = null;
if (!is_array($i)) {
$mylist[] = $i;
} else {
$mylist = $i;
}
foreach ($mylist as $myitem) {
parent::addRDF(parent::triplifyString($id, parent::getvoc() . "tag", $myitem));
}
}
if (isset($item['documentations'])) {
$i = $item['documentations']['documentation'];
$mylist = null;
if (!is_array($i)) {
$mylist[] = $i;
} else {
$mylist = $i;
}
foreach ($mylist as $myitem) {
if (strstr($myitem, "pubmed")) {
$uri = "pubmed:" . substr($myitem, strrpos($myitem, ":") + 1);
} else {
if (strstr($myitem, "doi")) {
$uri = "http://dx.doi.org/" . substr($myitem, strpos($myitem, "doi:"));
} else {
$uri = $myitem;
}
}
parent::addRDF(parent::triplify($id, parent::getvoc() . "documentation", $uri));
}
}
if (isset($item['restrictions'])) {
$mylist = null;
if (!isset($item['restrictions']['restriction']['statement'])) {
$mylist = $item['restrictions']['restriction'];
} else {
$mylist[] = $item['restrictions']['restriction'];
}
foreach ($mylist as $i => $myitem) {
$rid = parent::getRes() . str_replace(":", "", $id) . "_" . ($i + 1);
$a = $myitem['@attributes'];
$rid_type = parent::getVoc() . 'restriction_type_' . $a['type'];
parent::addRDF(parent::describeIndividual($rid, $a['desc'], parent::getVoc() . "Restriction") . parent::describeClass(parent::getVoc() . "Restriction", "Resource Restriction") . parent::triplify($rid, "rdf:type", $rid_type) . parent::describeClass($rid_type, $a['desc'], parent::getVoc() . "Restriction") . parent::triplifyString($rid, "dct:description", $myitem['statement']) . parent::triplify($rid, "foaf:page", isset($myitem['link']) ? $myitem['link'] : "") . parent::triplify($id, parent::getVoc() . "restriction", $rid));
}
}
/*
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>event</element>
<element>rule</element>
<element>species</element>
</elements>
</format>
*/
if (isset($item['annotation'])) {
$mylist = null;
if (!isset($item['annotation']['format']['elements'])) {
$mylist = $item['annotation']['format'];
} else {
$mylist[] = $item['annotation']['format'];
}
foreach ($mylist as $i => $myitem) {
$name = $myitem['@attributes']['name'];
$myid = str_replace("MIR:", parent::getRes(), $id) . "_annotation_" . ($i + 1) . "_" . urlencode($name);
parent::addRDF(parent::describeIndividual($myid, "{$label} used by {$name}", parent::getVoc() . "ValueSet") . parent::describeClass(parent::getVoc() . "ValueSet", "MIRIAM Value Set") . parent::triplifyString($myid, parent::getVoc() . "used-in", $name) . parent::triplify($myid, parent::getVoc() . "uses", $id));
$b = $myitem['elements']['element'];
$mylist2 = null;
if (!is_array($b)) {
$mylist2[] = $b;
} else {
$mylist2 = $b;
}
foreach ($mylist2 as $i => $e) {
parent::addRDF(parent::triplifyString($myid, parent::getVoc() . "used-for", $e));
}
}
}
}
private function process()
{
$z = 0;
$y = 1;
while ($l = $this->getReadFile()->Read(200000)) {
if ($z++ % 1000000 == 0) {
echo $z . PHP_EOL;
$odir = parent::getParameterValue('outdir');
$ofile = 'iproclass.' . $y++ . "." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
if (parent::getWriteFile() != null) {
parent::getWriteFile()->close();
parent::clear();
}
// generate a new file
parent::setWriteFile($odir . $ofile, $gz);
}
$fields = explode("\t", $l);
@($uniprot_acc = $fields[0]);
@($uniprot = $fields[1]);
@($gene = $fields[2]);
@($refseq = $fields[3]);
@($gi = $fields[4]);
@($pdb = $fields[5]);
@($pfam = $fields[6]);
@($go = $fields[7]);
@($pirsf = $fields[8]);
@($ipi = $fields[9]);
@($uniref_100 = $fields[10]);
@($uniref_90 = $fields[11]);
@($uniref_50 = $fields[12]);
@($uniparc = $fields[13]);
//skipping pir-psd because db no longer maintained
@($ncbi_taxonomy = $fields[15]);
@($mim = $fields[16]);
@($unigene = $fields[17]);
@($ensembl = $fields[18]);
@($pubmed = $fields[19]);
@($embl_genbank_ddbj = $fields[20]);
@($embl_protein = trim($fields[21]));
$id = $uniprot_acc;
$id_res = $this->getNamespace() . $id;
$id_label = "iproclass entry for uniprot:{$uniprot_acc}";
parent::addRDF(parent::triplify($id_res, $this->getVoc() . "x-uniprot", "uniprot:" . $uniprot_acc));
if (!empty($uniprot)) {
$uniprot_ids = explode("; ", $uniprot);
foreach ($uniprot_ids as $uniprot_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-uniprot", "uniprot:" . $uniprot_id));
}
}
if (!empty($gene)) {
$gene_ids = explode("; ", $gene);
foreach ($gene_ids as $gene_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ncbigene", "geneid:" . $gene_id));
}
}
if (!empty($refseq)) {
$refseq_ids = explode("; ", $refseq);
foreach ($refseq_ids as $refseq_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-refseq", "refseq:" . $refseq_id));
}
}
if (!empty($gi)) {
$gi_ids = explode("; ", $gi);
foreach ($gi_ids as $gi_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-gi", "gi:" . $gi_id));
}
}
if (!empty($pdb)) {
$pdb_ids = explode("; ", $pdb);
foreach ($pdb_ids as $pdb_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-pdb", "pdb:" . $pdb_id));
}
}
if (!empty($pfam)) {
$pfam_ids = explode("; ", $pfam);
foreach ($pfam_ids as $pfam_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-pfam", "pfam:" . $pfam_id));
}
}
if (!empty($go)) {
$go_ids = explode("; ", $go);
foreach ($go_ids as $go_id) {
$go_id = substr($go_id, 3);
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-go", "go:" . $go_id));
}
}
if (!empty($pirsf)) {
$pirsf_ids = explode("; ", $pirsf);
foreach ($pirsf_ids as $pirsf_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-pirsf", "pirsf:" . $pirsf_id));
}
}
if (!empty($ipi)) {
$ipi_ids = explode("; ", $ipi);
foreach ($ipi_ids as $ipi_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ipi", "ipi:" . $ipi_id));
}
}
if (!empty($uniref_100)) {
$uniref_100_ids = explode("; ", $uniref_100);
foreach ($uniref_100_ids as $uniref_100_id) {
parent::AddRDF(parent::QQuadO_URL($id_res, "rdfs:seeAlso", "http://uniprot.org/uniref/" . $uniref_100_id));
}
}
if (!empty($uniref_90)) {
$uniref_90_ids = explode("; ", $uniref_90);
foreach ($uniref_90_ids as $uniref_90_id) {
parent::AddRDF(parent::QQuadO_URL($id_res, "rdfs:seeAlso", "http://uniprot.org/uniref/" . $uniref_90_id));
}
}
if (!empty($uniref_50)) {
$uniref_50_ids = explode("; ", $uniref_50);
foreach ($uniref_50_ids as $uniref_50_id) {
parent::AddRDF(parent::QQuadO_URL($id_res, "rdfs:seeAlso", "http://uniprot.org/uniref/" . $uniref_50_id));
}
}
if (!empty($uniparc)) {
$uniparc_ids = explode("; ", $uniparc);
foreach ($uniparc_ids as $uniparc_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-uniparc", "uniparc:" . $uniparc_id) . parent::QQuadO_URL($id_res, "rdfs:seeAlso", "http://uniprot.org/uniparc/" . $uniparc_id));
}
}
if (!empty($ncbi_taxonomy)) {
$taxonomy_ids = explode("; ", $ncbi_taxonomy);
foreach ($taxonomy_ids as $taxonomy_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-taxon", "taxon:" . $taxonomy_id));
}
}
if (!empty($mim)) {
$mim_ids = explode("; ", $mim);
foreach ($mim_ids as $mim_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-omim", "omim:" . $mim_id));
}
}
if (!empty($unigene)) {
$unigene_ids = explode("; ", $unigene);
foreach ($unigene_ids as $unigene_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-unigene", "unigene:" . $unigene_id));
}
}
if (!empty($ensembl)) {
$ensembl_ids = explode("; ", $ensembl);
foreach ($ensembl_ids as $ensembl_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ensembl", "ensembl:" . $ensembl_id));
}
}
if (!empty($pubmed)) {
$pubmed_ids = explode("; ", $pubmed);
foreach ($pubmed_ids as $pubmed_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-pubmed", "pubmed:" . $pubmed_id));
}
}
if (!empty($embl_genbank_ddbj)) {
$genbank_ids = explode("; ", $embl_genbank_ddbj);
foreach ($genbank_ids as $genbank_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-genbank", "genbank:" . $genbank_id));
}
}
if (!empty($embl_protein)) {
$embl_protein_ids = explode(";", $embl_protein);
foreach ($embl_protein_ids as $embl_protein_id) {
parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-genbank", "genbank:" . $embl_protein_id));
}
}
//write rdf to file
$this->WriteRDFBufferToWriteFile();
}
//while
}
function gene_interactions()
{
while ($l = parent::getReadFile()->Read()) {
if ($l[0] == '#') {
continue;
}
$data = explode("\t", $l);
if (count($data) != 11) {
trigger_error("Found " . count($data) . " columns, expecting 11");
continue;
}
$interaction = $data[0];
$interaction_type = str_replace("_", "-", $data[1]);
$interaction_type_label = str_replace("_", " ", $data[1]);
$int_additional_info = $data[2];
$gene1 = $data[5];
$gene2 = $data[8];
$interaction_id = parent::getNamespace() . $interaction;
if ($interaction_type == "Genetic") {
$int_pred = parent::getVoc() . "genetically-interacts-with";
} elseif ($interaction_type == "Physical") {
$int_pred = parent::getVoc() . "physically-interacts-with";
} elseif ($interaction_type == "Predicted") {
