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, $kid));
}
}
}
}
}
/**
* process a results xml file from the download directory
**/
function process_file($infile)
{
$indir = parent::getParameterValue('indir');
$xml = new CXML($infile);
$this->setCheckPoint('file');
while ($xml->Parse("clinical_study") == TRUE) {
$this->setCheckPoint('record');
$this->root = $root = $xml->GetXMLRoot();
$this->nct_id = $nct_id = $this->getString("//id_info/nct_id");
$this->study_id = $study_id = parent::getNamespace() . "{$nct_id}";
### declare
$label = $this->getString("//brief_title");
if (!$label) {
$label = $this->getString("//official_title");
}
if (!$label) {
$label = "Clinical trial #" . $nct_id;
}
parent::addRDF(parent::describeIndividual($study_id, $label, parent::getVoc() . "Clinical-Study") . parent::describeClass(parent::getVoc() . "Clinical-Study", "Clinical Study"));
##########################################################################################
#required header
##########################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "download-date", $this->getString('//required_header/download_date')) . parent::triplify($study_id, parent::getVoc() . "url", $this->getString('//required_header/url')));
##########################################################################################
#identifiers
##########################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "nct-id", $this->getString('//id_info/nct_id'), "xsd:string") . parent::triplifyString($study_id, parent::getVoc() . "org-study-id", $this->getString('//id_info/org_study_id'), "xsd:string"));
$sids = $root->xpath('//id_info/secondary_id');
if (isset($sids)) {
foreach ($sids as $id) {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "secondary-id", (string) $id, "xsd:string"));
}
}
$nctaliases = $root->xpath('//id_info/nct-alias');
if (isset($nctaliases)) {
foreach ($nctaliases as $id) {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "nct-alias", (string) $id, "xsd:string"));
}
}
##########################################################################################
#titles
##########################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "brief-title", $this->getString("//brief_title")) . parent::triplifyString($study_id, parent::getVoc() . "official-title", $this->getString("//official_title")));
###################################################################################
#brief summary
###################################################################################
$brief_summary = str_replace(array("\r", "\n", "\t"), array("
", "
", "	"), $this->getString('//brief_summary/textblock'));
parent::addRDF(parent::triplifyString($study_id, $this->getVoc() . "brief-summary", $brief_summary));
####################################################################################
# detailed description
####################################################################################
$d = str_replace(array("\r", "\n", "\t"), array("
", "
", "	"), $this->getString('//detailed_description/textblock'));
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "detailed-description", $d));
#########################################################################################
#acronym
#########################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "acronym", $this->getString("//acronym")));
########################################################################################
#sponsors
########################################################################################
try {
$sponsors = array("lead_sponsor", "collaborator");
foreach ($sponsors as $sponsor) {
$a = @array_shift($root->xpath('//sponsors/' . $sponsor));
if ($a == null) {
break;
}
$agency = $this->getString("//agency", $a);
$agency_id = parent::getRes() . md5($agency);
$agency_class = $this->getString("//agency_class", $a);
$agency_class_id = parent::getRes() . md5($agency_class);
parent::addRDF(parent::describeIndividual($agency_id, $agency, parent::getVoc() . "Organization") . parent::describeClass(parent::getVoc() . "Organization", "Organization") . parent::triplify($study_id, parent::getVoc() . str_replace("_", "-", $sponsor), $agency_id) . parent::describeIndividual($agency_class_id, $agency_class, parent::getVoc() . "Organization") . parent::describeClass(parent::getVoc() . "Organization", "Organization") . parent::triplify($agency_id, parent::getVoc() . "organization", $agency_class_id));
}
} catch (Exception $e) {
echo "There was an error in the lead sponsor element: {$e}\n";
}
#################################################################################
# source
#################################################################################
$source = $this->getString('//source');
if ($source) {
$source_id = parent::getRes() . md5($source);
parent::addRDF(parent::describeIndividual($source_id, $source, parent::getVoc() . "Organization") . parent::triplify($study_id, parent::getVoc() . "source", $source_id));
}
######################################################################################
# oversight
######################################################################################
try {
$oversight = @array_shift($root->xpath('//oversight_info'));
$oversight_id = parent::getRes() . md5($oversight->asXML());
$authority = $this->getString('//authority', $oversight);
$authority_id = parent::getRes() . md5($authority);
