Ejemplo n.º 1
0
 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);
 }
Ejemplo n.º 2
0
 function functional_descriptions()
 {
     while ($l = $this->getReadFile()->read(2000000)) {
         if ($l[0] == "#") {
             continue;
         }
         if (strstr($l, "gene_id")) {
             continue;
         }
         // gene_id public_name molecular_name concise_description provisional_description detailed_description automated_description gene_class_description
         $a = explode("\t", $l);
         if (count($a) != 8) {
             trigger_error("Found one row that only has " . count($a) . " columns, expecting 8", E_USER_ERROR);
             continue;
         }
         $id = parent::getNamespace() . $a[0];
         $label = $a[1] . ($a[2] ? " (" . $a[2] . ")" : "");
         parent::addRDF(parent::describeIndividual($id, $label, parent::getVoc() . "Gene") . parent::describeClass(parent::getVoc() . "Gene", "Wormbase Gene") . parent::triplifyString($id, parent::getVoc() . "concise-description", $a[3]) . parent::triplifyString($id, parent::getVoc() . "provisional-description", $a[4]) . parent::triplifyString($id, parent::getVoc() . "detailed-description", $a[5]) . parent::triplifyString($id, parent::getVoc() . "automated-description", $a[6]) . parent::triplifyString($id, parent::getVoc() . "gene-class-description", trim($a[7])));
         parent::writeRDFBufferToWriteFile();
     }
 }
Ejemplo n.º 3
0
 public function makeAddress($address)
 {
     if ($address == null) {
         return null;
     }
     $address_uri = parent::getRes() . md5($address->asXML());
     parent::addRDF(parent::describeIndividual($address_uri, "address", parent::getVoc() . "Address") . parent::describeClass(parent::getVoc() . "Address", "Address") . parent::triplifyString($address_uri, parent::getVoc() . "city", $this->makeDescription($this->getString('./city', $address), "City")) . parent::triplifyString($address_uri, parent::getVoc() . "state", $this->makeDescription($this->getString('./state', $address), "State")) . parent::triplifyString($address_uri, parent::getVoc() . "zip", $this->makeDescription($this->getString('./zip', $address), "ZipCode")) . parent::triplifyString($address_uri, parent::getVoc() . "country", $this->makeDescription($this->getString('./country', $address), "Country")));
     return $address_uri;
 }
Ejemplo n.º 4
0
 function product($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();
     }
 }
Ejemplo n.º 5
0
 function process()
 {
     $refseq_record_str = "";
     while ($aLine = $this->getReadFile()->Read(40960)) {
         preg_match("/^\\/\\/\$/", $aLine, $matches);
         if (!count($matches)) {
             preg_match("/^\n\$/", $aLine, $matches);
             if (count($matches) == 0) {
                 $refseq_record_str .= $aLine . PHP_EOL;
             }
             continue;
         } else {
             //now remove the header if it is there
             $refseq_record_str = $this->removeHeader($refseq_record_str);
             $sectionsRaw = $this->parseGenbankRaw($refseq_record_str);
             /**
              * SECTIONS being parsed:
              * locus, definition, accession, version, keywords, source
              * features
              **/
             //get the locus section
             $locus = $this->retrieveSections("LOCUS", $sectionsRaw);
             $parsed_locus_arr = $this->parseLocus($locus);
             //get the definition
             $definition = $this->retrieveSections("DEFINITION", $sectionsRaw);
             $parsed_definition_arr = $this->parseDefinition($definition);
             //get the accession
             $accessions = $this->retrieveSections("ACCESSION", $sectionsRaw);
             $parsed_accession_arr = $this->parseAccession($accessions);
             //get the version
             $versions = $this->retrieveSections("VERSION", $sectionsRaw);
             $parsed_version_arr = $this->parseVersion($versions);
             //get the keywords
             $keywords = $this->retrieveSections("KEYWORDS", $sectionsRaw);
             $parsed_keyword_arr = $this->parseKeywords($keywords);
             //get the reference section
             $references = $this->retrieveSections("REFERENCE", $sectionsRaw);
             $parsed_refs_arr = $this->parseReferences($references);
             //get the source section
             $source = $this->retrieveSections("SOURCE", $sectionsRaw);
             $parsed_source_arr = $this->parseSource($source);
             //get the features
             $features = $this->retrieveSections("FEATURES", $sectionsRaw);
             $parsed_features_arr = $this->parseFeatures($features);
             //lets make some rdf
             $refseq_res = $this->getNamespace() . $parsed_version_arr['versioned_accession'];
             $refseq_label = utf8_encode(htmlspecialchars($parsed_definition_arr[0]));
             parent::AddRDF(parent::describeIndividual($refseq_res, $refseq_label, $this->getVoc() . 'refseq-record') . parent::triplifyString($refseq_res, $this->getVoc() . 'sequence-length', $parsed_locus_arr[0]['sequence_length']) . parent::triplifyString($refseq_res, $this->getVoc() . 'chromosome-shape', $parsed_locus_arr[0]['chromosome_shape']) . parent::triplifyString($refseq_res, $this->getVoc() . 'date-of-entry', $parsed_locus_arr[0]['date']) . parent::triplifyString($refseq_res, $this->getVoc() . 'source', utf8_encode($parsed_source_arr[0])) . parent::triplify($refseq_res, $this->getVoc() . 'fasta-seq', 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?sendto=on&db=nucest&dopt=fasta&val=' . $parsed_version_arr['gi']) . parent::triplify('https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?sendto=on&db=nucest&dopt=fasta&val=' . $parsed_version_arr['gi'], "rdf:type", $this->getVoc() . 'fasta-sequence'));
             //add the features to the rdf
             foreach ($parsed_features_arr as $aFeature) {
                 $type = $aFeature['type'];
                 $feat_desc = $this->getFeatures($type);
                 $label = $type;
                 $def = '';
                 if (isset($feat_desc['definition'])) {
                     $def = preg_replace('/\\s\\s*/', ' ', $feat_desc['definition']);
                 }
                 $comment = null;
                 //					$value = $aFeature['value'];
                 $value = str_replace("UniProtKB/Swiss-Prot", "UniProt", $aFeature['value']);
                 // imperfect solution.