$int_pred = parent::getVoc() . "predicted-to-interact-with";
} elseif ($interaction_type == "Regulatory") {
$int_pred = parent::getVoc() . "regulates";
}
//elseif
if ($int_additional_info == "No_interaction") {
$interaction_label = "No " . strtolower($interaction_type) . " interaction between " . $gene1 . " and " . $gene2;
parent::addRDF(parent::describeIndividual($interaction_id, $interaction_label, parent::getVoc() . $interaction_type . "-Non-Interaction") . parent::describeClass(parent::getVoc() . $interaction_type . "-Non-Interaction", $interaction_type_label . " non-interaction") . parent::triplify($interaction_id, parent::getVoc() . "involves", parent::getNamespace() . $gene1) . parent::triplify($interaction_id, parent::getVoc() . "involves", parent::getNamespace() . $gene2));
$npa_id = parent::getRes() . md5($interaction_id . "negative property assertion");
$npa_label = "Negative property assertion stating that " . $gene1 . " and " . $gene2 . " do not have a " . $interaction_type_label . " interaction";
parent::addRDF(parent::describeIndividual($npa_id, $npa_label, "owl:NegativeObjectPropertyAssertion") . parent::triplify($npa_id, "owl:sourceIndividual", parent::getNamespace() . $gene1) . parent::triplify($npa_id, "owl:targetIndividual", parent::getNamespace() . $gene2) . parent::triplify($npa_id, "owl:assertionProperty", $int_pred));
} elseif ($int_additional_info == "N/A" || $int_additional_info == "Genetic_interaction") {
$interaction_label = $interaction_type . " interaction between " . $gene1 . " and " . $gene2;
parent::addRDF(parent::describeIndividual($interaction_id, $interaction_label, parent::getVoc() . $interaction_type . "-Interaction") . parent::describeClass(parent::getVoc() . $interaction_type . "-Interaction", $interaction_type_label . " Interaction") . parent::triplify($interaction_id, parent::getVoc() . "involves", parent::getNamespace() . $gene1) . parent::triplify($interaction_id, parent::getVoc() . "involves", parent::getNamespace() . $gene2) . parent::triplify(parent::getNamespace() . $gene1, $int_pred, parent::getNamespace() . $gene2));
} else {
$interaction_label = ($int_additional_info != "" ? $int_additional_info . " " : "") . strtolower($interaction_type) . " interaction between " . $gene1 . " and " . $gene2;
$type = parent::getVoc() . ($int_additional_info != "" ? $int_additional_info . "-" : "") . $interaction_type . "-Interaction";
$type_label = ($int_additional_info != "" ? $int_additional_info . " " : "") . $interaction_type_label . " Interaction";
parent::addRDF(parent::describeIndividual($interaction_id, $interaction_label, $type) . parent::describeClass($type, $type_label, parent::getVoc() . $interaction_type . "-Interaction") . parent::describeClass(parent::getVoc() . $interaction_type . "-Interaction", $interaction_type . " Interation") . parent::triplify($interaction_id, parent::getVoc() . "involves", parent::getNamespace() . $gene1) . parent::triplify($interaction_id, parent::getVoc() . "involves", parent::getNamespace() . $gene2) . parent::triplify(parent::getNamespace() . $gene1, $int_pred, parent::getNamespace() . $gene2));
}
//else
parent::WriteRDFBufferToWriteFile();
}
//while
}
function Parse($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
}
$this->WriteRDFBufferToWriteFile();
}
}
function product($fpin)
{
$z = 0;
$list = '';
fgets($fpin);
// header
while ($l = fgets($fpin, 100000)) {
$a = explode("\t", $l);
if (count($a) != 18) {
trigger_error("Expected 18 coloumns, instead found" . count($a));
continue;
}
$product_id = parent::getNamespace() . $a[0];
$product_label = $a[3];
$product_type_label = ucfirst(strtolower($a[2]));
$product_type = parent::getVoc() . str_replace(" ", "-", $product_label);
parent::addRDF(parent::describeIndividual($product_id, $a[3], parent::getVoc() . "Product") . parent::describeClass(parent::getVoc() . "Product", "NDC Product") . parent::triplify($product_id, parent::getVoc() . "product-type", $product_type) . parent::describeIndividual($product_type, $product_type_label, parent::getVoc() . "Product-Type") . parent::describeClass(parent::getVoc() . "Product-Type", "Product Type") . parent::triplifyString($product_id, parent::getVoc() . "product-id", $a[1]) . parent::triplifyString($product_id, parent::getVoc() . "proprietary-name", $a[3]) . parent::triplifyString($product_id, parent::getVoc() . "trade-name-suffix", $a[4]));
if ($a[5]) {
$b = explode(";", $a[5]);
foreach ($b as $c) {
parent::addRDF(parent::triplifyString($product_id, parent::getVoc() . "non-proprietary-name", trim($c)));
}
}
if ($a[6]) {
$b = explode(",", $a[6]);
foreach ($b as $c) {
$dosageform = strtolower($c);
$dosageform_id = parent::getVoc() . str_replace(" ", "-", ucfirst(strtolower($c)));
parent::addRDF(parent::describeIndividual($dosageform_id, $dosageform, parent::getVoc() . "Dosage-Form") . parent::describeClass(parent::getVoc() . "Dosage-Form", "NDC Dosage Form") . parent::triplify($product_id, parent::getVoc() . "dosage-form", $dosageform_id));
}
}
if ($a[7]) {
// MV
$b = explode("; ", $a[7]);
foreach ($b as $c) {
$route = strtolower(trim($c));
$route_id = parent::getVoc() . str_replace(" ", "-", ucfirst(strtolower($c)));
parent::addRDF(parent::describeIndividual($route_id, $route, parent::getVoc() . "Route") . parent::describeClass(parent::getVoc() . "Route", "NDC Drug Route") . parent::triplify($product_id, parent::getVoc() . "route", $route_id));
}
}
if ($a[8]) {
$date = substr(0, 4, $a[8]) . "-" . substr(4, 2, $a[8]) . "-" . substr(6, 2, $a[8]);
parent::addRDF(parent::triplifyString($product_id, parent::getVoc() . "start-marketing-date", $date));
}
if ($a[9]) {
$date = substr(0, 4, $a[9]) . "-" . substr(4, 2, $a[9]) . "-" . substr(6, 2, $a[9]);
parent::addRDF(parent::triplifyString($product_id, parent::getVoc() . "end-marketing-date", $date));
}
if ($a[10]) {
parent::addRDF(parent::triplifyString($product_id, parent::getVoc() . "marketing-category", $a[10]));
}
if ($a[11]) {
parent::addRDF(parent::triplifyString($product_id, parent::getVoc() . "application-number", $a[11]));
}
// create a labeller node
if ($a[12]) {
$labeller_id = parent::getRes() . md5($a[12]);
$label = addslashes($a[12]);
parent::addRDF(parent::describeIndividual($labeller_id, $label, parent::getVoc() . "Labeller") . parent::describeClass(parent::getVoc() . "Labeller", "NDC Labeller") . parent::triplify($product_id, parent::getVoc() . "labeller", $labeller_id));
}
// the next three are together
if ($a[13]) {
// MV
$substances = explode(";", $a[13]);
$strengths = explode(";", $a[14]);
$units = explode(";", $a[15]);
$l = '';
foreach ($substances as $i => $substance) {
// list the active ingredient
$ingredient_label = strtolower($substance);
$strength = '';
if (isset($strengths[$i])) {
$strength = $strengths[$i];
}
$unit = $units[$i];
$ingredient_id = parent::getRes() . md5($ingredient_label);
parent::addRDF(parent::describeIndividual($ingredient_id, $ingredient_label, parent::getVoc() . "Ingredient") . parent::describeClass(parent::getVoc() . "Ingredient", "NDC Ingredient") . parent::triplify($product_id, parent::getVoc() . "ingredient", $ingredient_id));
// describe the substance composition
$substance_label = "{$strength} {$unit} {$ingredient_label}";
$substance_id = parent::getRes() . md5($substance_label);
parent::addRDF(parent::describeIndividual($substance_id, $substance_label, parent::getVoc() . "Substance") . parent::triplifyString($substance_id, parent::getVoc() . "amount", $strength) . parent::describeClass(parent::getVoc() . "Substance", "NDC Substance"));
$unit_id = parent::getVoc() . md5($unit);
parent::addRDF(parent::describeIndividual($unit_id, $unit, parent::getVoc() . "Unit") . parent::describeClass(parent::getVoc() . "Unit", "NDC Unit") . parent::triplify($substance_id, parent::getVoc() . "amount_unit", $unit_id) . parent::triplify($product_id, parent::getVoc() . "has-part", $substance_id));
}
}
if ($a[16]) {
// MV
$b = explode(",", $a[16]);
foreach ($b as $c) {
$cat_id = parent::getVoc() . md5($c);
parent::addRDF(parent::describeIndividual($cat_id, $c, parent::getVoc() . "Pharmacological-Class") . parent::describeClass(parent::getVoc() . "Pharmacological-Class", "NDC Pharmacological Class") . parent::triplify($product_id, parent::getVoc() . "pharmacological-class", $cat_id));
}
}
parent::WriteRDFBufferToWriteFile();
}
}
function ParseEntry($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()
{
$l = parent::getReadFile()->read(100000);
$header = explode("\t", trim(substr($l, 1)));
if (($c = count($header)) != 54) {
trigger_erorr("Expecting 54 columns, found {$c}!");
return FALSE;
}
// check # of columns
while ($l = parent::getReadFile()->read(500000)) {
$a = explode("\t", trim($l));
// irefindex identifiers
$rigid = "irefindex." . $a[34];