parent::addRDF(parent::describeIndividual($oversight_id, $authority, parent::getVoc() . "Organization") . parent::triplify($study_id, $this->getVoc() . "oversight", $oversight_id) . parent::triplify($study_id, $this->getVoc() . "authority", $authority_id) . parent::triplifyString($oversight_id, parent::getVoc() . "has-dmc", $this->getString('//has_dmc', $oversight)));
} catch (Exception $e) {
echo "There was an error in the oversight info element: {$e}\n";
}
#################################################################################
# overall status
#################################################################################
$overall_status = $this->getString('//overall_status');
if ($overall_status) {
$status_id = parent::getRes() . md5($overall_status);
parent::addRDF(parent::describeIndividual($status_id, $overall_status, parent::getVoc() . "Status") . parent::describeClass(parent::getVoc() . "Status", "Status") . parent::triplify($study_id, parent::getVoc() . "overall-status", $status_id));
}
#########################################################################################
#why stopped
#########################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "why-stopped", $this->getString("//why_stopped")));
##################################################################################
# dates
##################################################################################
$dates = array("start_date", "end_date", "completion_date", "primary_completion_date", "verification_date", "lastchanged_date", "firstreceived_date", "firstreceived_results_date");
foreach ($dates as $date) {
$d = $this->getString('//' . $date);
if ($d) {
$datetime = $this->getDatetimeFromDate($d);
if (isset($datetime)) {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . str_replace("_", "-", $date), $datetime));
} else {
trigger_error("unable to parse date: {$d}", E_USER_ERROR);
}
}
}
####################################################################################
# phase
####################################################################################
$phase = $this->getString('//phase');
if ($phase && $phase != "N/A") {
$phase_id = $this->getRes() . md5($phase);
parent::addRDF(parent::describeIndividual($phase_id, $phase, parent::getVoc() . "Phase", $phase) . parent::describeClass(parent::getVoc() . "Phase", $phase) . parent::triplify($study_id, parent::getVoc() . "phase", $phase_id));
}
###################################################################################
# study type
####################################################################################
$study_type = $this->getString('//study_type');
if ($study_type) {
$study_type_id = $this->getRes() . md5($study_type);
parent::addRDF(parent::describeClass($study_type_id, $study_type, parent::getVoc() . "Study-Type") . parent::describeClass(parent::getVoc() . "Study-Type", "Study Type") . parent::triplify($study_id, parent::getVoc() . "study-type", $study_type_id));
}
###############################################################################
# study design
###############################################################################
$study_design = $this->getString('//study_design');
if ($study_design) {
$study_design_id = parent::getRes() . md5($study_id . $study_design);
parent::addRDF(parent::describeIndividual($study_design_id, "{$study_id} study design", parent::getVoc() . "Study-Design") . parent::describeClass(parent::getVoc() . "Study-Design", "Study Design") . parent::triplify($study_id, parent::getVoc() . "study-design", $study_design_id));
// Intervention Model: Parallel Assignment, Masking: Double-Blind, Primary Purpose: Treatment
foreach (explode(", ", $study_design) as $i => $b) {
$c = explode(": ", $b);
if (isset($c[1])) {
$sdp = $study_design_id . "-" . ($i + 1);
$key = parent::getRes() . md5($c[0]);
$value = parent::getRes() . md5($c[1]);
parent::addRDF(parent::describeIndividual($sdp, $b, parent::getVoc() . "Study-Design-Parameter") . parent::describeClass(parent::getVoc() . "Study-Design-Parameter", "Study Design Parameter") . parent::triplify($sdp, parent::getVoc() . "key", $key) . parent::describeClass($key, $c[0]) . parent::triplify($sdp, parent::getVoc() . "value", $value) . parent::describeClass($value, $c[1]) . parent::triplify($study_design_id, parent::getVoc() . "study-design-parameter", $sdp));
}
}
}
####################################################################################
# target duration
####################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "target-duration", $this->getString('//target_duration')));
################################################################################
# outcomes
###############################################################################
$outcomes = array("primary_outcome", "secondary_outcome", "other_outcome");
foreach ($outcomes as $outcome) {
$o = $root->xpath('//' . $outcome);
if ($o) {
$os = $o;
if (!is_array($o)) {
$os = array($o);
}
foreach ($os as $o) {
try {
$po_id = parent::getRes() . md5($nct_id . $o->asXML());
$po_type = parent::getVoc() . str_replace("_", "-", $outcome);
$measure = $this->getString('//measure', $o);
$time_frame = $this->getString('//time_frame', $o);
$safety_issue = $this->getString('//saftey_issue', $o);
$description = $this->getString('//description', $o);