                 $value_arr = explode("/", $value);
                 $location = preg_replace('/\\n/', '', $value_arr[0]);
                 $class_id = parent::getVoc() . md5($type);
                 $feat_res = parent::getRes() . md5($type . $location . $refseq_res);
                 $feat_label = utf8_encode($type . " " . $location . " for " . $refseq_res);
                 if (isset($feat_desc['comment'])) {
                     $comment = $feat_desc['comment'];
                     $comment = preg_replace('/\\s\\s*/', ' ', $comment);
                     $label .= " " . $comment;
                 }
                 parent::AddRDF(parent::describeClass($class_id, $label, parent::getVoc() . "Feature", $label, $def) . parent::describeIndividual($feat_res, $feat_label, $class_id) . parent::triplify($refseq_res, $this->getVoc() . "has-feature", $feat_res));
                 foreach ($value_arr as $aL) {
                     //check if aL has an equals in it
                     $p = "/(\\S+)\\=(.*)/";
                     preg_match($p, $aL, $m);
                     if (count($m)) {
                         if ($m[1] == "db_xref") {
                             parent::AddRDF(parent::triplify($feat_res, "rdfs:seeAlso", str_replace("\"", "", $m[2])));
                         } else {
                             parent::AddRDF(parent::triplifyString($feat_res, $this->getVoc() . $m[1], utf8_encode(str_replace("\"", "", $m[2]))));
                         }
                     }
                 }
             }
             //add the accession
             foreach ($parsed_accession_arr[0] as $acc) {
                 parent::AddRDF(parent::triplifyString($refseq_res, $this->getVoc() . "accession", $acc));
             }
             //versioned accession
             if (isset($parsed_version_arr['versioned_accession'])) {
                 parent::AddRDF(parent::triplifyString($refseq_res, $this->getVoc() . "versioned-accession", $parsed_version_arr['versioned_accession']));
             }
             //keywords
             foreach ($parsed_keyword_arr as $akw) {
                 parent::AddRDF(parent::triplifyString($refseq_res, $this->getVoc() . "keyword", $akw));
             }
             //references
             foreach ($parsed_refs_arr as $aRef) {
                 $r = rand();
                 $ref_res = $this->getRes() . md5($r);
                 $ref_label = "reference for " . $refseq_res;
                 if (isset($aRef['TITLE'])) {
                     parent::AddRDF(parent::describeIndividual($ref_res, $ref_label, $this->getVoc() . "reference") . parent::triplifyString($ref_res, $this->getVoc() . "title", $aRef['TITLE']));
                 }
                 if (isset($aRef['PUBMED'])) {
                     parent::AddRDF(parent::triplify($ref_res, $this->getVoc() . "x-pubmed", 'pubmed:' . $aRef['PUBMED']));
                 }
                 if (isset($aRef['AUTHORS'])) {
                     parent::AddRDF(parent::triplifyString($ref_res, $this->getVoc() . "authors", $aRef['AUTHORS']));
                 }
                 if (isset($aRef['COORDINATES'])) {
                     parent::AddRDF(parent::triplify($refseq_res, $this->getVoc() . "reference", $ref_res) . parent::triplifyString($ref_res, $this->getVoc() . "coordinates", $aRef['COORDINATES']) . parent::triplifyString($ref_res, $this->getVoc() . "citation", $aRef['JOURNAL']));
                 } else {
                     parent::AddRDF(parent::triplify($refseq_res, $this->getVoc() . "reference", $ref_res) . parent::triplifyString($ref_res, $this->getVoc() . "citation", $aRef['JOURNAL']));
                 }
             }
             $refseq_record_str = "";
             $this->WriteRDFBufferToWriteFile();
             continue;
         }
     }
     //while
 }
Ejemplo n.º 6
0
 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();
     }
 }
Ejemplo n.º 7
0
 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", $a[7]));
     }
     parent::writeRDFBufferToWriteFile();
 }
Ejemplo n.º 8
0
 function ParseEntry($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
 }
Ejemplo n.º 9
0
 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", $icrogidb) . parent::describeClass(parent::getVoc() . "Taxon-Sequence-Similar-Group", "Taxon + Sequence Similar Group"));
         parent::writeRDFBufferToWriteFile();
     }
 }
Ejemplo n.º 10
0
 function psiblast()
 {
     while ($l = $this->GetReadFile()->Read(2048)) {
         $a = explode("\t", trim($l));
         $id1 = $a[0];
         $id2 = $a[7];
         $id = "aln_{$id1_}{$id2}";
         $this->AddRDF(parent::describeIndividual($this->getRes() . $id, "psiblast alignment between {$id1} and {$id2}", $this->getVoc() . "PSI-BLAST-Alignment") . parent::describeClass($this->getVoc() . "PSI-BLAST-Alignment", "PSI-Blast Alignment") . parent::triplify($this->getRes() . $id, $this->getVoc() . "query", $this->getNamespace() . $id1) . parent::triplify($this->getRes() . $id, $this->getVoc() . "target", $this->getNamespace() . $id2) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "query-start", $a[1]) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "query-stop", $a[2]) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "target-start", $a[3]) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "target-stop", $a[4]) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "percent-aligned", $a[5]) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "score", $a[6]) . parent::triplifyString($this->getRes() . $id, $this->getVoc() . "is-encoded-by", "taxon:" . $a[8]) . parent::describeProperty($this->getVoc() . "target-start", "Relationship between an SGD sequence alignment and its target sequence start position") . parent::describeProperty($this->getVoc() . "target-stop", "Relationship between an SGD sequence alignment and its target sequence stop position") . parent::describeProperty($this->getVoc() . "score", "Relationship between an SGD sequence alignment and its score") . parent::describeProperty($this->getVoc() . "percent-aligned", "Relationship between an SGD sequence alignment and its percent-aligned value") . parent::describeProperty($this->getVoc() . "is-encoded-by", "Relationship between an SGD sequence alignment and the taxon the aligned sequences are encoded by"));
         parent::writeRDFBufferToWriteFile();
     }
     //while
     return TRUE;
 }
Ejemplo n.º 11
0
 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));
                 }
             }
         }
         $this->writeRDFBufferToWriteFile();
     }
     //while
 }
Ejemplo n.º 12
0
 function parseDrugEntry(&$xml)
 {
     $declared = null;
     // a list of all the entities declared