# checksum for interaction
$rogida = "irefindex." . $a[32];
# checksum for A
$rogidb = "irefindex." . $a[33];
# checksum for B
$irigid = "irefindex.irigid:" . $a[44];
# integer id for interaction
$irogida = "irefindex.irogid:" . $a[42];
# integer id for A
$irogidb = "irefindex.irogid:" . $a[43];
# integer id for B
$crigid = "irefindex.crigid:" . $a[47];
# checksum for canonical interaction
$icrigid = "irefindex.icrigid:" . $a[50];
# integer id for canonical interaction
$crogida = "irefindex.crogid:" . $a[45];
# checksum for A's canonical group
$crogidb = "irefindex.crogid:" . $a[46];
# checksum for B's canonical group
$icrogida = "irefindex.icrogid:" . $a[48];
# integer for A's canonical group
$icrogidb = "irefindex.icrogid:" . $a[49];
# integer for B's canonical group
// 13 contains the original identifier, the rigid, and the edgetype
$ids = explode("|", $a[13]);
if (count($ids) != 3) {
trigger_error("Expecting 3 entries in column 14");
print_r($ids);
exit;
}
parent::getRegistry()->parseQName($ids[0], $ns, $id);
if ($id == '-') {
// this happens with hprd
$iid = "hprd:" . substr($ids[1], 6);
} else {
$iid = $ns . ":" . $id;
}
// get the type
if ($a[52] == "X") {
$label = "{$a['0']} - {$a['1']} Interaction";
$type = "Pairwise-Interaction";
} else {
if ($a[52] == "C") {
$label = $a[53] . " component complex";
#num of participants
$type = "Multimeric-Complex";
} else {
if ($a[52] == "Y") {
$label = "{$a['0']} homomeric complex";
$type = "Homopolymeric-Complex";
}
}
}
parent::addRDF(parent::describeIndividual($iid, $label, parent::getVoc() . $type) . parent::describeClass(parent::getVoc() . $type, str_replace("-", " ", $type)));
// interaction type[52] by method[6]
unset($method);
if ($a[6] != '-') {
$data = $this->ParseStringArray($a[6]);
$method = trim($data["label"]);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
if ($qname) {
parent::addRDF(parent::triplify($iid, parent::getVoc() . "method", $qname) . parent::describeClass($qname, $data['label']));
}
}
parent::addRDF(parent::triplify($iid, "rdfs:seeAlso", "http://wodaklab.org/iRefWeb/interaction/show/" . $a[50]));
// set the interactors
for ($i = 0; $i <= 1; $i++) {
$p = 'a';
if ($i == 1) {
$p = 'b';
}
$data = $this->ParseStringArray($a[$i]);
$interactor = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($iid, parent::getVoc() . "interactor_{$p}", $interactor));
// biological role
$role = $a[16 + $i];
if ($role != '-') {
$data = $this->ParseStringArray($role);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
if ($qname != "mi:0000") {
parent::addRDF(parent::triplify($iid, parent::getVoc() . "interactor_{$p}" . "_biological_role", $qname) . parent::describeClass($qname, $data['label']));
}
}
// experimental role
$role = $a[18 + $i];
if ($role != '-') {
$data = $this->ParseStringArray($role);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
if ($qname != "mi:0000") {
parent::addRDF(parent::triplify($iid, parent::getVoc() . "interactor_{$p}" . "_experimental_role", $qname) . parent::describeClass($qname, $data['label']));
}
}
// interactor type
$type = $a[20 + $i];
if ($type != '-') {
$data = $this->ParseStringArray($type);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($interactor, "rdf:type", $qname) . parent::describeClass($qname, $data['label']));
}
}
// add the alternatives through the taxon + seq redundant group
for ($i = 2; $i <= 3; $i++) {
$taxid = '';
$rogid = "irefindex." . $a[32 + ($i - 2)];
parent::addRDF(parent::describeIndividual($rogid, "", parent::getVoc() . "Taxon-Sequence-Identical-Group") . parent::describeClass(parent::getVoc() . "Taxon-Sequence-Identical-Group", "Taxon + Sequence Identical Group"));
$tax = $a[9 + ($i - 2)];
if ($tax && $tax != '-' && $tax != '-1') {
$data = $this->ParseStringArray($tax);
$taxid = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($rogid, parent::getVoc() . "x-taxonomy", $taxid));
}
$list = explode("|", $a[3 + ($i - 2)]);
foreach ($list as $item) {
$data = $this->ParseStringArray($item);
$ns = trim($data["ns"]);
$id = trim($data["id"]);
$qname = $ns . ":" . $id;
if ($ns && $ns != 'rogid' && $ns != 'irogid' and $id != '-') {
parent::addRDF(parent::triplify($rogid, parent::getVoc() . "has-member", $qname));
if ($taxid && $taxid != '-' && $taxid != '-1') {
parent::addRDF(parent::triplify($qname, parent::getVoc() . "x-taxonomy", $taxid));
}
}
}
}
// publications
$list = explode("|", $a[8]);
foreach ($list as $item) {
if ($item == '-' && $item != 'pubmed:0') {
continue;
}
$data = $this->ParseStringArray($item);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($iid, parent::getVoc() . "article", $qname));
}
// MI interaction type
if ($a[11] != '-' && $a[11] != 'NA') {
$data = $this->ParseStringArray($a[11]);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($iid, "rdf:type", $qname));
if (!isset($defined[$qname])) {
$defined[$qname] = '';
parent::addRDF(parent::triplifyString($qname, "rdfs:label", $data['label']));
}
}
// source
if ($a[12] != '-') {
$data = $this->ParseStringArray($a[12]);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($iid, parent::getVoc() . "source", $qname));
}
// confidence
$list = explode("|", $a[14]);
foreach ($list as $item) {
$data = $this->ParseStringArray($item);
$ns = trim($data["ns"]);
$id = trim($data["id"]);
if ($ns == 'lpr') {
// lowest number of distinct interactions that any one article reported
parent::addRDF(parent::triplifyString($iid, parent::getVoc() . "minimum-number-interactions-reported", $id));
} else {
if ($ns == "hpr") {
// higher number of distinct interactions that any one article reports
parent::addRDF(parent::triplifyString($iid, parent::getVoc() . "maximum-number-interactions-reported", $id));
} else {
if ($ns = 'hp') {
// total number of unique PMIDs used to support the interaction
parent::addRDF(parent::triplifyString($iid, parent::getVoc() . "number-supporting-articles", $id));
}
}
}
}
// expansion method
if ($a[15]) {
$id = parent::getRes() . md5($a[15]);
parent::addRDF(parent::describeIndividual($id, $a[15], parent::getVoc() . "Expansion-Method") . parent::describeClass(parent::getVoc() . "Expansion-Method", "Expansion Method") . parent::triplify($iid, parent::getVoc() . "expansion-method", $id));
}
// host organism
if ($a[28] != '-') {
$data = $this->ParseStringArray($a[28]);
$qname = trim($data["ns"]) . ":" . trim($data["id"]);
parent::addRDF(parent::triplify($iid, parent::getVoc() . "host-organism", $qname));
}
// @todo add to record
// created 2010/05/18
$date = str_replace("/", "-", $a[30]) . "T00:00:00Z";
parent::addRDF(parent::triplifyString($iid, "dc:created", $date, "xsd:dateTime"));
// taxon-sequence identical interaction group
parent::addRDF(parent::triplify($iid, parent::getVoc() . "taxon-sequence-identical-interaction", $rigid) . parent::triplify($rigid, "rdf:type", parent::getVoc() . "Taxon-Sequence-Identical-Interaction") . parent::describeClass(parent::getVoc() . "Taxon-Sequence-Identical-Interaction", "Taxon + Sequence Identical Interaction") . parent::triplify($rigid, parent::getVoc() . "irigid", $irigid) . parent::triplify($rigid, parent::getVoc() . "interactor-a", $rogida) . parent::triplify($rogida, parent::getVoc() . "irogid", $irogida) . parent::triplify($rigid, parent::getVoc() . "interactor-b", $rogidb) . parent::triplify($rogidb, parent::getVoc() . "irogid", $irogidb) . parent::triplify($rogida, parent::getVoc() . "canonical-group", $crogida) . parent::triplify($rogidb, parent::getVoc() . "canonical-group", $crogidb) . parent::triplify($rigid, parent::getVoc() . "taxon-sequence-similar-interaction", $crigid) . parent::triplify($crigid, "rdf:type", parent::getVoc() . "Taxon-Sequence-Canonical-Interaction") . parent::describeClass(parent::getVoc() . "Taxon-Sequence-Canonical-Interaction", "Taxon + Sequence Canonical Interaction") . parent::triplify($crigid, parent::getVoc() . "icrigid", $icrigid) . parent::triplify($crigid, parent::getVoc() . "interactor-a-canonical-group", $crogida) . parent::triplify($crogida, "rdf:type", parent::getVoc() . "Taxon-Sequence-Similar-Group") . parent::triplify($crogida, parent::getVoc() . "icrogid", $icrogida) . parent::triplify($crigid, parent::getVoc() . "interactor-b-canonical-group", $crogidb) . parent::triplify($crogidb, "rdf:type", parent::getVoc() . "Taxon-Sequence-Similar-Group") . parent::triplify($crogidb, parent::getVoc() . "icrogid", $icrogidb) . parent::describeClass(parent::getVoc() . "Taxon-Sequence-Similar-Group", "Taxon + Sequence Similar Group"));
parent::writeRDFBufferToWriteFile();
}
}
function AddCategory(&$x, $id, $list_name, $item_name, $predicate, $list_item_name = null)
{
if (isset($x->{$list_name})) {
foreach ($x->{$list_name} as $item) {
if (isset($item->{$item_name}) && $item->{$item_name} != '') {
$l = $item->{$item_name};
$att = $l->attributes();
foreach ($l as $key => $item_value) {