parent::addRDF(parent::describeIndividual($po_id, $measure . " " . $time_frame, ucfirst($po_type)) . parent::describeClass(ucfirst($po_type), str_replace("_", " ", ucfirst($outcome))) . parent::triplifyString($po_id, "dc:description", $description) . parent::triplifyString($po_id, parent::getVoc() . "measure", $measure) . parent::triplifyString($po_id, parent::getVoc() . "time-frame", $time_frame) . parent::triplifyString($po_id, parent::getVoc() . "safety-issue", $safety_issue) . parent::triplify($study_id, parent::getVoc() . $po_type, $po_id));
} catch (Exception $e) {
echo "There was an error parsing the primary outcome element: {$e} \n";
}
}
}
}
##############################################################################
#number of arms
##############################################################################
try {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "number-of-arms", $this->getString('//number_of_arms')));
} catch (Exception $e) {
echo "There was an exception parsing the number of arms element: {$e}\n";
}
##############################################################################
#number of groups
##############################################################################
try {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "number-of-arms", $this->getString('//number_of_groups')));
} catch (Exception $e) {
echo "There was an exception parsing the number of groups: {$e}\n";
}
##############################################################################
#enrollment
##############################################################################
try {
$e = $root->xpath('//enrollment');
if ($e) {
$type = strtolower((string) $e[0]->attributes()->type);
$value = $this->getString('//enrollment');
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . ($type ? $type . "-" : "") . "enrollment", $value));
}
} catch (Exception $e) {
echo "There was an exception parsing the enrollment element: {$e}\n";
}
###############################################################################
#condition
###############################################################################
try {
$conditions = $root->xpath('//condition');
foreach ($conditions as $condition) {
$mesh_label_id = parent::getRes() . md5($condition);
parent::addRDF(parent::triplify($study_id, parent::getVoc() . "condition", $mesh_label_id) . parent::describeClass($mesh_label_id, $condition, parent::getVoc() . "Condition") . parent::describeClass(parent::getVoc() . "Condition", "Condition"));
}
} catch (Exception $e) {
echo "There was an exception parsing condition element: {$e}\n";
}
################################################################################
# arm_group
################################################################################
try {
$arm_groups = $root->xpath('//arm_group');
foreach ($arm_groups as $arm_group) {
$arm_group_id = $this->getString('./arm_group_label', $arm_group);
$arm_group_id = md5($arm_group_id);
$arm_group_uri = parent::getRes() . $this->nct_id . "/arm-group/" . $arm_group_id;
$arm_group_label = $this->nct_id . " arm group " . $arm_group_id;
$arm_group_type = ucfirst(str_replace(" ", "_", $this->getString('./arm_group_type', $arm_group)));
if (!$arm_group_type) {
$arm_group_type = "Clinical-Arm";
}
$description = $this->getString('./description', $arm_group);
parent::addRDF(parent::describeIndividual($arm_group_uri, $arm_group_label, parent::getVoc() . $arm_group_type) . parent::describeClass(parent::getVoc() . $arm_group_type, ucfirst(str_replace("_", " ", $arm_group_type))) . parent::triplifyString($arm_group_uri, parent::getVoc() . "description", $description) . parent::describeIndividual($arm_group_uri, $arm_group, parent::getVoc() . "Arm-Group") . parent::describeClass(parent::getVoc() . "Arm-Group", "Arm Group") . parent::triplify($study_id, parent::getVoc() . "arm-group", $arm_group_uri));
}
} catch (Exception $e) {
echo "There was an exception in arm groups: {$e}\n";
}
##############################################################################
#intervention
##############################################################################
try {
$interventions = $root->xpath('//intervention');
foreach ($interventions as $intervention) {
$intervention_id = parent::getRes() . md5($intervention->asXML());
$intervention_name = $this->getString('./intervention_name', $intervention);
$intervention_type = $this->getString('./intervention_type', $intervention);
$intervention_type_uri = parent::getVoc() . ucfirst(str_replace(" ", "_", $intervention_type));
$intervention_desc = $this->getString('./description', $intervention);
$intervention_on = $this->getString('./other_name', $intervention);
parent::addRDF(parent::describeIndividual($intervention_id, $intervention_name, $intervention_type_uri) . parent::describeClass($intervention_type_uri, $intervention_type) . parent::triplifyString($intervention_id, parent::getVoc() . "intervention-name", $intervention_name) . parent::triplifyString($intervention_id, parent::getVoc() . "intervention-desc", $intervention_desc) . parent::triplifyString($intervention_id, parent::getVoc() . "other-name", $intervention_on) . parent::triplify($study_id, parent::getvoc() . "intervention", $intervention_id));
$agl = $intervention->xpath("./arm_group_label");
foreach ($agl as $a) {
$arm_group_id = md5($a);
$ag = parent::getRes() . $this->nct_id . "/arm-group/" . $arm_group_id;