     $counter = 1;
     $x = $xml->GetXMLRoot();
     $dbid = (string) $x->{"drugbank-id"};
     $did = "drugbank:" . $dbid;
     $name = (string) $x->name;
     $type = ucfirst((string) str_replace(" ", "-", $x->attributes()->type));
     $type_label = ucfirst($x->attributes()->type);
     $description = null;
     if (isset($this->id_list)) {
         if (!isset($this->id_list[$dbid])) {
             return;
         }
         unset($this->id_list[$dbid]);
     }
     echo "Processing {$dbid}" . PHP_EOL;
     if (isset($x->description) && $x->description != '') {
         $description = trim((string) $x->description);
     }
     parent::addRDF(parent::describeIndividual($did, $name, parent::getVoc() . "Drug", $name, $description) . parent::describeClass(parent::getVoc() . "Drug", "Drug") . parent::triplify($did, "owl:sameAs", "http://identifiers.org/drugbank/" . $dbid) . parent::triplify($did, "rdfs:seeAlso", "http://www.drugbank.ca/drugs/" . $dbid) . parent::triplify($did, "rdf:type", parent::getVoc() . $type) . parent::describeClass(parent::getVoc() . $type, $type_label));
     foreach ($x->{'drugbank-id'} as $id) {
         parent::addRDF(parent::triplifyString($did, parent::getVoc() . "drugbank-id", $id));
     }
     if (isset($x->{'cas-number'})) {
         parent::addRDF(parent::triplify($did, parent::getVoc() . "x-cas", "cas:" . $x->{'cas-number'}));
     }
     $literals = array("indication", "pharmacodynamics", "mechanism-of-action", "toxicity", "biotransformation", "absorption", "half-life", "protein-binding", "route-of-elimination", "volume-of-distribution", "clearance");
     foreach ($literals as $l) {
         if (isset($x->{$l}) and $x->{$l} != '') {
             $lid = parent::getRes() . md5($l . $x->{$l});
             parent::addRDF(parent::describeIndividual($lid, "{$l} for {$did}", parent::getVoc() . ucfirst($l), "{$l} for {$did}", $x->{$l}) . parent::describeClass(parent::getVoc() . ucfirst($l), ucfirst(str_replace("-", " ", $l))) . parent::triplify($did, parent::getVoc() . $l, $lid));
         }
     }
     // TODO:: Replace the next two lines
     $this->AddList($x, $did, "groups", "group", parent::getVoc() . "group");
     $this->AddList($x, $did, "categories", "category", parent::getVoc() . "category");
     if (isset($x->classification)) {
         foreach ($x->classification->children() as $k => $v) {
             $cid = parent::getRes() . md5($v);
             parent::addRDF(parent::describeIndividual($cid, $v, parent::getVoc() . "Drug-Classification-Category") . parent::describeClass(parent::getVoc() . "Drug-Classification-Category", "Drug Classification Category") . parent::triplify($did, parent::getVoc() . "drug-classification-category", $cid));
         }
     }
     $this->addLinkedResource($x, $did, 'atc-codes', 'atc-code', 'atc');
     $this->addLinkedResource($x, $did, 'ahfs-codes', 'ahfs-code', 'ahfs');
     // taxonomy
     $this->AddText($x, $did, "taxonomy", "kingdom", parent::getVoc() . "kingdom");
     // substructures
     $this->AddText($x, $did, "taxonomy", "substructures", parent::getVoc() . "substructure", "substructure");
     // synonyms
     $this->AddCategory($x, $did, "synonyms", "synonym", parent::getVoc() . "synonym");
     // brand names
     $this->AddCategory($x, $did, "international-brands", "international-brand", parent::getVoc() . "brand");
     // salt
     if (isset($x->salts->salt)) {
         foreach ($x->salts->salt as $s) {
             $sid = parent::getPrefix() . ':' . $s->{'drugbank-id'};
             parent::addRDF(parent::describeIndividual($sid, $s->name, parent::getVoc() . "Salt") . parent::describeClass(parent::getVoc() . "Salt", "Salt") . parent::triplify($did, parent::getVoc() . "salt", $sid) . parent::triplify($sid, parent::getVoc() . "x-cas", "cas:" . $s->{'cas-number'}) . parent::triplify($sid, parent::getVoc() . "x-inchikey", "inchikey:" . $s->{'inchikey'}));
         }
     }
     // mixtures
     // <mixtures><mixture><name>Cauterex</name><ingredients>dornase alfa + fibrinolysin + gentamicin sulfate</ingredients></mixture>
     if (isset($x->mixtures)) {
         $id = 0;
         foreach ($x->mixtures->mixture as $item) {
             if (isset($item)) {
                 $o = $item;
                 $mid = parent::getRes() . str_replace(" ", "-", $o->name[0]);
                 parent::addRDF(parent::triplify($did, parent::getVoc() . "mixture", $mid) . parent::describeIndividual($mid, $o->name[0], parent::getVoc() . "Mixture") . parent::describeClass(parent::getVoc() . "Mixture", "mixture") . parent::triplifyString($mid, $this->getVoc() . "ingredients", "" . $o->ingredients[0]));
                 $a = explode(" + ", $o->ingredients[0]);
                 foreach ($a as $b) {
                     $b = trim($b);
                     $iid = parent::getRes() . str_replace(" ", "-", $b);
                     parent::addRDF(parent::describeClass($iid, $b, parent::getVoc() . "Ingredient") . parent::describeClass(parent::getVoc() . "Ingredient", "Ingredient") . parent::triplify($mid, parent::getVoc() . "ingredient", $iid));
                 }
             }
         }
     }
     // packagers
     // <packagers><packager><name>Cardinal Health</name><url>http://www.cardinal.com</url></packager>
     if (isset($x->packagers)) {
         foreach ($x->packagers as $items) {
             if (isset($items->packager)) {
                 foreach ($items->packager as $item) {
                     $pid = parent::getRes() . md5($item->name);
                     parent::addRDF(parent::triplify($did, parent::getVoc() . "packager", $pid));
                     if (!isset($defined[$pid])) {
                         $defined[$pid] = '';
                         parent::addRDF(parent::describe($pid, "" . $item->name[0]));
                         if (strstr($item->url, "http://") && $item->url != "http://BASF Corp.") {
                             parent::addRDF($this->triplify($pid, "rdfs:seeAlso", "" . $item->url[0]));
                         }
                     }
                 }
             }
         }
     }
     // manufacturers
     $this->AddText($x, $did, "manufacturers", "manufacturer", parent::getVoc() . "manufacturer");
     // @TODO RESOURCE
     // prices
     if (isset($x->prices->price)) {
         foreach ($x->prices->price as $product) {
             $pid = parent::getRes() . md5($product->description);
             parent::addRDF(parent::describeIndividual($pid, $product->description, parent::getVoc() . "Pharmaceutical", $product->description) . parent::describeClass(parent::getVoc() . "Pharmaceutical", "pharmaceutical") . parent::triplifyString($pid, parent::getVoc() . "price", "" . $product->cost, "xsd:float") . parent::triplify($did, parent::getVoc() . "product", $pid));