$kid = parent::getvoc() . md5($item_value);
$this->addRDF($this->describeIndividual($kid, "" . $item_value, parent::getVoc() . ucfirst($item_name)) . $this->describeClass(parent::getVoc() . ucfirst($item_name), ucfirst("" . $item_name)) . $this->triplify($id, $predicate, $kid));
foreach ($att as $ka => $va) {
parent::addRDF($this->triplifyString($kid, parent::getVoc() . $ka, "" . $va));
}
}
$kid = parent::getvoc() . md5($l->asXML());
foreach ($l->children() as $k2 => $v2) {
$this->addRDF($this->describeIndividual($kid, $k2 == "name" ? $v2 : $predicate, parent::getVoc() . ucfirst($k2)) . $this->describeClass(parent::getVoc() . ucfirst($k2), ucfirst("" . $v2)) . $this->triplifyString($kid, parent::getVoc() . $k2, $v2) . $this->triplify($id, $predicate, $kid));
}
}
}
}
}
private function citations()
{
while ($l = $this->getReadFile()->read(2000000)) {
$a = explode("\t|\t", rtrim($l, "\t|\n"));
if (!isset($a[1]) or !isset($a[2])) {
continue;
}
$c = parent::getRes() . "citation-id-" . $a[0];
$seealso = isset($a[4]) ? trim($a[4]) : "";
if ($seealso) {
$seealso = str_replace(array("lx: DOI ", "http;//"), array("http://dx.doi.org/", "http://"), $seealso);
if (strlen($seealso) > 2 and !strstr($seealso, "http")) {
$seealso = "http://" . $seealso;
}
$seealso = parent::triplify($c, "rdfs:seeAlso", $seealso);
}
parent::addRDF(parent::describeIndividual($c, $a[1], $this->getVoc() . "Citation") . parent::describeClass($this->getVoc() . "Citation", "Citation") . parent::triplifyString($c, parent::getVoc() . "citation-key", $a[1]) . ($a[2] == "0" ? "" : parent::triplify($c, parent::getVoc() . "x-pubmed", "pubmed:" . $a[2])) . $seealso . ((isset($a[5]) and $a[5]) ? parent::triplifyString($c, parent::getVoc() . "text", str_replace("\"", "", $a[5])) : ""));
if (isset($a[6])) {
$taxids = explode(" ", trim($a[6]));
if (count($taxids)) {
foreach ($taxids as $taxid) {
parent::addRDF(parent::triplify("taxonomy:{$taxid}", $this->getVoc() . "citation", $c));
}
}
}
$this->writeRDFBufferToWriteFile();
}
//while
}
function genes($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 freq()
{
$cols = 10;
$i = 1;
parent::setCheckpoint('file');
while ($l = parent::getReadFile()->read()) {
$a = explode("\t", str_replace("%", "", $l));
if (count($a) != $cols) {
trigger_error("Expecting {$cols}, but found " . count($a) . " instead... skipping file!", E_USER_ERROR);
return false;
}
list($stitch_flat, $stitch_stereo, $cui, $placebo, $freq, $freq_lower, $freq_upper, $concept_type, $meddra_concept_id, $meddra_concept_label) = $a;
if ($concept_type == "LLT") {
continue;
}
$meddra_concept_label = trim($meddra_concept_label);
$id = "stitch_resource:" . md5("se_freq" . $l);
$stitch_flat = "stitch:{$stitch_flat}";
$label = "{$meddra_concept_label} frequency for {$stitch_flat}";
parent::addRDF(parent::describeIndividual($id, $label, parent::getVoc() . "Drug-Effect-Frequency") . parent::describeClass(parent::getVoc() . "Drug-Effect-Frequency", "SIDER Drug-Effect and Frequency") . parent::triplify($id, parent::getVoc() . "drug", $stitch_flat) . parent::triplify($id, parent::getVoc() . "effect", "umls:" . $meddra_concept_id));
if ($placebo) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "placebo", "true", "xsd:boolean"));
}
$number = false;
if (is_numeric($freq)) {
$flabel = $freq . "%";
$ftype_label = "Exact-Frequency";
$ftype = parent::getVoc() . $ftype_label;
$number = true;
} else {
$flabel = $freq;
$ftype_label = "Qualitative-Frequency";
$ftype = parent::getVoc() . "{$ftype_label}";
}
if ($freq_lower != $freq_upper) {
$flabel .= "({$freq_lower}-{$freq_upper})";
$ftype_label = "Range-Frequency";
$ftype = parent::getVoc() . $ftype_label;
}
$fid = $id . md5($a[5] . $a[6] . $a[8]);
parent::addRDF(parent::triplify($id, parent::getVoc() . "frequency", $fid) . parent::describeIndividual($fid, $flabel, $ftype) . parent::describeClass($ftype, $ftype_label));
if ($number == true) {
parent::addRDF(parent::triplifyString($fid, parent::getVoc() . "frequency-value", $freq / 100));
} else {
parent::addRDF(parent::triplifyString($fid, parent::getVoc() . "frequency-value", $freq));
}
parent::addRDF(parent::triplifyString($fid, parent::getVoc() . "lower-frequency", sprintf("%.3f", $freq_lower)) . parent::triplifyString($fid, parent::getVoc() . "upper-frequency", sprintf("%.3f", $freq_upper)));
parent::setCheckpoint('record');
}
parent::setCheckpoint('file');
}
function parse($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);
}
function Run()
{
// get the work
if ($this->GetParameterValue('files') == 'all') {
$sources = explode("|", parent::getParameterList('files'));
array_shift($sources);
} else {
// comma separated list
$sources = explode(",", parent::getParameterValue('files'));
}
$download_files = array("h**o-sapiens" => "Pathway%20Commons%202%20homo%20sapiens.BIOPAX.owl.gz", "hprd" => "Pathway%20Commons%202%20HPRD.BIOPAX.owl.gz", "humancyc" => "Pathway%20Commons%202%20HumanCyc.BIOPAX.owl.gz", "nci-nature" => "Pathway%20Commons%202%20NCI_Nature.BIOPAX.owl.gz", "panther-pathway" => "Pathway%20Commons%202%20PANTHER%20Pathway.BIOPAX.owl.gz", "phosphositeplus" => "Pathway%20Commons%202%20PhosphoSitePlus.BIOPAX.owl.gz", "reactome" => "Pathway%20Commons%202%20Reactome.BIOPAX.owl.gz");
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$dataset_description = '';
// iterate over the requested data
foreach ($sources as $source) {
echo "processing {$source}... ";
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
// set the remote and input files
$file = $source . ".owl";
$zfile = $source . ".owl.gz";
$rfile = $rdir . $download_files[$source];
$lfile = $ldir . $zfile;
// download if if the file doesn't exist locally or we are told to
if (!file_exists($lfile) || $this->GetParameterValue('download') == 'true') {
// download
echo "downloading... ";
file_put_contents($lfile, file_get_contents($rfile));
}
// extract the file out of the ziparchive
// and load into a buffer
echo 'extracting... ';
if (($fpin = gzopen($lfile, "r")) === FALSE) {
trigger_error("Unable to open {$lfile}", E_USER_ERROR);
exit;
}
$data = '';
while (!gzeof($fpin)) {
$buffer = gzgets($fpin, 4096);
$data .= $buffer;
}
gzclose($fpin);
// set the output file
$suffix = parent::getParameterValue('output_format');
$outfile = $source . '.' . $suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
parent::setWriteFile($odir . $outfile, $gz);
// send for parsing
$p = new BioPAX2Bio2RDF($this);
$p->SetBuffer($data)->SetBioPAXVersion(3)->SetBaseNamespace("http://purl.org/pc2/3/")->SetBio2RDFNamespace("http://bio2rdf.org/pathwaycommons:")->SetDatasetURI(parent::getDatasetURI());
$rdf = $p->Parse();
parent::addRDF($rdf);
// write to output
parent::writeRDFBufferToWriteFile();
parent::getWriteFile()->Close();
echo "done!" . PHP_EOL;
//generate dataset description
echo "Generating dataset description for {$zfile}... ";
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Pathway Commons")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("rdf/xml")->setPublisher("http://www.pathwaycommons.org/")->setHomepage("http://www.pathwaycommons.org/")->setRights("use")->setRights("restricted-by-source-license")->setLicense("http://www.pathwaycommons.org/pc2/home.html#data_sources")->setDataset("http://identifiers.org/pathwaycommons/");
$dataset_description .= $source_file->toRDF();
echo "done!" . PHP_EOL;
}
echo "Generating dataset description for Bio2RDF Pathways Commons dataset... ";
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/pathwaycommons/pathwaycommons.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $output_file->toRDF();
//write dataset description to file
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function parseKGML($lfile)
{
$pathway = simplexml_load_file($lfile);
if ($pathway === false) {
echo "Error in parsing {$lfile}" . PHP_EOL;
return;
}
$pathway_id = str_replace("path", "kegg", $pathway['name']);
$base_id = str_replace("kegg", "kegg_resource", $pathway_id) . ".";
parent::addRDF(parent::describeIndividual($pathway_id, $pathway['title'], parent::getVoc() . "Pathway") . parent::triplify($pathway_id, "rdfs:seeAlso", $pathway['link']) . parent::triplify($pathway_id, "foaf:depiction", $pathway['image']));
// get the entries
foreach ($pathway->children() as $type => $item) {
if ($type == "entry") {
$eid = $base_id . $item['id'];
$entries["" . $item['id']] = "" . $item['name'];
parent::addRDF(parent::describeIndividual($eid, $item['name'], parent::getVoc() . "Ortholog-Group") . parent::describeClass(parent::getVoc() . "Ortholog-Group", "KEGG Ortholog Group"));
$mids = explode(" ", $item['name']);
foreach ($mids as $mid) {
if ($item['type'] == 'path') {
$mid = str_replace($mid, ":", "_");
} else {
$mid = substr($mid, strpos($mid, ":") + 1);
}