parent::addRDF(parent::describeIndividual($ag, $a, parent::getVoc() . "Arm-Group") . parent::describeClass(parent::getVoc() . "Arm-Group", "Arm Group") . parent::triplify($intervention_id, parent::getVoc() . "arm-group", $ag));
}
}
} catch (Exception $e) {
echo "There was an error in interventions {$e}\n";
}
###############################################################################
#eligibility
################################################################################
try {
$eligibility = @array_shift($root->xpath('//eligibility'));
if ($eligibility !== null) {
$eligibility_label = "eligibility for " . $study_id;
$eligibility_id = parent::getRes() . md5($eligibility->asXML());
parent::addRDF(parent::describeIndividual($eligibility_id, $eligibility_label, parent::getVoc() . "Eligibility") . parent::describeClass(parent::getVoc() . "Eligibility", "Eligibility") . parent::triplify($study_id, parent::getVoc() . "eligibility", $eligibility_id));
if ($criteria = @array_shift($eligibility->xpath('./criteria'))) {
$text = @array_shift($criteria->xpath('./textblock'));
parent::addRDF(parent::triplifyString($eligibility_id, parent::getVoc() . "text", $text));
$c = preg_split("/(Inclusion Criteria\\:|Exclusion Criteria\\:)/", $text);
//inclusion
if (isset($c[1])) {
$d = explode(" - ", $c[1]);
// the lists are separated by a hyphen
foreach ($d as $inclusion) {
$inc = trim($inclusion);
if ($inc != '') {
$inc_id = parent::getRes() . md5($inc);
parent::addRDF(parent::describeIndividual($inc_id, $inc, parent::getVoc() . "Inclusion-Criteria") . parent::describeClass(parent::getVoc() . "Inclusion-Criteria", "Inclusion Criteria") . parent::triplify($eligibility_id, parent::getVoc() . "inclusion-criteria", $inc_id));
}
}
}
//exclusion
if (isset($c[2])) {
$d = explode(" - ", $c[1]);
foreach ($d as $exclusion) {
$exc = trim($exclusion);
if ($exc != '') {
$exc_id = parent::getRes() . md5($exc);
parent::addRDF(parent::describeIndividual($exc_id, $exc, parent::getVoc() . "Exclusion-Criteria") . parent::describeClass(parent::getVoc() . "Exclusion-Criteria", "Exclusion Criteria") . parent::triplify($eligibility_id, parent::getVoc() . "exclusion-criteria", $exc_id));
}
}
}
}
parent::addRDF(parent::triplifyString($eligibility_id, parent::getVoc() . "gender", $this->getString('./gender', $eligibility)));
parent::addRDF(parent::triplifyString($eligibility_id, parent::getVoc() . "healthy-volunteers", $this->getString('./healthy_volunteers', $eligibility)));
$attributes = array('minimum_age', 'maximum_age');
foreach ($attributes as $a) {
$s = $this->getString('./' . $a, $eligibility);
if ($s != 'N/A') {
$age = trim(str_replace("Years", "", $s));
parent::addRDF(parent::triplifyString($eligibility_id, parent::getVoc() . str_replace("_", "-", $a), $age));
}
}
$attributes = array("study_pop" => "study-population", "sampling_method" => "sampling-method");
foreach ($attributes as $a => $r) {
$e = @array_shift($eligibility->xpath('./' . $a));
if ($s = $this->getString('./' . $a, $eligibility)) {
parent::addRDF(parent::triplifyString($eligibility_id, parent::getVoc() . $r, $this->getString('./textblock', $e)));
}
}
}
} catch (Exception $e) {
echo "There was an error in eligibility: {$e}\n";
}
######################################################################################
#biospec
#####################################################################################
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "biospec-retention", $this->getString('//biospec_retention')));
try {
$b = @array_shift($root->xpath('//biospec_descr'));
if ($b) {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "biospec_descr", $this->getString('./textblock', $b)));
}
} catch (Exception $e) {
echo "There was an error in biospec_descr: {$e}\n";
}
###################################################################
# contacts
###################################################################
$contacts = array("overall_official", "overall_contact", "overall_contact_backup");
try {
foreach ($contacts as $c) {
$d = @array_shift($root->xpath('//' . $c));
if ($d) {
parent::addRDF(parent::triplify($study_id, parent::getVoc() . str_replace("_", "-", $c), $this->makeContact($d)));
}
}
} catch (Exception $e) {
echo "There was an error parsing overall contact: {$e}" . "\n";
}
##############################################################
# location of facility doing the testing
##############################################################
try {
$location = @array_shift($root->xpath('//location'));
if ($location) {
$location_uri = parent::getRes() . md5($location->asXML());
$name = $this->getString('//facility/name', $location);
$address = @array_shift($location->xpath('//facility/address'));
$contact = @array_shift($location->xpath('//contact'));
$backups = @array_shift($location->xpath('//contact_backup'));
$investigators = @array_shift($location->xpath('//investigator'));
parent::addRDF(parent::describeIndividual($location_uri, $name, parent::getVoc() . "Location") . parent::describeClass(parent::getVoc() . "Location", "Location") . parent::triplifyString($location_uri, parent::getVoc() . "status", $this->getString('//status', $location)) . parent::triplify($study_id, parent::getVoc() . "location", $location_uri) . parent::triplify($location_uri, parent::getVoc() . "address", $this->makeAddress($address)) . ($contact != null ? parent::triplify($location_uri, parent::getVoc() . "contact", $this->makeContact($contact)) : ""));
if ($backups) {