             $uid = parent::getVoc() . md5($product->unit);
             parent::addRDF(parent::describeIndividual($uid, $product->unit, parent::getVoc() . "Unit", $product->unit) . parent::describeClass(parent::getVoc() . "Unit", "unit") . parent::triplify($pid, parent::getVoc() . "form", $uid));
         }
     }
     // dosages <dosages><dosage><form>Powder, for solution</form><route>Intravenous</route><strength></strength></dosage>
     if (isset($x->dosages->dosage)) {
         foreach ($x->dosages->dosage as $dosage) {
             $id = parent::getRes() . md5($dosage->strength . $dosage->form . $dosage->route);
             $label = ($dosage->strength != '' ? $dosage->strength . " " : "") . $dosage->form . " form with " . $dosage->route . " route";
             parent::addRDF(parent::describeIndividual($id, $label, parent::getVoc() . "Dosage") . parent::describeClass(parent::getVoc() . "Dosage", "Dosage") . parent::triplify($did, parent::getVoc() . "dosage", $id));
             $rid = parent::getVoc() . md5($dosage->route);
             $this->typify($id, $rid, "Route", "" . $dosage->route);
             $fid = parent::getVoc() . md5($dosage->form);
             $this->typify($id, $fid, "Form", "" . $dosage->form);
             if ($dosage->strength != '') {
                 parent::addRDF(parent::triplifyString($id, parent::getVoc() . "strength", $dosage->strength));
             }
         }
     }
     // experimental-properties
     $props = array("experimental-properties", "calculated-properties");
     foreach ($props as $prop) {
         $subtype = substr($prop, 0, strpos("-", $prop));
         if (isset($x->{$prop})) {
             foreach ($x->{$prop} as $properties) {
                 foreach ($properties as $property) {
                     $type = (string) $property->kind;
                     $value = (string) $property->value;
                     $type_uri = parent::getVoc() . ucfirst(str_replace(" ", "-", $type));
                     $id = parent::getRes() . $prop . "-" . $dbid . "-" . $counter++;
                     $label = $property->kind . ": {$value}" . ($property->source == '' ? '' : " from " . $property->source);
                     parent::addRDF(parent::describeIndividual($id, $label, $type_uri) . parent::describeClass($type_uri, $type, parent::getVoc() . ucfirst($prop)) . parent::describeClass(parent::getVoc() . ucfirst($prop), str_replace("-", " ", $prop)) . parent::triplifyString($id, $this->getVoc() . "value", $value) . parent::triplify($did, $this->getVoc() . $prop, $id));
                     // Source
                     if (isset($property->source)) {
                         foreach ($property->source as $source) {
                             $s = (string) $source;
                             if ($s == '') {
                                 continue;
                             }
                             $sid = parent::getRes() . md5($s);
                             parent::addRDF(parent::describeIndividual($sid, $s, parent::getVoc() . "Source") . parent::describeClass(parent::getVoc() . "Source", "Source") . parent::triplify($id, parent::getVoc() . "source", $sid));
                         }
                     }
                 }
             }
         }
     }
     // identifiers
     // <patents><patent><number>RE40183</number><country>United States</country><approved>1996-04-09</approved>        <expires>2016-04-09</expires>
     if (isset($x->patents->patent)) {
         foreach ($x->patents->patent as $patent) {
             $id = "uspto:" . $patent->number;
             parent::addRDF(parent::triplify($did, $this->getVoc() . "patent", $id) . parent::describeIndividual($id, $patent->country . " patent " . $patent->number, $this->getVoc() . "Patent") . parent::describeClass(parent::getVoc() . "Patent", "patent") . parent::triplifyString($id, $this->getVoc() . "approved", "" . $patent->approved) . parent::triplifyString($id, $this->getVoc() . "expires", "" . $patent->expires));
             $cid = parent::getRes() . md5($patent->country);
             $this->typify($id, $cid, "Country", "" . $patent->country);
         }
     }
     // partners
     $partners = array('target', 'enzyme', 'transporter', 'carrier');
     foreach ($partners as $partner) {
         $plural = $partner . 's';
         if (isset($x->{$plural})) {
             foreach ($x->{$plural} as $list) {
                 foreach ($list->{$partner} as $item) {
                     $this->parsePartnerRelation($did, $item, $partner);
                     parent::writeRDFBufferToWriteFile();
                 }
             }
         }
     }
     // drug-interactions
     $y = (int) substr($dbid, 2);
     if (isset($x->{"drug-interactions"})) {
         foreach ($x->{"drug-interactions"} as $ddis) {
             foreach ($ddis->{"drug-interaction"} as $ddi) {
                 $dbid2 = $ddi->{'drugbank-id'};
                 if ($dbid < $dbid2) {
                     // don't repeat
                     $ddi_id = parent::getRes() . $dbid . "_" . $dbid2;
                     parent::addRDF(parent::triplify("drugbank:" . $dbid, parent::getVoc() . "ddi-interactor-in", "" . $ddi_id) . parent::triplify("drugbank:" . $dbid2, parent::getVoc() . "ddi-interactor-in", "" . $ddi_id) . parent::describeIndividual($ddi_id, "DDI between {$name} and " . $ddi->name . " - " . $ddi->description, parent::getVoc() . "Drug-Drug-Interaction") . parent::describeClass(parent::getVoc() . "Drug-Drug-Interaction", "drug-drug interaction"));
                 }
             }
         }
     }
     // food-interactions
     $this->AddText($x, $did, "food-interactions", "food-interaction", parent::getVoc() . "food-interaction");
     // affected-organisms
     $this->AddCategory($x, $did, "affected-organisms", "affected-organism", parent::getVoc() . "affected-organism");
     //  <external-identifiers>
     if (isset($x->{"external-identifiers"})) {
         foreach ($x->{"external-identifiers"} as $objs) {
             foreach ($objs as $obj) {
                 $ns = $this->NSMap($obj->resource);
                 $id = $obj->identifier;
                 if ($ns == "genecards") {
                     $id = str_replace(array(" "), array("_"), $id);
                 }
                 parent::addRDF(parent::triplify($did, parent::getVoc() . "x-{$ns}", "{$ns}:{$id}"));
                 if ($ns == "pubchemcompound") {
                     parent::addRDF(parent::triplify("{$ns}:{$id}", "skos:exactMatch", "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/{$id}"));
