function phenotype()
{
/** get the ontology terms **/
$apofile = $this->GetParameterValue('ncbo_download_dir') . "apo.obo";
if (!file_exists($apofile)) {
GetLatestNCBOOntology('1222', $this->GetParameterValue('ncbo_api_key'), $apofile);
}
$apoin = fopen($apofile, "r");
if ($apoin === FALSE) {
trigger_error("Unable to open {$apofile}");
exit;
}
$terms = OBOParser($apoin);
fclose($apoin);
BuildNamespaceSearchList($terms, $searchlist);
while ($l = $this->GetReadFile()->Read(96000)) {
if (trim($l) == '') {
continue;
}
$a = explode("\t", $l);
$eid = md5($a[3] . $a[5] . $a[6] . $a[9]);
$label = "{$a['0']} - {$a['5']} experiment with {$a['6']} resulting in phenotype of {$a['9']}";
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "rdfs:label", "{$label} [sgd_resource:{$eid}]"));
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "void:inDataset", $this->GetDatasetURI()));
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "rdf:type", "sgd_vocabulary:Phenotype_Experiment"));
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "sgd_vocabulary:has-participant", "sgd:{$a['3']}"));
// reference
// PMID: 12140549|SGD_REF: S000071347
$b = explode("|", $a[4]);
foreach ($b as $c) {
$d = explode(" ", $c);
if ($d[0] == "PMID:") {
$ns = "pubmed";
} else {
$ns = "sgd";
}
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "sgd_vocabulary:article", "{$ns}:" . $d[1]));
}
// experiment type [5]
$p = strpos($a[5], '(');
if ($p !== FALSE) {
$label = substr($a[5], 0, $p - 1);
$details = substr($a[5], $p + 1);
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "dc:description", "{$details}"));
} else {
$label = $a[5];
}
$id = array_search($label, $searchlist['experiment_type']);
if ($id !== FALSE) {
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "sgd_vocabulary:experiment-type", strtolower($id)));
} else {
trigger_error("No match for experiment type {$label}");
}
// mutant type [6]
$id = array_search($a[6], $searchlist['mutant_type']);
if ($id !== FALSE) {
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "sgd_vocabulary:mutant-type", strtolower($id)));
}
// phenotype [9]
// presented as observable: qualifier
$b = explode(": ", $a[9]);
$id = array_search($b[0], $searchlist['observable']);
if ($id !== FALSE) {
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "sgd_vocabulary:observable", strtolower($id)));
}
if (!empty($b[1])) {
$id = array_search($b[1], $searchlist['qualifier']);
if ($id !== FALSE) {
$this->AddRDF($this->QQuad("sgd_resource:{$eid}", "sgd_vocabulary:qualifier", strtolower($id)));
}
}
/*
7) Allele (Optional) -Allele name and description, if applicable
8) Strain Background (Optional) -Genetic background in which the phenotype was analyzed
10) Chemical (Optional) -Any chemicals relevant to the phenotype
11) Condition (Optional) -Condition under which the phenotype was observed
12) Details (Optional) -Details about the phenotype
13) Reporter (Optional) -The protein(s) or RNA(s) used in an experiment to track a process
*/
if (trim($a[7]) != '') {
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "sgd_vocabulary:allele", $a[7]));
}
if (trim($a[8]) != '') {
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "sgd_vocabulary:background", $a[8]));
}
if (trim($a[10]) != '') {
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "sgd_vocabulary:chemical", $a[10]));
}
if (trim($a[11]) != '') {
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "sgd_vocabulary:condition", $a[11]));
}
if (trim($a[12]) != '') {
$this->AddRDF($this->QQuadL("sgd_resource:{$eid}", "sgd_vocabulary:details", str_replace('"', '\\"', $a[12])));
}
//if($a[13] != '') $buf .= "sgd:$eid sgd_vocabulary:reporter \"$a[13]\".".PHP_EOL;
}
//while
return TRUE;
}
function phenotype()
{
/** get the ontology terms **/
$apofile = $this->GetParameterValue('ncbo_download_dir') . "apo.obo";
if (!file_exists($apofile)) {
GetLatestNCBOOntology('APO', $this->GetParameterValue('ncbo_api_key'), $apofile);
}
$apoin = fopen($apofile, "r");
if ($apoin === FALSE) {
trigger_error("Unable to open {$apofile}", E_USER_ERROR);
exit;
}
$terms = OBOParser($apoin);
fclose($apoin);
BuildNamespaceSearchList($terms, $searchlist);
while ($l = $this->GetReadFile()->Read(96000)) {
if (trim($l) == '') {
continue;
}