foreach ($backups as $backup) {
parent::addRDF(parent::triplify($location_uri, parent::getVoc() . "contact-backup", $this->makeContact($backup)));
}
}
if ($investigators) {
foreach ($investigators as $investigator) {
parent::addRDF(parent::triplify($location_uri, parent::getVoc() . "investigator", $this->makeContact($investigator)));
}
}
}
} catch (Exception $e) {
echo "There was an error parsing location: {$e}" . "\n";
}
######################################################################
#countries
######################################################################
try {
$a = array("location_countries", "removed_countries");
foreach ($a as $country) {
$lc = @array_shift($root->xpath('//' . $country));
if ($lc) {
$label = $this->getString('//country', $lc);
$cid = parent::getRes() . md5($label);
parent::addRDF(parent::describeIndividual($cid, $label, parent::getVoc() . "Country") . parent::describeClass(parent::getVoc() . "Country", "Country") . parent::triplify($study_id, parent::getVoc() . "country", $cid));
}
}
} catch (Exception $e) {
echo "There was an error parsing country: {$e}" . "\n";
}
######################################################################
#reference
######################################################################
try {
$a = array("reference", "result_reference");
foreach ($a as $ref_type) {
$references = $root->xpath('//' . $ref_type);
foreach ($references as $reference) {
$p = $this->getString('./PMID', $reference);
if ($p) {
$pmid = "pubmed:{$p}";
parent::addRDF(parent::describeIndividual($pmid, $p, parent::getVoc() . "Reference") . parent::describeClass(parent::getVoc() . "Reference", "Reference") . parent::triplifyString($pmid, parent::getVoc() . "citation", $this->getString('./citation', $reference)) . parent::triplify($study_id, parent::getVoc() . str_replace("_", "-", $ref_type), $pmid));
}
}
}
} catch (Exception $e) {
echo "There was an error parsing references element: {$e}\n";
}
#######################################################################
#link
#######################################################################
try {
$links = $root->xpath('//link');
foreach ($links as $i => $link) {
$url = $this->getString('./url', $link);
$url = preg_replace("/>.*\$/", "", $url);
$lid = parent::getRes() . md5($url);
parent::addRDF(parent::describeIndividual($lid, $this->getString('./description', $link), parent::getVoc() . "Link") . parent::describeClass(parent::getVoc() . "Link", "Link") . parent::triplify($lid, parent::getVoc() . "url", $url) . parent::triplify($study_id, parent::getVoc() . "link", $lid));
}
} catch (Exception $e) {
echo "There was an error parsing link element: {$e}\n";
}
############################################################################
#responsible party
############################################################################
try {
$rp = @array_shift($root->xpath('//responsible_party'));
if ($rp) {
$rp_id = parent::getRes() . md5($rp->asXML());
$label = $this->getString('./name_title', $rp);
if (!$label) {
$label = $this->getString('./organization', $rp);
} else {
$label .= ", " . $this->getString('./organization', $rp);
}
if (!$label) {
$label = $this->getString('./party_type', $rp);
}
$org_id = parent::getRes() . md5($this->getString('./organization', $rp));
parent::addRDF(parent::describeIndividual($rp_id, $label, parent::getVoc() . "Responsible-Party") . parent::describeClass(parent::getVoc() . "Responsible-Party", "Responsible Party") . parent::triplify($study_id, parent::getVoc() . "responsible-party", $rp_id) . parent::triplify($rp_id, parent::getVoc() . "organization", $org_id) . parent::describeIndividual($org_id, $this->getString('./organization', $rp), parent::getVoc() . "Organization") . parent::describeClass(parent::getVoc() . "Organization", "Organization") . parent::triplifyString($rp_id, parent::getVoc() . "name-title", $this->getString('./name_title', $rp)) . parent::triplifyString($rp_id, parent::getVoc() . "party-type", $this->getString('./party_type', $rp)) . parent::triplifyString($rp_id, parent::getVoc() . "investigator-affiliation", $this->getString('./investigator_affiliation', $rp)) . parent::triplifyString($rp_id, parent::getVoc() . "investigator-full-name", $this->getString('./investigator_full_name', $rp)) . parent::triplifyString($rp_id, parent::getVoc() . "investigator-title", $this->getString('./investigator_title', $rp)));
}
} catch (Exception $e) {
echo "There was an error parsing the responsible_party element: {$e}\n";
}
##############################################################################
# keywords
##############################################################################
try {
$keywords = $root->xpath('//keyword');
foreach ($keywords as $keyword) {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "keyword", (string) $keyword));
}
} catch (Exception $e) {
echo "There was an error parsing the keywords element: {$e}";
}
# mesh terms
# note: mesh terms are assigned using an imperfect algorithm
try {
$mesh_terms = $root->xpath('//condition_browse/mesh_term');
foreach ($mesh_terms as $mesh_term) {
$term = (string) $mesh_term;
$mesh_id = parent::getRes() . md5($term);
parent::addRDF(parent::triplify($study_id, parent::getVoc() . "condition-mesh", $mesh_id));
parent::addRDF(parent::triplifyString($mesh_id, "rdfs:label", $term));
}
} catch (Exception $e) {
echo "There was an error in mesh_terms: {$e}\n";