                 }
             }
         }
     }
     // <external-links>
     if (isset($x->{"external-links"})) {
         foreach ($x->{"external-links"}->{'external-link'} as $el) {
             if (strpos($el->url, 'http') !== false) {
                 parent::addRDF(parent::triplify($did, "rdfs:seeAlso", "" . $el->url));
             }
         }
     }
     parent::writeRDFBufferToWriteFile();
 }
Ejemplo n.º 13
0
 function genes($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);
 }
Ejemplo n.º 14
0
 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", $freq_upper)));
         parent::setCheckpoint('record');
     }
     parent::setCheckpoint('file');
 }
Ejemplo n.º 15
0
 function addDate($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"));
 }
Ejemplo n.º 16
0
 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="--&gt;"/>
             	</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;
 }
Ejemplo n.º 17
0
 private function process()
 {
     //read the file into a string
     $xml_str = '';
     while ($l = $this->getReadFile()->Read(4096)) {
         $xml_str .= $l;
     }
     $xml = new SimpleXMLElement($xml_str);
     foreach ($xml->{'sts'} as $sts) {
         $uid = (string) $sts->uid;
         $uid_res = $this->getNamespace() . $uid;
         $name = (string) $sts->name;
         $uid_label = $name;
         parent::AddRDF(parent::describeIndividual($uid_res, $uid_label, $this->getVoc() . "sequence_tagged_site"));
         //split by semicolon
         $genbank_accession_arr = explode(";", (string) $sts->gbacc);
         foreach ($genbank_accession_arr as $gb) {
             parent::AddRDF(parent::triplify($uid_res, $this->getVoc() . 'x-genbank', 'genbank:' . $gb));
         }
         //split by semicolon
         $gi_arr = explode(';', (string) $sts->gi);
         foreach ($gi_arr as $gi) {
             parent::AddRDF(parent::triplify($uid_res, $this->getVoc() . 'x-gi', 'gi:' . $gi));
         }
         $links = (string) $sts->links;
         if (isset($links)) {
             parent::AddRDF(parent::triplifyString($uid_res, $this->getVoc() . 'links', utf8_encode($links)));
         }
         $forward_primer = (string) $sts->pcrfor;
         if (isset($forward_primer)) {
             parent::AddRDF(parent::triplifyString($uid_res, $this->getVoc() . 'forward-primer', $forward_primer));
         }
         $reverse_primer = (string) $sts->pcrrev;
         if (isset($reverse_primer)) {
             parent::AddRDF(parent::triplifyString($uid_res, $this->getVoc() . 'reverse-primer', $reverse_primer));
         }
         $epcr_summary = (string) $sts->EPCR_Summary;
         if (isset($epcr_summary)) {
             parent::AddRDF(parent::triplifyString($uid_res, $this->getVoc() . 'epcr-summary', $epcr_summary));
         }
         $dbsts = (string) $sts->dbsts;
         if (isset($dbsts)) {
             parent::AddRDF(parent::triplifyString($uid_res, $this->getVoc() . 'dbsts', $dbsts));
         }
         foreach ($sts->{'Map_Gene_Summary_List'} as $gsl) {
             foreach ($gsl->{'Map_Gene_Summary'} as $mgs) {
                 $r = rand();
                 $org = (string) $mgs->Org;
                 $taxid = (string) $mgs->taxid;
                 $chromosome = (string) $mgs->Chr;
                 $locus = (string) $mgs->Locus;
                 $polymorphic = (string) $mgs->Polymorphic;
                 $lbl = "map gene summary for :" . $org . " " . $taxid;
                 $u_res = $this->getRes() . md5($r . $org);
                 parent::AddRDF(parent::describeIndividual($u_res, $lbl, $this->getVoc() . "map-gene-summary") . parent::triplify($uid_res, $this->getVoc() . "has-map-gene-summary", $u_res));
                 if (isset($polymorphic)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "polymorphic", $polymorphic));
                 }
                 if (isset($locus)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "locus", $locus));
                 }
                 if (isset($chromosome)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "chromosome", $chromosome));
                 }
                 if (isset($taxid)) {
                     parent::AddRDF(parent::triplify($u_res, $this->getVoc() . "x-taxonomy", "taxon:" . $taxid));
                 }
                 if (isset($org)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "org-name", $org));
                 }
             }
         }
         foreach ($sts->{'org'} as $anOrg) {
             $r = rand();
             $taxname = (string) $anOrg->taxname;
             $taxid = (string) $anOrg->taxid;
             $name = (string) $anOrg->name;
             $keyword = (string) $anOrg->keyword;
             $alias = (string) $anOrg->alias;
             $polymorphic = (string) $anOrg->polymorphic;
             $dseg = (string) $anOrg->dseg;
             $gdb = (string) $anOrg->gdb;
             $rgd = (string) $anOrg->rgd;
             $mgd = (string) $anOrg->mgd;
             $zfin = (string) $anOrg->zfin;
             $pcrsize = (string) $anOrg->pcrsize;
             $dbsnp = (string) $anOrg->dbsnp;
             $warn = (string) $anOrg->warn;
             $wloc = (string) $anOrg->wloc;
             $wmap = (string) $anOrg->wmap;
             $wctg = (string) $anOrg->wctg;
             $wdrift = (string) $anOrg->wdrift;
             $mapview = (string) $anOrg->mapview;
             $u_res = $this->getRes() . md5($r . $taxname . $taxid);
             $u_lbl = "org entry for " . $taxname . " " . $taxid;
             parent::AddRDF(parent::describeIndividual($u_res, $u_lbl, $this->getVoc() . "organism") . parent::triplify($uid_res, $this->getVoc() . "has-organism", $u_res));
             if (isset($mapview) && strlen($mapview)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "mapview", $mapview));
             }
             if (isset($wdrift) && strlen($wdrift)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "wdrift", $wdrift));
             }
             if (isset($wctg) && strlen($wctg)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "wctg", $wctg));
             }
             if (isset($wmap) && strlen($wmap)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "wmap", $wmap));
             }
             if (isset($wloc) && strlen($wloc)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "wloc", $wloc));
             }
             if (isset($warn) && strlen($warn)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "warn", $warn));
             }
             if (isset($taxname) && strlen($taxname)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "taxname", $taxname));
             }