parent::addRDF(parent::triplify($eid, parent::getVoc() . "member", "kegg:" . $mid));
}
}
}
// iterate over the relations, reactions
foreach ($pathway->children() as $type => $item) {
if ($type == "relation") {
/*
<relation entry1="70" entry2="73" type="ECrel">
<subtype name="compound" value="86"/>
</relation>
<relation entry1="26" entry2="25" type="PPrel">
<subtype name="compound" value="17"/>
<subtype name="activation" value="-->"/>
</relation>
*/
$id1 = "" . $item['entry1'];
$id2 = "" . $item['entry2'];
$type = "" . $type;
$relation_id = str_replace("kegg", "kegg_resource", $pathway_id) . "." . $id1 . "." . $id2 . "." . $type;
$label = $type . " relation between " . $entries[$id1] . " and " . $entries[$id2];
parent::addRDF(parent::describeIndividual($relation_id, $label, parent::getVoc() . "Pathway-Relation") . parent::describeClass(parent::getVoc() . "Pathway-Relation", "KEGG Pathway Relation") . parent::triplify($relation_id, parent::getVoc() . "source", $base_id . $id1) . parent::triplify($relation_id, parent::getVoc() . "target", $base_id . $id2) . parent::triplify($relation_id, parent::getVoc() . "pathway", $pathway_id) . parent::triplifyString($relation_id, parent::getVoc() . "type", $item['type']));
foreach ($item->children() as $subtype) {
parent::addRDF(parent::triplifyString($relation_id, parent::getVoc() . "subtype", '' . $subtype['name']));
}
} else {
if ($type == "reaction") {
/* <reaction id="133" name="rn:R09085" type="irreversible">
<substrate id="86" name="cpd:C00267"/>
<product id="90" name="cpd:C00668"/>
</reaction>
*/
$reaction_id = str_replace("kegg", "kegg_resource", $pathway_id) . "." . substr($item['name'], strpos($item['name'], ":") + 1);
$reaction_type = parent::getVoc() . ucfirst($item['type']) . "-Reaction";
parent::addRDF(parent::describeIndividual($reaction_id, $item['name'], parent::getVoc() . "Reaction") . parent::describeClass(parent::getVoc() . "Reaction", "KEGG Reaction") . parent::triplify($reaction_id, "rdf:type", $reaction_type));
foreach ($item->children() as $k => $v) {
$cid = str_replace("cpd:", "kegg:", $v['name']);
parent::addRDF(parent::triplify($reaction_id, parent::getVoc() . $k, $cid));
}
}
}
}
return;
}
function models()
{
$tax_ids = array("Caenorhabditis elegans" => "6239", "Mus musculus" => "10090", "Saccharomyces cerevisiae" => "4932", "Drosophila melanogaster" => "7227", "Podospora anserina" => "5145", "Mesocricetus auratus" => "10036", "Schizosaccharomyces pombe" => "4896", "Danio rerio" => "7955");
$h = explode(",", parent::getReadFile()->read());
$expected_columns = 8;
if (($n = count($h)) != $expected_columns) {
trigger_error("Found {$n} columns in gene file - expecting {$expected_columns}!", E_USER_WARNING);
return false;
}
/*
[0] GenAge ID
[1] symbol
[2] name
[3] organism
[4] entrez gene id
[5] avg lifespan change (max obsv)
[6] lifespan effect
[7] longevity influence
*/
while ($l = parent::getReadFile()->read(200000)) {
$data = str_getcsv($l);
$genage = str_pad($data[0], 4, "0", STR_PAD_LEFT);
$gene_symbol = $data[1];
$name = $data[2];
$organism = $data[3];
$ncbi_gene_id = $data[4];
$max_percent_obsv_avg_lifespan_change = $data[5];
$lifespan_effect = $data[6];
$longevity_influence = $data[7];
$genage_id = parent::getNamespace() . $genage;
parent::addRDF(parent::describeIndividual($genage_id, $name, parent::getVoc() . "Aging-Related-Gene") . parent::describeClass(parent::getVoc() . "Aging-Related-Gene", "Aging Related Gene"));
parent::addRDF(parent::triplifyString($genage_id, parent::getVoc() . "gene-symbol", parent::safeLiteral($gene_symbol)));
parent::addRDF(parent::triplify($genage_id, parent::getVoc() . "taxon", "ncbitaxon:" . $tax_ids[$organism]));
if ($ncbi_gene_id !== "") {
parent::addRDF(parent::triplify($genage_id, parent::getVoc() . "x-ncbigene", "ncbigene:" . $ncbi_gene_id));
}
if ($max_percent_obsv_avg_lifespan_change !== "") {
parent::addRDF(parent::triplifyString($genage_id, parent::getVoc() . "maximum-percent-observed-average-lifespan-change", parent::safeLiteral($max_percent_obsv_avg_lifespan_change)));
}
if ($lifespan_effect == "Increase and Decrease") {
parent::addRDF(parent::triplifyString($genage_id, parent::getVoc() . "lifespan-effect", "increase") . parent::triplifyString($genage_id, parent::getVoc() . "lifespan-effect", "decrease"));
} else {
parent::addRDF(parent::triplifyString($genage_id, parent::getVoc() . "lifespan-effect", strtolower($lifespan_effect)));
}
parent::addRDF(parent::triplifyString($genage_id, parent::getVoc() . "longevity-influence", strtolower($longevity_influence)));
parent::WriteRDFBufferToWriteFile();
}
}
function MGI_Geno_NotDisease()
{
$line = 1;
while ($l = $this->getReadFile()->read(248000)) {
$a = explode("\t", $l);
if (count($a) != 8) {
trigger_error("Incorrect number of columns", E_USER_WARNING);
continue;
}
$genotype = $a[0];
$alleles = explode("|", strtolower($a[2]));
$diseases = explode(",", $a[7]);
foreach ($diseases as $d) {
$disease = "omim:{$d}";
foreach ($alleles as $allele) {
$id = parent::getRes() . md5($allele . $disease);
$label = "{$allele} {$disease} absent association";
parent::addRDF(parent::describeIndividual($id, $label, $this->getVoc() . "Allele-Disease-Non-Association") . parent::describeClass($this->getVoc() . "Allele-Disease-Non-Association", "MGI Allele-Disease Non-Association") . parent::triplify($id, $this->getVoc() . "allele", $allele) . parent::triplifyString($id, $this->getVoc() . "genotype-string", $genotype) . parent::triplify($id, $this->getVoc() . "disease", $disease) . parent::triplifyString($id, $this->getVoc() . "is-negated", "true"));
if ($a[5]) {
$pmids = explode(",", $a[5]);
foreach ($pmids as $pmid) {
parent::addRDF(parent::triplify($id, $this->getVoc() . "x-pubmed", "pubmed:" . $pmid));
}
}
}
}
$this->writeRDFBufferToWriteFile();
}
}
function twosides()
{
$items = null;
$id = 0;
$this->GetReadFile()->Read();
while ($l = $this->GetReadFile()->Read()) {
$a = explode("\t", $l);
$id++;
if ($id % 10000 == 0) {
$this->WriteRDFBufferToWriteFile();
}
$uid = "twosides:{$id}";
$d1 = "pubchemcompound:" . (int) sprintf("%d", substr($a[0], 4));
$d1_name = $a[2];
$d2 = "pubchemcompound:" . (int) sprintf("%d", substr($a[1], 4));
$d2_name = $a[3];
$e = "umls:" . $a[4];
$e_name = strtolower($a[5]);
$uid_label = "DDI between {$d1_name} and {$d2_name} leading to {$e_name}";
if (!isset($items[$d1])) {
parent::addRDF(parent::describeIndividual($d1, $d1_name, parent::getVoc() . "Chemical") . parent::describeClass(parent::getVoc() . "Chemical", "PharmGKB Chemical"));
$items[$d1] = '';
}
if (!isset($items[$d2])) {
parent::addRDF(parent::describeIndividual($d2, $d2_name, parent::getVoc() . "Chemical") . parent::describeClass(parent::getVoc() . "Chemical", "PharmGKB Chemical"));
$items[$d2] = '';
}
if (!isset($items[$e])) {
parent::addRDF(parent::describeIndividual($e, $e_name, parent::getVoc() . "Event") . parent::describeClass(parent::getVoc() . "Event", "PharmGKB side effect event"));
$items[$e] = '';
}
parent::addRDF(parent::describeIndividual($uid, $uid_label, parent::getVoc() . "Drug-Drug-Association") . parent::describeClass(parent::getVoc() . "Drug-Drug-Association", "PharmGKB Twosides Drug-Drug Association") . parent::triplify($uid, parent::getVoc() . "chemical", $d1) . parent::triplify($uid, parent::getVoc() . "chemical", $d2) . parent::triplify($uid, parent::getVoc() . "event", $e) . parent::triplifyString($uid, parent::getVoc() . "p-value", $a[7]));
}
parent::writeRDFBufferToWriteFile();
}
function gene_expression()
{
$h = explode(",", parent::getReadFile()->read());
$expected_columns = 8;
if (($n = count($h)) != $expected_columns) {
trigger_error("Found {$n} columns in gene file - expecting {$expected_columns}!", E_USER_WARNING);
return false;
}
while ($l = parent::getReadFile()->read(200000)) {
$data = str_getcsv($l);
$mgi_symbol = $data[0];
$mgi_description = $data[1];
$geneid = $data[2];
$total_datasets = $data[3];
$total_ovexp = $data[4];
$total_underexp = $data[5];
$p_value = $data[6];
$expression = $data[7];
$id = parent::getRes() . md5($geneid . $total_datasets . $total_ovexp . $total_underexp . $p_value . $expression);
$evidence_id = parent::getRes() . md5($geneid . $total_datasets . $total_ovexp . $total_underexp . $p_value . $expression . "_evidence");
$label = "Dietary restriction induced " . $expression . "-expression of " . $mgi_symbol . " based on microarray results from " . $total_datasets . " datasets, with p-value " . $p_value;
$type_label = "Gene " . ucfirst($expression) . " Expression";
$type = parent::getVoc() . str_replace(" ", "-", $type_label);