}
################################################################################
# regulated by fda? is section 801? has expanded access?
################################################################################
try {
parent::addRDF(parent::triplifyString($study_id, parent::getVoc() . "is-fda-regulated", $this->getString('is_fda_regulated')) . parent::triplifyString($study_id, parent::getVoc() . "is-section-801", $this->getString('is_section_801')) . parent::triplifyString($study_id, parent::getVoc() . "has-expanded-access", $this->getString('has_expanded_access')));
} catch (Exception $e) {
echo "There was an error parsing the is_fda_regulated element: {$e}\n";
}
###############################################################################
# mesh terms for the intervention browse
###############################################################################
try {
$a = array("condition_browse", "intervention_browse");
foreach ($a as $browse_type) {
$terms = $root->xpath("//{$browse_type}/mesh_term");
foreach ($terms as $term) {
$term_label = (string) $term;
$term_id = parent::getRes() . md5($term);
parent::addRDF(parent::describeIndividual($term_id, $term_label, parent::getVoc() . "Term") . parent::describeClass(parent::getVoc() . "Term", "Term") . parent::triplify($study_id, parent::getVoc() . str_replace("_", "-", $browse_type), $term_id));
}
}
} catch (Exception $e) {
echo "There was an error parsing {$browse_type}/mesh_term element: {$e}\n";
}
################################################################################
# clinical results
################################################################################
try {
$cr = @array_shift($root->xpath('//clinical_results'));
if ($cr) {
$cr_id = parent::getRes() . md5($study_id . $cr->asXML());
parent::addRDF(parent::describeIndividual($cr_id, "clinical results for {$study_id}", parent::getVoc() . "Clinical-Result") . parent::describeClass(parent::getVoc() . "Clinical-Result", "Clinical Result") . parent::triplifyString($cr_id, parent::getVoc() . "description", $this->getString('./desc', $cr)) . parent::triplifyString($cr_id, parent::getVoc() . "restrictive-agreement", $this->getString('./restrictive_agreement', $cr)) . parent::triplifyString($cr_id, parent::getVoc() . "limitations-and-caveats", $this->getString('./limitations_and_caveats', $cr)) . parent::triplify($study_id, parent::getVoc() . "clinical-result", $cr_id));
}
} catch (Exception $e) {
echo "There was an error parsing clinical results: {$e}\n";
}
################################################################################
# Participant Flow
################################################################################
try {
$pc = 1;
$mc = 1;
$wc = 1;
$pf = @array_shift($root->xpath('//clinical_results/participant_flow'));
if ($pf) {
$pf_id = parent::getRes() . md5($pf->asXML());
parent::addRDF(parent::describeIndividual($pf_id, "participant flow for {$study_id}", parent::getVoc() . "Participant-Flow") . parent::describeClass(parent::getVoc() . "Participant-Flow", "Participant-Flow") . parent::triplify($study_id, parent::getVoc() . "participant-flow", $pf_id) . parent::triplifyString($pf_id, parent::getVoc() . "recruitment-details", $this->getString('./recruitment_details', $pf)) . parent::triplifyString($pf_id, parent::getVoc() . "pre-assignment-details", $this->getString('./pre_assignment_details', $pf)));
$groups = @array_shift($pf->xpath('./group_list'));
foreach ($groups as $group) {
parent::addRDF(parent::triplify($pf_id, parent::getVoc() . "group", $this->makeGroup($group)));
}
//period_list
$periods = @array_shift($pf->xpath('./period_list'));
foreach ($periods as $period) {
$period_id = parent::getRes() . $nct_id . "/period/" . $pc++;
$period_title = $this->getString('./title', $period);
parent::addRDF(parent::describeIndividual($period_id, $period_title . " for {$nct_id}", parent::getVoc() . "Period") . parent::describeClass(parent::getVoc() . "Period", "Period") . parent::triplify($pf_id, parent::getVoc() . "period", $period_id));
// milestones
$milestones = @array_shift($period->xpath('./milestone_list'));
if ($milestones) {
foreach ($milestones as $milestone) {
$milestone_id = parent::getRes() . $nct_id . "/milestone/" . $mc++;
$label = $this->getString('./title', $milestone);