             if (isset($name)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "name", $name));
             }
             if (isset($keyword) && strlen($keyword)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "keyword", $keyword));
             }
             if (isset($alias) && strlen($alias)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "alias", $alias));
             }
             if (isset($polymorphic) && strlen($polymorphic)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "polymorphic", $polymorphic));
             }
             if (isset($dseg) && strlen($dseg)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "dseg", $dseg));
             }
             if (isset($gdb) && strlen($gdb)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "gdb", $gdb));
             }
             if (isset($rgd) && strlen($rgd)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "rgd", $rgd));
             }
             if (isset($mgd) && strlen($mgd)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "mgd", $mgd));
             }
             if (isset($zfin) && strlen($zfin)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "zfin", $zfin));
             }
             if (isset($pcrsize) && strlen($pcrsize)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "pcrsize", $pcrsize));
             }
             if (isset($dbsnp) && strlen($dbsnp)) {
                 parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . "dbsnp", $dbsnp));
             }
             foreach ($anOrg->{'rhdb'} as $rh) {
                 $id = (string) $rh->id;
                 $panel = (string) $rh->panel;
                 $r = rand();
                 $u_res = $this->getRes() . md5($r . $id . $panel);
                 $u_label = "rhdb for " . $id . " " . $panel;
                 parent::AddRDF(parent::describeIndividual($u_res, $u_label, $this->getVoc() . "rhdb") . parent::triplify($uid_res, $this->getVoc() . 'has-rhdb', $u_res) . parent::triplifyString($u_res, $this->getVoc() . 'id', $id) . parent::triplifyString($u_res, $this->getVoc() . 'panel', $panel));
             }
             foreach ($anOrg->{'unigene'} as $u) {
                 $ugid = (string) $u->unigene;
                 $ugname = (string) $u->ugname;
                 $r = rand();
                 $u_res = $this->getRes() . md5($r . $ugid . $ugname);
                 $u_label = "unigene for " . $ugid . " " . $ugname;
                 if (strlen($ugid) > 0 && strlen($ugname) > 0) {
                     parent::AddRDF(parent::describeIndividual($u_res, $u_label, $this->getVoc() . "unigene") . parent::triplify($uid_res, $this->getVoc() . 'has-unigene', $u_res) . parent::triplify($u_res, $this->getVoc() . 'x-unigene', $ugid) . parent::triplifyString($u_res, $this->getVoc() . 'ugname', $ugname));
                 }
             }
             foreach ($anOrg->{'locus'} as $aLocus) {
                 $lid = (string) $aLocus->lid;
                 $lsymbol = (string) $aLocus->lsymbol;
                 $lname = (string) $aLocus->lname;
                 $lcyto = (string) $aLocus->lcyto;
                 $ltype = (string) $aLocus->ltype;
                 $r = rand();
                 $u_res = $this->getRes() . md5($r . $lid);
                 $u_label = "locus for " . $lid . " " . $lname . " " . $lsymbol;
                 parent::AddRDF(parent::describeIndividual($u_res, $u_label, $this->getVoc() . "locus") . parent::triplify($uid_res, $this->getVoc() . 'has-locus', $u_res));
                 if (isset($lcyto) && strlen($lcyto)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'cyto', $lcyto));
                 }
                 if (isset($ltype) && strlen($ltype)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'ltype', $ltype));
                 }
                 if (isset($lname) && strlen($lname)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'name', $lname));
                 }
             }
             foreach ($anOrg->{'mappos'} as $aMapPos) {
                 $map = (string) $aMapPos->map;
                 $marker = (string) $aMapPos->marker;
                 $chr = (string) $aMapPos->chr;
                 $chrpos = (string) $aMapPos->chrpos;
                 $ctg = (string) $aMapPos->ctg;
                 $ctgpos = (string) $aMapPos->ctgpos;
                 $coord = (string) $aMapPos->coord;
                 $lod = (string) $aMapPos->lod;
                 $bin = (string) $aMapPos->bin;
                 $binpos = (string) $aMapPos->binpos;
                 $het = (string) $aMapPos->het;
                 $lab = (string) $aMapPos->lab;
                 $unit = (string) $aMapPos->unit;
                 $r = rand();
                 $u_res = $this->getRes() . md5($r . $map);
                 $u_label = "locus for " . $map . " " . $marker . " " . $chr;
                 parent::AddRDF(parent::describeIndividual($u_res, $u_label, $this->getVoc() . "mappos") . parent::triplify($uid_res, $this->getVoc() . 'has-mappos', $u_res));
                 if (isset($unit) && strlen($unit)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'unit', $unit));
                 }
                 if (isset($lab) && strlen($lab)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'lab', $lab));
                 }
                 if (isset($het) && strlen($het)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'het', $het));
                 }
                 if (isset($binpos) && strlen($binpos)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'binpos', $binpos));
                 }
                 if (isset($bin) && strlen($bin)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'bin', $bin));
                 }
                 if (isset($lod) && strlen($lod)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'lod', $lod));
                 }
                 if (isset($coord) && strlen($coord)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'coord', $coord));
                 }
                 if (isset($ctgpos) && strlen($ctgpos)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'ctgpos', $ctgpos));
                 }
                 if (isset($ctg) && strlen($ctg)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'ctg', $ctg));
                 }
                 if (isset($chrpos) && strlen($chrpos)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'chrpos', $chrpos));
                 }
                 if (isset($chr) && strlen($chr)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'chr', $chr));
                 }
                 if (isset($marker) && strlen($marker)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'marker', $marker));
                 }
             }
             foreach ($anOrg->{'epcr'} as $aEpcr) {