parent::addRDF(parent::describeIndividual($id, $label, $type) . parent::describeClass($type, $type_label) . parent::triplify($id, parent::getVoc() . "gene", "ncbigene:" . $geneid) . parent::triplifyString("ncbigene:" . $geneid, parent::getVoc() . "mgi-gene-symbol", $mgi_symbol) . parent::triplifyString("ncbigene:" . $geneid, parent::getVoc() . "mgi-gene-description", $mgi_description) . parent::triplify($id, parent::getVoc() . "evidence", $evidence_id) . parent::triplifyString($id, parent::getVoc() . "perturbation-context", "dietary restriction") . parent::triplifyString($evidence_id, parent::getVoc() . "total-number-datasets", $total_datasets) . parent::triplifyString($evidence_id, parent::getVoc() . "total-number-datasets-overexpressed", $total_ovexp) . parent::triplifyString($evidence_id, parent::getVoc() . "total-number-datasets-underexpressed", $total_underexp) . parent::triplifyString($evidence_id, parent::getVoc() . "p-value", $p_value));
parent::writeRDFBufferToWriteFile();
}
//while
}
private function gene2accession()
{
$this->getReadFile()->read(200000);
$header = array(0 => array('rel' => "x-taxonomy", 'ns' => "taxonomy"), 1 => array('rel' => "ncbigene", 'ns' => "ncbigene"), 2 => array('rel' => "status"), 3 => array('rel' => "rna-nucleotide-accession.version", 'ns' => "genbank"), 4 => array('rel' => "rna-nucleotide-gi", 'ns' => "gi"), 5 => array('rel' => "protein-accession.version", 'ns' => "genbank"), 6 => array('rel' => "protein-gi", 'ns' => "gi"), 7 => array('rel' => "genomic-nucleotide-accession.version", 'ns' => "genbank"), 8 => array('rel' => "genomic-nucleotide-gi", 'ns' => "gi"), 9 => array('rel' => "genomic-start-position"), 10 => array('rel' => "genomic-end-position"), 11 => array('rel' => "orientation"), 12 => array('rel' => "assembly"), 13 => array('rel' => "mature-peptide-accession.version", 'ns' => "genbank"), 14 => array('rel' => "mature-peptide-gi", 'ns' => "gi"), 15 => array('rel' => "symbol"));
//(tab is used as a separator, pound sign - start of a comment) */
$z = 1;
while ($l = $this->getReadFile()->read(200000)) {
if ($l[0] == "#") {
continue;
}
if ($z++ % 10000 == 0) {
echo $z . PHP_EOL;
parent::clear();
}
$a = explode("\t", rtrim($l));
if (count($a) != 16) {
trigger_error("gene2accession: expecting 16 columns, found " . count($a) . " instead", E_USER_ERROR);
}
$taxid = $a[0];
if (isset($this->taxids) and !isset($this->taxids[$taxid])) {
continue;
}
$id = parent::getNamespace() . $a[1];
$refseq = false;
if ($a[2] != '-') {
$refseq = true;
}
if ($a[9] != '-' and $a[10] != '-') {
$region = parent::getRes() . $a[7] . "/" . $a[9] . "-" . $a[10];
$start_pos = parent::getRes() . $a[7] . "/" . $a[9];
$stop_pos = parent::getRes() . $a[7] . "/" . $a[10];
if ($a[11] == "+") {
$orientation = "faldo:ForwardStrandPosition";
} else {
if ($a[11] == "-") {
$orientation = "faldo:ReverseStrandPosition";
} else {
$orientation = "faldo:StrandedPosition";
}
}
parent::addRDF(parent::describeIndividual($region, "location of ncbigene:" . $a[1] . " on " . $a[7], "faldo:Region") . parent::describeIndividual($start_pos, "start of ncbigene:" . $a[1] . " on " . $a[7], "faldo:ExactPosition") . parent::describeIndividual($stop_pos, "stop position of ncbigene:" . $a[1] . " on " . $a[7], "faldo:ExactPosition") . parent::triplify($id, "faldo:location", $region) . parent::triplify($region, "faldo:begin", $start_pos) . parent::triplify($start_pos, "rdf:type", $orientation) . parent::triplifyString($start_pos, "faldo:position", $a[9], "xsd:integer") . parent::triplify($start_pos, "faldo:reference", "refseq:" . $a[7]) . parent::triplify($region, "faldo:end", $stop_pos) . parent::triplify($stop_pos, "rdf:type", $orientation) . parent::triplifyString($stop_pos, "faldo:position", $a[10], "xsd:integer") . parent::triplify($stop_pos, "faldo:reference", "refseq:" . $a[7]));
}
foreach ($header as $i => $v) {
if ($a[$i] == "-") {
continue;
}
if ($i == 1 or $i == 9 or $i == 10 or $i == 11) {
continue;
}
/// ncbigene
if (isset($v['ns'])) {
$ns = $v['ns'];
if ($ns == 'genbank' and $refseq == true) {
$ns = 'refseq';
}
parent::addRDF(parent::triplify($id, parent::getVoc() . $v['rel'], "{$ns}:" . $a[$i]));
} else {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . $v['rel'], $a[$i]));
}
}
parent::writeRDFBufferToWriteFile();
}
//while
}
function process($file)
{
$z = 1;
while ($l = parent::getReadFile()->read(100000)) {
if ($z % 100000 == 0) {
parent::clear();
}
if ($l[0] == "!") {
continue;
}
$fields = explode("\t", $l);
if (count($fields) != 17) {
trigger_error("Expected 17 columns, but found " . count($fields), E_USER_ERROR);
return false;
}
//get the Go id
$db = $fields[0];
$id = $fields[1];
$symbol = $fields[2];
$qualifier = $fields[3];
$goid = substr($fields[4], 3);
$refs = $this->getDbReferences($fields[5]);
$eco = $this->getEvidenceCodeLabelArr($fields[6]);
$aspect = $this->getAspect($fields[8]);
$label = $fields[9];
$synonyms = explode("|", $fields[10]);
$taxid = $fields[12];
$date = $this->parseDate($fields[13]);
$assignedBy = $fields[14];
//entity id
$eid = $this->getdbURI($db, $id);
if (!$eid) {
print_r($fields);
continue;
}
parent::addRDF(parent::describeIndividual($eid, $label, parent::getVoc() . "GO-Annotation") . parent::describeClass(parent::getVoc() . "GO-Annotation", "GO Annotation") . parent::triplifyString($eid, parent::getVoc() . "symbol", $symbol));
parent::addRDF(parent::triplify($eid, parent::getVoc() . "x-taxonomy", $taxid));
foreach ($synonyms as $s) {
if (!empty($s)) {
parent::addRDF(parent::triplifyString($eid, parent::getVoc() . "synonym", $s));
}
}
$rel = $aspect;
if ($qualifier == 'NOT') {
if ($aspect == 'process') {
$rel = 'not-in-process';
}
if ($aspect == 'function') {
$rel = 'not-has-function';
}
if ($aspect == 'component') {
$rel = 'not-in-component';
}
}
parent::addRDF(parent::describeObjectProperty(parent::getVoc() . $rel, str_replace("-", " ", $rel)) . parent::triplify($eid, parent::getVoc() . $rel, "go:" . $goid));
$type = key($eco);
$aid = parent::getRes() . $file . "_" . $z++;
parent::addRDF(parent::describeObjectProperty(parent::getVoc() . "go-annotation", "GO annotation") . parent::triplify($eid, parent::getVoc() . "go-annotation", $aid));
$cat = parent::getRes() . md5($aspect);
parent::addRDF(parent::describeIndividual($aid, "{$id}-go:{$goid} association", parent::getVoc() . "GO-Annotation") . parent::triplify($aid, parent::getVoc() . "target", $eid) . parent::triplify($aid, parent::getVoc() . "go-term", "go:" . $goid) . parent::triplify($aid, parent::getVoc() . "evidence", "eco:" . $eco[$type][1]) . parent::triplify($aid, parent::getVoc() . "go-category", $cat) . parent::describeClass($cat, $aspect) . parent::triplifyString($aid, parent::getVoc() . "assigned-by", $assignedBy));
if ($date != '') {
parent::addRDF(parent::triplifyString($aid, parent::getVoc() . "entry-date", $date . "T00:00:00Z", "xsd:dateTime"));
}
foreach ($refs as $ref) {
$b = explode(":", $ref);
if ($b[0] == 'PMID') {
parent::addRDF(parent::triplify($aid, parent::getVoc() . "article", "pubmed:" . $b[1]));
}
}
//write RDF to file
parent::writeRDFBufferToWriteFile();
}
}
/**
* Convert pubchem substance XML record to RDF
**/
function parse_substance_record(&$xml)
{
$root = $xml->GetXMLRoot();
// pubchem identifier and version
$sid = array_shift($root->xpath('//PC-Substance_sid/PC-ID/PC-ID_id'));
$sid_version = array_shift($root->xpath('//PC-Substance_sid/PC-ID/PC-ID_version'));
$psid = $this->getPcsNs() . $sid;
parent::addRDF(parent::describeIndividual($psid, null, $this->getPcsVoc() . "Substance"));
parent::addRDF(parent::triplifyString($psid, $this->getPcsVoc() . "version", parent::safeLiteral($sid_version)));
// reference to pubchem compounds
$pc_compounds = $root->xpath('//PC-Substance_compound/PC-Compounds/PC-Compound');
foreach ($pc_compounds as $compound) {
$cid = array_shift($compound->xpath('./PC-Compound_id/PC-CompoundType/PC-CompoundType_id/PC-CompoundType_id_cid'));
$cid_type = array_shift($compound->xpath('./PC-Compound_id/PC-CompoundType/PC-CompoundType_type'));
if ($cid != "") {
$pcid = $this->getPccNs() . $cid;
parent::addRDF(parent::triplify($psid, $this->getPcsVoc() . "compound", $pcid));
}
}
// database cross references (xref)
// source identifier
$source_id = array_shift($root->xpath('//PC-Substance_source/PC-Source/PC-Source_db/PC-DBTracking/PC-DBTracking_source-id/Object-id/Object-id_str'));
parent::addRDF(parent::triplifyString($psid, $this->getPcsVoc() . "source-identifier", parent::safeLiteral($source_id)));
// synonyms
$synonyms = $root->xpath('//PC-Substance_synonyms/PC-Substance_synonyms_E');
foreach ($synonyms as $synonym) {
parent::addRDF(parent::triplifyString($psid, $this->getPcsVoc() . "synonym", parent::safeLiteral($synonym)));
}
//comment
$comments = $root->xpath('//PC-Substance_comment/PC-Substance_comment_E');
foreach ($comments as $comment) {
if ($comment !== "") {
parent::addRDF(parent::triplifyString($psid, "rdfs:comment", parent::safeLiteral($comment)));
}
}
}
/**
* add an RDF representation of the incoming param to the model.
