function Run()
{
echo "processing miriam database";
// directory shortcuts
$ldir = $this->getParameterValue('indir');
$odir = $this->getParameterValue('outdir');
// download and set the read file
$file = 'miriam.xml';
$rfile = $this->getParameterValue("download_url");
$lfile = $ldir . $file;
if (!file_exists($lfile) || $this->getParameterValue("download") == "true") {
utils::downloadSingle($rfile, $lfile);
}
parent::setReadFile($lfile);
// set the write file
$outfile = "miriam." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile(parent::getParameterValue("outdir") . $outfile, $gz);
$this->parse();
parent::WriteRDFBufferToWriteFile();
$this->getWriteFile()->Close();
return true;
}
function CTD_chem_gene_ixn_types()
{
$first = true;
while ($l = $this->GetReadFile()->Read()) {
if ($l[0] == '#') {
continue;
}
$a = explode("\t", $l);
// check number of columns
if ($first) {
if (($c = count(explode("\t", $l))) != 4) {
trigger_error("CTD_chem_gene_ixn_types function expects 4 fields, found {$c}!" . PHP_EOL, E_USER_WARNING);
return FALSE;
}
$first = false;
}
$id = $this->getVoc() . $a[1];
$parent = trim($a[3]);
if (isset($parent) && !empty($parent)) {
$this->AddRDF(parent::describeClass($id, $a[0], $this->getVoc() . $parent, null, $a[2]));
} else {
$this->AddRDF(parent::describeClass($id, $a[0], null, null, $a[2]));
}
parent::WriteRDFBufferToWriteFile();
}
return TRUE;
}
function gene_interactions()
{
while ($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() . $gene2));
}
//else
parent::WriteRDFBufferToWriteFile();
}
//while
}
function product($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 drugs()
{
$declared = '';
$h = explode("\t", $this->GetReadFile()->Read(1000));
// first line is header
if (count($h) != 10) {
trigger_error("Change in number of columns for drugs file", E_USER_ERROR);
return FALSE;
}
while ($l = $this->GetReadFile()->Read(200000)) {
$a = explode("\t", $l);
$id = parent::getNamespace() . $a[0];
$this->drugs[$a[0]] = $a[1];
parent::addRDF(parent::describeIndividual($id, $a[1], parent::getVoc() . "Drug") . parent::describeClass(parent::getVoc() . "Drug", "PharmGKB Drug"));
if (trim($a[2])) {
// generic names
// Entacapona [INN-Spanish],Entacapone [Usan:Inn],Entacaponum [INN-Latin],entacapone
$b = explode(',', trim($a[2]));
foreach ($b as $c) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "generic_name", str_replace('"', '', $c)));
}
parent::addRDF(parent::describeProperty(parent::getVoc() . "generic_name", "Relationship between a PharmGKB drug and a generic name"));
}
if (trim($a[3])) {
// trade names
//Disorat,OptiPranolol,Trimepranol
$b = explode(',', trim($a[3]));
foreach ($b as $c) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "trade_name", str_replace(array("'", "\""), array("\\\\'", ""), $c)));
}
parent::addRDF(parent::describeProperty(parent::getVoc() . "trade_name", "Relationship between a PharmGKB drug and a trade name"));
}
if (trim($a[4])) {
// Brand Mixtures
// Benzyl benzoate 99+ %,"Dermadex Crm (Benzoic Acid + Benzyl Benzoate + Lindane + Salicylic Acid + Zinc Oxide + Zinc Undecylenate)",
$b = explode(',', trim($a[4]));
foreach ($b as $c) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "brand_mixture", str_replace(array("'", "\""), array("\\\\'", ""), $c)));
}
parent::addRDF(parent::describeProperty(parent::getVoc() . "brand_mixture", "Relationship between a PharmGKB drug and a brand mixture"));
}
if (trim($a[5])) {
// Type
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "drug_class", str_replace(array("'", "\""), array("\\\\'", ""), $a[5])) . parent::describeProperty(parent::getVoc() . "drug_class", "Relationship between a PharmGKB drug and its drug class"));
}
if (trim($a[6])) {
// Cross References
// drugBank:DB00789,keggDrug:D01707,pubChemCompound:55466,pubChemSubstance:192903,url:http://en.wikipedia.org/wiki/Gadopentetate_dimeglumine
$b = explode(',', trim(str_replace('"', '', $a[6])));
foreach ($b as $c) {
$this->getRegistry()->parseQName($c, $ns, $id1);
$ns = str_replace(array('"', ' '), '', $ns);
$ns = str_replace(array('keggcompound', 'keggdrug', 'drugbank', 'uniprotkb', 'clinicaltrials.gov', 'drugsproductdatabase(dpd)', 'nationaldrugcodedirectory', 'therapeutictargetsdatabase', 'fdadruglabelatdailymed'), array('kegg', 'kegg', 'drugbank', 'uniprot', 'clinicaltrials', 'dpd', 'ndc', 'ttd', 'dailymed'), strtolower(str_replace('"', '', $ns)));
if ($ns == "url") {
parent::addRDF(parent::QQuadO_URL($id, "rdfs:seeAlso", $id));
} else {
parent::addRDF(parent::triplify($id, parent::getVoc() . "x-" . $ns, $ns . ":" . $id1));
}
}
}
if (trim($a[9])) {
// External Vocabulary
// ATC:H01AC(Somatropin and somatropin agonists),ATC:V04CD(Tests for pituitary function)
// ATC:D07AB(Corticosteroids, moderately potent (group II)) => this is why you don't use brackets and commas as separators.
$b = explode(',', trim($a[9]), 2);
foreach ($b as $c) {
preg_match_all("/ATC:([A-Z0-9]+)\\((.*)\\)\$/", $c, $m);
if (isset($m[1][0])) {
$atc = "atc:" . $m[1][0];
parent::addRDF(parent::triplify($id, parent::getVoc() . "x-atc", $atc));
if (!isset($declared[$atc])) {
$declared[$atc] = '';
parent::addRDF(parent::triplifyString($atc, "rdfs:label", $m[2][0]));
}
}
}
}
parent::WriteRDFBufferToWriteFile();
}
}
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();
}
}