                 $seqType = (string) $aEpcr->seqtype;
                 $acc = (string) $aEpcr->acc;
                 $gi = (string) $aEpcr->gi;
                 $pos1 = (string) $aEpcr->pos1;
                 $pos2 = (string) $aEpcr->pos2;
                 $epcr_size = (string) $aEpcr->epcrsize;
                 $r = rand();
                 $u_res = $this->getRes() . md5($r . $gi . $pos1);
                 $u_label = "epcr for " . $pos1 . " " . $pos2;
                 parent::AddRDF(parent::describeIndividual($u_res, $u_label, $this->getVoc() . "epcr") . parent::triplify($uid_res, $this->getVoc() . 'has-epcr', $u_res));
                 if (isset($seqtype) && strlen($seqtype)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'seqtype', $seqtype));
                 }
                 if (isset($acc) && strlen($acc)) {
                     parent::AddRDF(parent::triplify($u_res, $this->getVoc() . 'x-genbank', 'genbank:' . $acc));
                 }
                 if (isset($gi) && strlen($gi)) {
                     parent::AddRDF(parent::triplify($u_res, $this->getVoc() . 'x-gi', 'gi:' . $gi));
                 }
                 if (isset($pos1) && strlen($pos1)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'pos1', $pos1));
                 }
                 if (isset($pos2) && strlen($pos2)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'pos2', $pos2));
                 }
                 if (isset($epcr_size) && strlen($epcr_size)) {
                     parent::AddRDF(parent::triplifyString($u_res, $this->getVoc() . 'epcr_size', $epcr_size));
                 }
             }
         }
         $this->WriteRDFBufferToWriteFile();
     }
 }
Ejemplo n.º 18
0
 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));
                     }
                 }
             }
         }
         $this->writeRDFBufferToWriteFile();
     }
 }
Ejemplo n.º 19
0
 function Parse($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
         }
         $this->WriteRDFBufferToWriteFile();
     }
 }
Ejemplo n.º 20
0
 function process()
 {
     while ($aLine = $this->GetReadFile()->Read(200000)) {
         $parsed_line = $this->parse_homologene_tab_line($aLine);
         $hid = "homologene:" . $parsed_line["hid"];
         $hid_label = "homologene group " . $parsed_line['hid'];
         parent::AddRDF(parent::describeIndividual($hid, $hid_label, $this->getVoc() . "Homologene-Group") . parent::describeClass($this->getVoc() . "Homologene-Group", "Homologene Group"));
         $geneid = "ncbigene:" . $parsed_line["geneid"];
         $taxid = "taxid:" . $parsed_line["taxid"];
         $gi = "gi:" . $parsed_line["gi"];
         $genesymbol = str_replace("\\", "", $parsed_line["genesymbol"]);
         $refseq = "refseq:" . $parsed_line["refseq"];
         parent::AddRDF(parent::triplify($hid, $this->getVoc() . "x-taxid", $taxid) . parent::describeProperty($this->getVoc() . "x-taxid", "Link to NCBI taxonomy"));
         parent::AddRDF(parent::triplify($hid, $this->getVoc() . "x-ncbigene", $geneid) . parent::describeProperty($this->getVoc() . "x-ncbigene", "Link to NCBI GeneId"));
         parent::AddRDF(parent::triplifyString($hid, $this->getVoc() . "gene-symbol", utf8_encode(htmlspecialchars($genesymbol)), "xsd:string") . parent::describeProperty($this->getVoc() . "gene-symbol", "Link to gene symbol"));
         parent::AddRDF(parent::triplify($hid, $this->getVoc() . "x-gi", $gi) . parent::describeProperty($this->getVoc() . "x-gi", "Link to NCBI GI"));
         parent::AddRDF(parent::triplify($hid, $this->getVoc() . "x-refseq", $refseq) . parent::describeProperty($this->getVoc() . "x-refseq", "Link to NCBI Refseq"));
         $this->WriteRDFBufferToWriteFile();
     }
 }
Ejemplo n.º 21
0
 function process()
 {
     $header = $this->GetReadFile()->Read(200000);
     $header_arr = explode("\t", $header);
     $n = 41;
     $c = count($header_arr);
     if ($c != $n) {
         echo PHP_EOL;
         print_r($header_arr);
         trigger_error("Expected {$n} columns, found {$c} . please update the script", E_USER_ERROR);
         exit;
     }
     while ($l = $this->GetReadFile()->Read(4096)) {
         $fields = explode("\t", $l);
         $id = strtolower($fields[0]);
         $approved_symbol = $fields[1];
         $approved_name = $fields[2];
         $status = $fields[3];
         $locus_type = $fields[4];
         $locus_group = $fields[5];
         $previous_symbols = $fields[6];
         $previous_names = $fields[7];
         $synonyms = $fields[8];
         $name_synonyms = $fields[9];
         $chromosome = $fields[10];
         $date_approved = $fields[11];
         $date_modified = $fields[12];
         $date_symbol_changed = $fields[13];
         $date_name_changed = $fields[14];
         $accession_numbers = $fields[15];
         $enzyme_ids = $fields[16];
         $entrez_gene_id = $fields[17];
         $ensembl_gene_id = $fields[18];
         $mouse_genome_database_id = $fields[19];
         $specialist_database_links = $fields[20];
         $specialist_database_ids = $fields[21];
         $pubmed_ids = $fields[22];
         $refseq_ids = $fields[23];
         $gene_family_tag = $fields[24];
         $gene_family_description = $fields[25];
         $record_type = $fields[26];
         $primary_ids = $fields[27];
         $secondary_ids = $fields[28];
         $ccd_ids = $fields[29];
         $vega_ids = $fields[30];
         $locus_specific_databases = $fields[31];
         $entrez_gene_id_mappeddatasuppliedbyNCBI = $fields[32];
         $omim_id_mappeddatasuppliedbyNCBI = $fields[33];
         $refseq_mappeddatasuppliedbyNCBI = $fields[34];
         $uniprot_id_mappeddatasuppliedbyUniProt = $fields[35];
         $ensembl_id_mappeddatasuppliedbyEnsembl = $fields[36];
         $vega_id_mappeddatasuppliedbyVega = $fields[37];
         $ucsc_id_mappeddatasuppliedbyUCSC = $fields[38];
         $mouse_genome_database_id_mappeddatasuppliedbyMGI = $fields[39];
         $rat_genome_database_id_mappeddatasuppliedbyRGD = $fields[40];
         $id_res = $id;
         $id_label = "Gene Symbol for " . $approved_symbol;
         parent::AddRDF(parent::triplify($id_res, "rdf:type", $this->getVoc() . "Gene-Symbol") . parent::describeIndividual($id_res, $id_label, $this->getVoc() . "Gene-Symbol") . parent::describeClass($this->getVoc() . "Gene-Symbol", "HGNC Official Gene Symbol"));
         if (!empty($approved_symbol)) {
             $s = "hgnc.symbol:" . $approved_symbol;