* @$desc_record_arr is an assoc array with the contents of one qualifier record
*/
private function makeDescriptorRecord($desc_record_arr)
{
//get the UI of the descriptor record
$dr_ui = $desc_record_arr["UI"][0];
$dr_res = $this->getNamespace() . $dr_ui;
$dr_label = $desc_record_arr['MH'][0];
parent::AddRDF(parent::describeIndividual($dr_res, $dr_label, $this->getVoc() . "Descriptor", $dr_label) . parent::describeClass($this->getVoc() . "Descriptor", "MeSH Descriptor"));
//now get the descriptor_data_elements
$qde = $this->getDescriptorDataElements();
//iterate over the properties
foreach ($desc_record_arr as $k => $v) {
if (array_key_exists($k, $qde)) {
if ($k == "AN") {
foreach ($v as $kv => $vv) {
//explode by semicolon
$vvrar = explode(";", $vv);
foreach ($vvrar as $anAn) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde["AN"], $anAn) . parent::describeProperty($this->getVoc() . $qde["AN"], "Relationship between a descriptor and its annotation"));
}
//foreach
}
//foreach
}
//if
//add allowable topical qualifiers
if ($k == "AQ") {
//$x = $this->getDescriptorDataElements();
foreach ($v as $kv => $vv) {
$vvrar = explode(" ", $vv);
foreach ($vvrar as $aq) {
$aq_res = $this->getRes() . $aq;
parent::AddRDF(parent::triplify($aq_res, "rdf:type", $this->getVoc() . "allowable-topical-qualifier") . parent::describeClass($this->getVoc() . "allowable-topical-qualifier", "allowable topical qualifier: " . $qde['AQ']));
parent::AddRDF(parent::triplify($dr_res, $this->getVoc() . $qde['AQ'], $aq_res) . parent::describeProperty($this->getVoc() . $qde['AQ'], "Relationship between a descriptor and its allowable topical qualifiers"));
}
//foreach
}
//foreach
}
//if
//add CATALOGING SUBHEADINGS LIST NAME
if ($k == "CATSH") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['CATSH'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['CATSH'], "Relationship between a descriptor and its cataloging subheadings list name"));
}
}
//if
if ($k == "CX") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['CX'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['CATSH'], "Relationship between a descriptor and xrefs"));
}
}
//if
//add date of entry
if ($k == "DA") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['DA'], $this->formatDate($vv), "xsd:date") . parent::describeProperty($this->getVoc() . $qde['DA'], "Relationship between a descriptor and its date of entry"));
}
}
//if
//descriptor class
if ($k == "DC") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['DC'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['DC'], "Relationship between a descriptor and its descriptor class"));
}
}
//if
//descriptor entry version
if ($k == "DE") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['DE'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['DE'], "Relationship between a descriptor record and its entry version"));
}
}
//if
//descriptor sort version
if ($k == "DS") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['DS'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['DS'], "Relationship between a descriptor record and its sort version"));
}
}
//if
//date major descriptor established
if ($k == "DX") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['DX'], $this->formatDate($vv), "xsd:date") . parent::describeProperty($this->getVoc() . $qde['DX'], "Relationship between a descriptor and its date of major descriptor established"));
}
}
//if
if ($k == "EC") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['EC'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['EC'], "Relationship between a descriptor and its entry combination"));
}
}
if ($k == "PRINT ENTRY") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['PRINT ENTRY'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['PRINT ENTRY'], "Relationship between a descriptor and its print entry term"));
}
}
if ($k == "ENTRY") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['ENTRY'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['ENTRY'], "Relationship between a descriptor and its entry term"));
}
}
if ($k == "FX") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['FX'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['FX'], "Relationship between a descriptor and its forward cross reference"));
}
}
if ($k == "GM") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['GM'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['GM'], "Relationship between a descriptor and its grateful med note"));
}
}
if ($k == "HN") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['HN'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['HN'], "Relationship between a descriptor record and its history note"));
}
}
if ($k == "MED") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['MED'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['MED'], "Relationship between a descriptor and its backfile postings"));
}
}
if ($k == "M94") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['M94'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M94'], "Relationship between a descriptor and its backfile postings"));
}
}
if ($k == "M90") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['M90'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M90'], "Relationship between a descriptor and its backfile postings"));
}
}
if ($k == "M85") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['M85'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M85'], "Relationship between a descriptor record and its backfile postings"));
}
}
if ($k == "M80") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['M80'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M80'], "Relationship between a descriptor record and its backfile postings"));
}
}
if ($k == "M75") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['M75'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M75'], "Relationship between a descriptor record and its backfile postings"));
}
}
if ($k == "M66") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['M66'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M66'], "Relationship between a descriptor record and its backfile postings"));
}
}
if ($k == "MH_TH") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['MH_TH'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['MH_TH'], "Relationship between a descriptor record and its MeSH Heading thesaurus id"));
}
}
if ($k == "MH") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['MH'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['MH'], "Relationship between a descriptor record and its MeSH Heading"));
}
}
if ($k == "MN") {
foreach ($v as $kv => $vv) {
$vid = parent::getNamespace() . $vv;
$vlabel = utf8_encode(htmlspecialchars($vv));
parent::AddRDF(parent::describeIndividual($vid, $dr_label, parent::getVoc() . "Tree-Entry", $vlabel) . parent::triplify($dr_res, $this->getVoc() . $qde['MN'], $vid) . parent::describeProperty($this->getVoc() . $qde['MN'], "Relationship between a descriptor record and its MeSH Tree Number"));
if (FALSE !== ($pos = strrpos($vv, "."))) {
$pid = parent::getNamespace() . substr($vv, 0, $pos);
parent::addRDF(parent::triplify($vid, "rdfs:subClassOf", $pid));
}
}
}
if ($k == "MR") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['MR'], $this->formatDate($vv), "xsd:date") . parent::describeProperty($this->getVoc() . $qde['MR'], "Relationship between a descriptor record and its major revision date"));
}
}
if ($k == "MS") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['MS'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['MS'], "Relationship between a descriptor record and its MeSH scope note"));
}
}
if ($k == "N1") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['N1'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['N1'], "Relationship between a descriptor record and its CAS 1 name"));
}
}
if ($k == "OL") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['OL'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['OL'], "Relationship between a descriptor record and its online note"));
}
}
if ($k == "PA") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['PA'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['PA'], "Relationship between a descriptor record and its pharmacological action"));
}
}
if ($k == "PI") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['PI'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['PI'], "Relationship between a descriptor record and its previous indexing"));
}
}
if ($k == "PM") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['PM'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['PM'], "Relationship between a descriptor record and its public mesh note"));
}
}
if ($k == "PX") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['PX'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['PX'], "Relationship between a descriptor record and its pre explosion"));
}
}
if ($k == "RECTYPE") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['RECTYPE'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['RECTYPE'], "Relationship between a descriptor record and its record type"));
}
}
if ($k == "RH") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['RH'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['RH'], "Relationship between a descriptor record and its running head, in relation to mesh tree structures"));
}
}
if ($k == "RN") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['RN'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['RN'], "Relationship between a descriptor record and its CAS registry"));
}
}
if ($k == "RR") {
foreach ($v as $kv => $vv) {
parent::AddRDF(parent::triplifyString($dr_res, $this->getVoc() . $qde['RR'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['RR'], "Relationship between a descriptor record and its registry number"));
}
}
if ($k == "ST") {
foreach ($v as $kv => $vv) {
$vid = parent::getNamespace() . $vv;
$pid = parent::getNamespace() . substr($vv, 0, strrpos($vv, ".") - 1);
$vlabel = utf8_encode(htmlspecialchars($vv));
parent::AddRDF(parent::describeIndividual($vid, $vlabel, parent::getVoc() . "Semantic-Type", $vlabel) . parent::triplify($dr_res, $this->getVoc() . $qde['ST'], $vid) . parent::describeProperty($this->getVoc() . $qde['ST'], "Relationship between a descriptor record and its semantic type"));
}
}
} else {
trigger_error("Please add key to descriptor record map: " . $k . PHP_EOL, E_USER_ERROR);
}
$this->WriteRDFBufferToWriteFile();
}
//foreach
$this->WriteRDFBufferToWriteFile();
}
function CTD_Genes()
{
$first = true;
while ($l = $this->GetReadFile()->Read()) {
if ($l[0] == '#') {
continue;
}
$a = explode("\t", $l);
// check number of columns
if ($first) {
if (($c = count(explode("\t", $l))) != 8) {
trigger_error("CTD_genes function expects 8 fields, found {$c}!" . PHP_EOL, E_USER_WARNING);
return FALSE;
}
$first = false;
}
$symbol = str_replace(array("\\/"), array('|'), $a[0]);
$label = str_replace("\\+/", '+', $a[1]);
$geneid = "ncbigene:" . $a[2];
$synonyms = $a[4];
$this->addRDF(parent::describeIndividual($geneid, $label, $this->getVoc() . "Gene") . parent::triplifyString($geneid, $this->getVoc() . "gene-symbol", $symbol) . parent::describeClass($this->getVoc() . "Gene", "CTD Gene"));