$a = explode("\t", $l);
$eid = md5($a[3] . $a[5] . $a[6] . $a[9]);
$label = "{$a['0']} - {$a['5']} experiment with {$a['6']} resulting in phenotype of {$a['9']}";
$this->AddRDF(parent::triplify($this->getRes() . $eid, $this->getVoc() . "has-participant", $this->getNamespace() . $a[3]) . parent::describeClass($this->getVoc() . "Phenotype_Experiment", "SGD phenotype experiment [" . $this->getVoc() . "Phenotype_Experiment]") . parent::describeProperty($this->getVoc() . "has-participant", "Relationship between an SGD entity and its participant"));
// reference
// PMID: 12140549|SGD_REF: S000071347
$b = explode("|", $a[4]);
foreach ($b as $c) {
$d = explode(" ", $c);
if ($d[0] == "PMID:") {
$ns = "pubmed";
} else {
$ns = "sgd";
}
$this->AddRDF(parent::triplify($this->getRes() . $eid, $this->getVoc() . "article", $ns . ":" . $d[1]));
}
// experiment type [5]
$details = null;
$p = strpos($a[5], '(');
if ($p !== FALSE) {
$label = substr($a[5], 0, $p - 1);
$details = substr($a[5], $p + 1);
} else {
$label = $a[5];
}
$this->AddRDF(parent::describeIndividual($this->getRes() . $eid, $label, $this->getVoc() . "Phenotype_Experiment", null, $details, null));
$id = array_search($label, $searchlist['experiment_type']);
if ($id !== FALSE) {
$this->AddRDF(parent::triplify($this->getRes() . $eid, $this->getVoc() . "experiment-type", strtolower($id)) . parent::describeProperty($this->getVoc() . "experiment-type", "Relationship between an SGD experiment and the experiment type"));
} else {
trigger_error("No match for experiment type {$label}", E_USER_WARNING);
}
// mutant type [6]
$id = array_search($a[6], $searchlist['mutant_type']);
if ($id !== FALSE) {
$this->AddRDF(parent::triplify($this->getRes() . $eid, $this->getVoc() . "mutant-type", strtolower($id)) . parent::describeProperty($this->getVoc() . "mutant-type", "Relationship between an SGD experiment and the mutant type"));
}
// phenotype [9]
// presented as observable: qualifier
$b = explode(": ", $a[9]);
$id = array_search($b[0], $searchlist['observable']);
if ($id !== FALSE) {
$this->AddRDF(parent::triplify($this->getRes() . $eid, $this->getVoc() . "observable", strtolower($id)) . parent::describeProperty($this->getVoc() . "observable", "Relationship between an SGD entity and its observable qualifier"));
}
if (!empty($b[1])) {
$id = array_search($b[1], $searchlist['qualifier']);
if ($id !== FALSE) {
$this->AddRDF(parent::triplify($this->getRes() . $eid, $this->getVoc() . "qualifier", strtolower($id)));
}
}
/*
7) Allele (Optional) -Allele name and description, if applicable
8) Strain Background (Optional) -Genetic background in which the phenotype was analyzed
10) Chemical (Optional) -Any chemicals relevant to the phenotype
11) Condition (Optional) -Condition under which the phenotype was observed
12) Details (Optional) -Details about the phenotype
13) Reporter (Optional) -The protein(s) or RNA(s) used in an experiment to track a process
*/
if (trim($a[7]) != '') {
$this->AddRDF(parent::triplifyString($this->getRes() . $eid, $this->getVoc() . "allele", $a[7]) . parent::describeProperty($this->getVoc() . "allele", "Relationship between an SGD experiment and an allele"));
}
if (trim($a[8]) != '') {
$this->AddRDF(parent::triplifyString($this->getRes() . $eid, $this->getVoc() . "background", $a[8]) . parent::describeProperty($this->getVoc() . "background", "Relationship betweeen an SGD experiment and its background"));
}
if (trim($a[10]) != '') {
$this->AddRDF(parent::triplifyString($this->getRes() . $eid, $this->getVoc() . "chemical", $a[10]) . parent::describeProperty($this->getVoc() . "chemical", "Relationship between an SGD experiment and a chemical"));
}
if (trim($a[11]) != '') {
$this->AddRDF(parent::triplifyString($this->getRes() . $eid, $this->getVoc() . "condition", $a[11]) . parent::describeProperty($this->getVoc() . "condition", "Relationship between an SGD experiment and a condition"));
}
if (trim($a[12]) != '') {
$this->AddRDF(parent::triplifyString($this->getRes() . $eid, $this->getVoc() . "details", str_replace('"', '\\"', $a[12])) . parent::describeProperty($this->getVoc() . "details", "Relationship between an SGD experiment and its details"));
}
parent::writeRDFBufferToWriteFile();
}
//while
return TRUE;
}