parent::addRDF(parent::describeIndividual($milestone_id, $label, parent::getVoc() . "Milestone") . parent::describeClass(parent::getVoc() . "Milestone", "Milestone") . parent::triplify($period_id, parent::getVoc() . "milestone", $milestone_id));
// participants
$p = 1;
$ps_list = @array_shift($milestone->xpath('./participants_list'));
foreach ($ps_list as $ps) {
$ps_id = $milestone_id . "/p/" . $p++;
$group_id = parent::getRes() . $this->nct_id . "/group/" . $ps->attributes()->group_id;
$count = (string) $ps->attributes()->count;
parent::addRDF(parent::describeIndividual($ps_id, "participant counts in " . $ps->attributes()->group_id . " for milestone {$mc} of {$nct_id}", parent::getVoc() . "Participant-Count") . parent::describeClass(parent::getVoc() . "Participant-Count", "Participant Count") . parent::triplify($ps_id, parent::getVoc() . "group", $group_id) . parent::triplifyString($ps_id, parent::getVoc() . "count", $count) . parent::triplify($milestone_id, parent::getVoc() . "participant-counts", $ps_id));
}
}
}
// milestones
$withdraws = @array_shift($period->xpath('./drop_withdraw_reason_list'));
if ($withdraws) {
foreach ($withdraws as $withdraw) {
$wid = parent::getRes() . $this->nct_id . "/withdraw/" . $wc++;
$label = $this->getString('./title', $withdraw);
parent::addRDF(parent::describeIndividual($wid, $label, parent::getVoc() . "Withdraw-Reason") . parent::describeClass(parent::getVoc() . "Withdraw-Reason", "Withdraw Reason"));
// participants
$ps_list = @array_shift($withdraw->xpath('./participants_list'));
foreach ($ps_list as $ps) {
$group_id = parent::getRes() . $nct_id . "/group/" . $ps->attributes()->group_id;
$count = (string) $ps->attributes()->count;
parent::addRDF(parent::triplify($wid, parent::getVoc() . "group", $group_id) . parent::triplifyString($wid, parent::getVoc() . "count", $count));
}
}
}
}
}
} catch (Exception $e) {
echo "There was an error parsing participant flow element: {$e}\n";
}
################################################################################
# baseline
################################################################################
try {
$baseline = @array_shift($root->xpath('//baseline'));
if ($baseline) {
$b_id = $this->nct_id . "/baseline";
$b_uri = parent::getRes() . $b_id;
// group list
$groups = @array_shift($baseline->xpath('./group_list'));
foreach ($groups as $group) {
parent::addRDF(parent::describeIndividual($b_uri, "baseline for {$nct_id}", parent::getVoc() . "Baseline") . parent::describeClass(parent::getVoc() . "Baseline", "Baseline") . parent::triplify($b_uri, parent::getVoc() . "group", $this->makeGroup($group)) . parent::triplify($study_id, parent::getVoc() . "baseline", $b_uri));
}
// measure list
$measures = @array_shift($baseline->xpath('./measure_list'));
foreach ($measures as $measure) {
parent::addRDF(parent::triplify($b_uri, parent::getVoc() . "measure", $this->makeMeasure($measure)));
}
}
} catch (Exception $e) {
echo "Error in parsing baseline" . PHP_EOL;
}
################################################################################
# outcomes
################################################################################
try {
$outcomes = @array_shift($root->xpath('//outcome_list'));
if ($outcomes) {
foreach ($outcomes as $i => $outcome) {
$outcome_id = $this->nct_id . "/outcome/" . ($i + 1);
$outcome_uri = parent::getRes() . $outcome_id;
$outcome_label = $this->getString("./title", $outcome);
if (!$outcome_label) {
$outcome_label = "outcome for " . $this->nct_id;
}
parent::addRDF(parent::describeIndividual($outcome_uri, $outcome_label, parent::getVoc() . "Outcome", $this->getString("./description", $outcome)) . parent::describeClass(parent::getVoc() . "Outcome", "Outcome") . parent::triplify($study_id, parent::getVoc() . "outcome", $outcome_uri) . parent::triplifyString($outcome_uri, parent::getVoc() . "type", $this->getString("./type", $outcome)) . parent::triplifyString($outcome_uri, parent::getVoc() . "time-frame", $this->getString("./time_frame", $outcome)) . parent::triplifyString($outcome_uri, parent::getVoc() . "safety-issue", $this->getString("./safety_issue", $outcome)) . parent::triplifyString($outcome_uri, parent::getVoc() . "posting-date", $this->getString("./posting-date", $outcome)) . parent::triplifyString($outcome_uri, parent::getVoc() . "population", $this->getString("./population", $outcome)));
$groups = @array_shift($outcome->xpath('./group_list'));