$ids = array(3 => array('rel' => "alternative-ncbigene-id", 'ns' => "ncbigene"), 4 => array('rel' => 'synonym'), 5 => array('rel' => 'x-biogrid', 'ns' => 'biogrid'), 6 => array('rel' => 'x-pharmgkb', 'ns' => 'pharmgkb'), 7 => array('rel' => 'x-uniprot', 'ns' => 'uniprot'));
foreach ($ids as $i => $v) {
if (!trim($a[$i])) {
continue;
}
$b = explode("|", $a[$i]);
foreach ($b as $c) {
if (isset($v['ns'])) {
parent::addRDF(parent::triplify($geneid, parent::getVoc() . $v['rel'], $v['ns'] . ":" . $c));
} else {
parent::addRDF(parent::triplifyString($geneid, parent::getVoc() . $v['rel'], $c));
}
}
}
parent::WriteRDFBufferToWriteFile();
}
return TRUE;
}
function Run()
{
// directory shortcuts
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
// get the work specified
$list = trim(parent::getParameterValue('files'));
if ($list == 'all') {
// call the getAllModelsId webservice
$file = $ldir . "all_models.json";
if (!file_exists($file)) {
try {
$x = @new SoapClient("http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl");
} catch (Exception $e) {
echo $e->getMessage();
}
$entries = $x->getAllModelsId();
file_put_contents($file, json_encode($entries));
} else {
$entries = json_decode(file_get_contents($file));
}
} elseif ($list == 'curated') {
// call the getAllCuratedModelsId webservice
$file = $ldir . "curated_models.json";
if (!file_exists($file)) {
try {
$x = @new SoapClient("http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl");
} catch (Exception $e) {
echo $e->getMessage();
}
$entries = $x->getAllCuratedModelsId();
file_put_contents($file, json_encode($entries));
} else {
$entries = json_decode(file_get_contents($file));
}
} else {
// check if a hyphenated list was provided
if (($pos = strpos($list, "-")) !== FALSE) {
$start_range = substr($list, 0, $pos);
$end_range = substr($list, $pos + 1);
for ($i = $start_range; $i <= $end_range; $i++) {
$entries[] = "BIOMD" . str_pad($i, 10, "0", STR_PAD_LEFT);
}
} else {
// for comma separated list
$b = explode(",", $this->GetParameterValue('files'));
foreach ($b as $e) {
$entries[] = "BIOMD" . str_pad($e, 10, "0", STR_PAD_LEFT);
}
}
}
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
// set the write file
$suffix = parent::getParameterValue('output_format');
$outfile = 'biomodels' . '.' . $suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
$dataset_description = '';
parent::setWriteFile($odir . $outfile, $gz);
// iterate over the entries
$i = 0;
$total = count($entries);
foreach ($entries as $id) {
echo "processing " . ++$i . " of {$total} - biomodel# " . $id;
$download_file = $ldir . $id . ".owl.gz";
$url = parent::getParameterValue('download_url') . "publ/{$id}/{$id}-biopax3.owl";
// download if the file doesn't exist or we are told to
if (!file_exists($download_file) || $this->GetParameterValue('download') == 'true') {
// download
echo " - downloading";
$ret = utils::downloadsingle($url, 'compress.zlib://' . $download_file, true);
if ($ret === false) {
echo "\nTrying non-curated model";
$url = parent::getParametervalue('download_url') . "uncura_publ/{$id}/{$id}-biopax3.owl";
$ret = utils::downloadsingle($url, 'compress.zlib://' . $download_file, true);
if ($ret === false) {
continue;
}
}
echo " - downloaded";
}
// load entry, parse and write to file
echo " - parsing... ";
// $this->SetReadFile($download_file,true);
$buf = file_get_contents("compress.zlib://" . $download_file);
$converter = new BioPAX2Bio2RDF($this);
$converter->SetBuffer($buf)->SetBioPAXVersion(3)->SetBaseNamespace("http://identifiers.org/biomodels.db/{$id}/")->SetBio2RDFNamespace("http://bio2rdf.org/biomodels:" . $id . "_")->SetDatasetURI($this->GetDatasetURI());
$rdf = $converter->Parse();
parent::addRDF($rdf);
parent::writeRDFBufferToWriteFile();
//generate dataset description
$source_file = (new DataResource($this))->setURI($url)->setTitle("EBI BioModels Database - BioModel # {$id}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($download_file)))->setFormat("rdf/xml")->setPublisher("http://www.ebi.ac.uk/")->setHomepage("http://www.ebi.ac.uk/biomodels-main/")->setRights("use-share-modify")->setLicense("http://www.ebi.ac.uk/biomodels-main/termsofuse")->setDataset("http://identifiers.org/biomodels.db/");
$dataset_description .= $source_file->toRDF();
echo "done!" . PHP_EOL;
}
//foreach
parent::getWriteFile()->close();
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/biomodels/biomodels.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $output_file->toRDF();
//write dataset description to file
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function Parse($xml)
{
// state the dataset info
foreach ($xml->release->dbinfo as $o) {
$db = $o->attributes()->dbname . " v" . $o->attributes()->version . " (" . $o->attributes()->entry_count . " entries) [" . $o->attributes()->file_date . "]";
parent::addRDF(parent::triplifyString(parent::getDatasetURI(), parent::getVoc() . "contains", $db));
if ((string) $o->attributes()->dbname === "INTERPRO") {
parent::setDatasetVersion($o->attributes()->version);
}
}
// get a potential id list
if (parent::getParameterValue("id_list") != '') {
$id_list = explode(",", parent::getParameterValue("id_list"));
}
// now interate over the entries
foreach ($xml->interpro as $o) {
parent::writeRDFBufferToWriteFile();
$interpro_id = $o->attributes()->id;
if (isset($id_list) && !in_array($interpro_id, $id_list)) {
continue;
}
echo "Processing {$interpro_id}" . PHP_EOL;
$name = $o->name;
$short_name = $o->attributes()->short_name;
$type = $o->attributes()->type;
$s = parent::getNamespace() . $interpro_id;
//echo "Adding... $s rdfs:label $name ($short_name) $type [$s]".PHP_EOL;
parent::addRDF(parent::describeIndividual($s, "{$name} ({$short_name}) {$type}", parent::getVoc() . $type));
// get the pubs
unset($pubs);
foreach ($o->pub_list->publication as $p) {
$pid = (string) $p->attributes()->id;
if (isset($p->db_xref)) {
if ($p->db_xref->attributes()->db == "PUBMED") {
$pmid = (string) $p->db_xref->attributes()->dbkey;
$pubs['pid'][] = '<cite idref="' . $pid . '"/>';
$pubs['pmid'][] = '<a href="http://www.ncbi.nlm.nih.gov/pubmed/' . $pmid . '">pubmed:' . $pmid . '</a>';
parent::addRDF(parent::triplify($s, parent::getVoc() . "x-pubmed", "pubmed:{$pmid}"));
}
}
}
$abstract = (string) $o->abstract->p->asXML();
if (isset($pubs)) {
$abstract = str_replace($pubs['pid'], $pubs['pmid'], $abstract);
}
parent::addRDF(parent::triplifyString($s, "dc:description", $abstract));
if (isset($o->example_list)) {
foreach ($o->example_list->example as $example) {
$db = (string) $example->db_xref->attributes()->db;
$id = (string) $example->db_xref->attributes()->dbkey;
parent::addRDF(parent::triplify($s, parent::getVoc() . "example-entry", "{$db}:{$id}"));
}
}
if (isset($o->parent_list->rel_ref)) {
foreach ($o->parent_list->rel_ref as $parent) {
$id = (string) $parent->attributes()->ipr_ref;
parent::addRDF(parent::triplify($s, parent::getVoc() . "parent", "interpro:{$id}"));
}
}
if (isset($o->child->rel_ref)) {
foreach ($o->child->rel_ref as $child) {
$id = (string) $child->attributes()->ipr_ref;
parent::addRDF(parent::triplify($s, parent::getVoc() . "child", "interpro:{$id}"));
}
}
if (isset($o->contains->rel_ref)) {
foreach ($o->contains->rel_ref as $contains) {
$id = (string) $contains->attributes()->ipr_ref;
parent::addRDF(parent::triplify($s, parent::getVoc() . "contains", "interpro:{$id}"));
}
}
if (isset($o->found_in->rel_ref)) {
foreach ($o->found_in->rel_ref as $f) {
$id = (string) $f->attributes()->ipr_ref;
parent::addRDF(parent::triplify($s, parent::getVoc() . "found-in", "interpro:{$id}"));
}
}
if (isset($o->sec_list->sec_ac)) {
foreach ($o->sec_ac as $s) {
$id = (string) $s->attributes()->acc;
parent::addRDF(parent::triplify($s, parent::getVoc() . "secondary-accession", "interpro:{$id}"));
}
}
// xrefs
if (isset($o->member_list->dbxref)) {
foreach ($o->member_list->db_xref as $dbxref) {
$db = (string) $dbxref->attributes()->db;
$id = (string) $dbxref->attributes()->dbkey;
parent::addRDF(parent::triplify($s, parent::getVoc() . "x-" . strtolower($db), "{$db}:{$id}"));
}
}
if (isset($o->external_doc_list)) {
foreach ($o->external_doc_list->db_xref as $dbxref) {
$db = (string) $dbxref->attributes()->db;
$id = (string) $dbxref->attributes()->dbkey;
parent::addRDF(parent::triplify($s, parent::getVoc() . "x-" . strtolower($db), "{$db}:{$id}"));
}
}
if (isset($o->structure_db_links->db_xref)) {
foreach ($o->structure_db_links->db_xref as $dbxref) {
$db = (string) $dbxref->attributes()->db;
$id = (string) $dbxref->attributes()->dbkey;
parent::addRDF(parent::triplify($s, parent::getVoc() . "x-" . strtolower($db), "{$db}:{$id}"));
}
}
// taxon distribution
foreach ($o->taxonomy_distribution->taxon_data as $t) {
$organism = (string) $t->attributes()->name;
$number = (string) $t->attributes()->proteins_count;
parent::addRDF(parent::triplifyString($s, parent::getVoc() . "taxon-distribution", "{$organism} ({$number})"));
}
}
}
public function TriplifyMap($a, $prefix)
{
$defaults = parent::getRegistry()->getDefaultURISchemes();
$bio2rdf_priority = false;
$mapping = true;
// subject
if ($a['s_type'] == 'bnode') {
$a['s'] = 'http://bio2rdf.org/' . $prefix . '_resource:' . substr($a['s'], 2);
}
$u = $this->parseURI($a['s']);
$s_uri = $u['uri'];
if (isset($u['prefix'])) {
if (!in_array($u['prefix'], $defaults)) {
if ($bio2rdf_priority) {
$s_uri = $u['bio2rdf_uri'];
if ($mapping) {
parent::addRDF(parent::triplify($s_uri, 'owl:sameAs', $u['uri']));
}
} else {
if ($mapping) {
parent::addRDF(parent::triplify($u['uri'], 'owl:sameAs', $u['bio2rdf_uri']));
}
}
}
} else {
// add to the registry of uris not found
if (!isset($this->unmapped_uri[$u['base_uri']])) {
$this->unmapped_uri[$u['base_uri']] = 1;
} else {
$this->unmapped_uri[$u['base_uri']]++;
}
}
// predicate
$u = $this->parseURI($a['p']);
$p_uri = $u['uri'];
if (isset($u['prefix'])) {
if (!in_array($u['prefix'], $defaults)) {
if ($bio2rdf_priority) {
$p_uri = $u['bio2rdf_uri'];
if ($mapping) {
parent::addRDF(parent::triplify($p_uri, 'owl:sameAs', $u['uri']));
}
} else {
if ($mapping) {
parent::addRDF(parent::triplify($u['uri'], 'owl:sameAs', $u['bio2rdf_uri']));
}
}
}
} else {
// add to the registry of uris not found
if (!isset($this->unmapped_uri[$u['base_uri']])) {
$this->unmapped_uri[$u['base_uri']] = 1;
} else {
$this->unmapped_uri[$u['base_uri']]++;
}
}
if ($a['o_type'] == 'uri' || $a['o_type'] == 'bnode') {
if ($a['o_type'] == 'bnode') {
$a['o'] = 'http://bio2rdf.org/' . $prefix . '_resource:' . substr($a['o'], 2);
}
$u = $this->parseURI($a['o']);
$o_uri = $u['uri'];
if (isset($u['prefix'])) {
if (!in_array($u['prefix'], $defaults)) {
if ($bio2rdf_priority) {
$o_uri = $u['bio2rdf_uri'];
if ($mapping) {
parent::addRDF(parent::triplify($o_uri, 'owl:sameAs', $u['uri']));
}
} else {
if ($mapping) {
parent::addRDF(parent::triplify($u['uri'], 'owl:sameAs', $u['bio2rdf_uri']));
}
}
}
} else {
// add to the registry of uris not found
if (!isset($this->unmapped_uri[$u['base_uri']])) {
$this->unmapped_uri[$u['base_uri']] = 1;
} else {
$this->unmapped_uri[$u['base_uri']]++;
}
}
// add the triple
parent::addRDF(parent::triplify($s_uri, $p_uri, $o_uri));
} else {
parent::addRDF(parent::triplifyString($s_uri, $p_uri, $a['o'], $a['o_datatype'] == '' ? null : $a['o_datatype'], $a['o_lang'] == '' ? null : $a['o_lang']));
}
}