if ($groups) {
foreach ($groups as $group) {
parent::addRDF(parent::triplify($outcome_uri, parent::getVoc() . "group", $this->makeGroup($group)));
}
}
// measure list
$measures = @array_shift($outcome->xpath('./measure_list'));
if ($measures) {
foreach ($measures as $measure) {
parent::addRDF(parent::triplify($outcome_uri, parent::getVoc() . "measure", $this->makeMeasure($measure)));
}
}
// analysis list
$analyses = @array_shift($outcome->xpath('./analysis_list'));
if ($analyses) {
foreach ($analyses as $analysis) {
parent::addRDF(parent::triplify($outcome_uri, parent::getVoc() . "analysis", $this->makeAnalysis($analysis)));
}
}
}
}
} catch (Exception $e) {
echo "Error in parsing outcomes" . PHP_EOL;
}
################################################################################
# events
################################################################################
try {
$c_ev = $c_c = 1;
$reported_events = @array_shift($root->xpath('//reported_events'));
if ($reported_events) {
$rp_id = parent::getRes() . md5($reported_events->asXML());
$groups = @array_shift($reported_events->xpath('./group_list'));
parent::addRDF(parent::describeIndividual($rp_id, "Reported events for {$nct_id}", parent::getVoc() . "Reported-Events") . parent::describeClass(parent::getVoc() . "Reported-Events", "Reported Events") . parent::triplify($study_id, parent::getVoc() . "reported-events", $rp_id));
foreach ($groups as $group) {
parent::addRDF(parent::triplify($rp_id, parent::getVoc() . "group", $this->makeGroup($group)));
}
// events
$event_list = array("serious_events" => "Serious Event", "other_events" => "Other Event");
foreach ($event_list as $ev => $ev_label) {
$et = @array_shift($reported_events->xpath('./' . $ev));
if (!$et) {
continue;
}
$ev_uri = parent::getVoc() . str_replace(" ", "-", $ev_label);
$categories = @array_shift($et->xpath('./category_list'));
foreach ($categories as $category) {
$major_title = $this->getString('./title', $category);
$major_title_uri = parent::getRes() . md5($major_title);
$events = @array_shift($category->xpath('./event_list'));
foreach ($events as $event) {
$e_uri = parent::getRes() . $this->nct_id . "/{$ev}/" . $c_ev++;
$subtitle = (string) $this->getString('./sub_title', $event) . " for " . $this->nct_id;
$subtitle_uri = parent::getRes() . md5($subtitle);
parent::addRDF(parent::describeIndividual($e_uri, $subtitle, $ev_uri) . parent::describeClass($ev_uri, $ev_label) . parent::triplify($e_uri, parent::getVoc() . "sub-title", $subtitle_uri) . parent::describeIndividual($subtitle_uri, $subtitle, parent::getVoc() . "Event") . parent::describeClass(parent::getVoc() . "Event", "Event") . parent::triplify($e_uri, parent::getVoc() . "major-title", $major_title_uri) . parent::describeClass($major_title_uri, $major_title) . parent::triplify($rp_id, parent::getVoc() . str_replace("_", "-", $ev), $e_uri));
$counts = $event->xpath('./counts');
foreach ($counts as $c) {
$group_id = $c->attributes()->group_id;
$group_uri = parent::getRes() . $nct_id . "/group/" . $group_id;
$c_uri = $e_uri . "/count/" . $c_c++;
parent::addRDF(parent::describeIndividual($c_uri, $subtitle . " for " . $group_id . " in " . $this->nct_id, parent::getVoc() . "Event-Count") . parent::describeClass(parent::getVoc() . "Event-Count", "Event Count") . parent::triplify($c_uri, parent::getVoc() . "group", $group_uri) . parent::triplify($e_uri, parent::getVoc() . "count", $c_uri) . parent::triplifyString($c_uri, parent::getVoc() . "default-vocabulary", $this->getString('./default_vocab', $et)) . parent::triplifyString($c_uri, parent::getVoc() . "frequency-threshold", $this->getString('./frequency_threshold', $et)) . parent::triplifyString($c_uri, parent::getVoc() . "default-assessment", $this->getString('./default_assessment', $et)) . parent::triplifyString($c_uri, parent::getVoc() . "number-events", $c->attributes()->events) . parent::triplifyString($c_uri, parent::getVoc() . "subjects-affected", $c->attributes()->subjects_affected) . parent::triplifyString($c_uri, parent::getVoc() . "subjects-at-risk", $c->attributes()->subjects_at_risk));
}
}
}
}
}
} catch (Exception $e) {
echo "Error in parsing reported events" . PHP_EOL;
}
parent::writeRDFBufferToWriteFile();
}
$this->setCheckPoint('record');
$this->setCheckPoint('dataset');
}
function parseItem($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));
}
}
}
}