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "approved-symbol", utf8_encode(htmlspecialchars($approved_symbol))) . parent::describeProperty($this->getVoc() . "approved-symbol", "HGNC approved gene symbol", "The official gene symbol that has been approved by the HGNC and is publicly available. Symbols are approved based on specific HGNC nomenclature guidelines. In the HTML results page this ID links to the HGNC Symbol Report for that gene") . parent::describeIndividual($s, $approved_symbol, parent::getVoc() . "Approved-Gene-Symbol") . parent::describeClass(parent::getVoc() . "Approved-Gene-Symbol", "Approved Gene Symbol") . parent::triplify($id_res, parent::getVoc() . "has-approved-symbol", $s) . parent::triplify($s, parent::getVoc() . "is-approved-symbol-of", $id_res));
         }
         if (!empty($approved_name)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "approved-name", utf8_encode(htmlspecialchars($approved_name))) . parent::describeProperty($this->getVoc() . "approved-name", "HGNC approved name", "The official gene name that has been approved by the HGNC and is publicly available. Names are approved based on specific HGNC nomenclature guidelines."));
         }
         if (!empty($status)) {
             $s = $this->getVoc() . str_replace(" ", "-", $status);
             parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "status", $s) . parent::describeProperty($this->getVoc() . "status", "HGNC status", "Indicates whether the gene is classified as: Approved - these genes have HGNC-approved gene symbols. Entry withdrawn - these previously approved genes are no longer thought to exist. Symbol withdrawn - a previously approved record that has since been merged into a another record.") . parent::describeClass($s, $status, $this->getVoc() . "Status"));
         }
         if (!empty($locus_id)) {
             $locus_res = $this->getRes() . $id . "_LOCUS";
             parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "locus", $locus_res) . parent::triplifyString($locus_res, $this->getVoc() . "locus-type", utf8_encode(htmlspecialchars($locus_type))) . parent::triplifyString($locus_res, $this->getVoc() . "locus-group", utf8_encode(htmlspecialchars($locus_group))) . parent::describeProperty($this->getVoc() . "locus-type", "locus type", "Specifies the type of locus described by the given entry") . parent::describeProperty($this->getVoc() . "locus-group", "locus group", "Groups locus types together into related sets. Below is a list of groups and the locus types within the group"));
         }
         if (!empty($previous_symbols)) {
             $previous_symbols = explode(", ", $previous_symbols);
             foreach ($previous_symbols as $previous_symbol) {
                 $previous_symbol_uri = "hgnc.symbol:" . $previous_symbol;
                 parent::AddRDF(parent::describeIndividual($previous_symbol_uri, $previous_symbol, parent::getVoc() . "Previous-Symbol") . parent::describeClass(parent::getVoc() . "Previous-Symbol", "Previous Symbol") . parent::triplify($id_res, $this->getVoc() . "previous-symbol", $previous_symbol_uri) . parent::describeProperty($this->getVoc() . "previous-symbol", "HGNC previous symbol", "Symbols previously approved by the HGNC for this gene"));
             }
         }
         if (!empty($previous_names)) {
             $previous_names = explode(", ", $previous_names);
             foreach ($previous_names as $previous_name) {
                 $previous_name = str_replace("\"", "", $previous_name);
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "previous-name", utf8_encode(htmlspecialchars($previous_name))) . parent::describeProperty($this->getVoc() . "previous-name", "HGNC previous name", "Gene names previously approved by the HGNC for this gene"));
             }
         }
         if (!empty($synonyms)) {
             $synonyms = explode(", ", $synonyms);
             foreach ($synonyms as $synonym) {
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "synonym", utf8_encode(htmlspecialchars($synonym))) . parent::describeProperty($this->getVoc() . "synonym", "synonym", "Other symbols used to refer to this gene"));
             }
         }
         if (!empty($name_synonyms)) {
             $name_synonyms = explode(", ", $name_synonyms);
             foreach ($name_synonyms as $name_synonym) {
                 $name_synonym = str_replace("\"", "", $name_synonym);
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "name-synonym", utf8_encode(htmlspecialchars($name_synonym))) . parent::describeProperty($this->getVoc() . "name-synonym", "name synonym", "Other names used to refer to this gene"));
             }
         }
         if (!empty($chromosome)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "chromosome", utf8_encode(htmlspecialchars($chromosome))) . parent::describeProperty($this->getVoc() . "chromosome", "chromosome", "Indicates the location of the gene or region on the chromosome"));
         }
         if (!empty($date_approved)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "date-approved", $date_approved, "xsd:date") . parent::describeProperty($this->getVoc() . "date-approved", "date approved", "Date the gene symbol and name were approved by the HGNC"));
         }
         if (!empty($date_modified)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "date-modified", $date_modified, "xsd:date") . parent::describeProperty($this->getVoc() . "date-modified", "date modified", "the date the entry was modified by the HGNC"));
         }
         if (!empty($date_symbol_changed)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "date-symbol-changed", $date_symbol_changed, "xsd:date") . parent::describeProperty($this->getVoc() . "date-symbol-changed", "date symbol changed", "The date the gene symbol was last changed by the HGNC from a previously approved symbol. Many genes receive approved symbols and names which are viewed as temporary (eg C2orf#) or are non-ideal when considered in the light of subsequent information. In the case of individual genes a change to the name (and subsequently the symbol) is only made if the original name is seriously misleading"));
         }
         if (!empty($date_name_changed)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "date-name-changed", $date_name_changed, "xsd:date") . parent::describeProperty($this->getVoc() . "date-name-changed", "date name changed", "The date the gene name was last changed by the HGNC from a previously approved name"));
         }
         if (!empty($accession_numbers)) {
             $accession_numbers = explode(", ", $accession_numbers);
             foreach ($accession_numbers as $accession_number) {
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "accession", utf8_encode(htmlspecialchars($accession_number))) . parent::describeProperty($this->getVoc() . "accession", "accession number", "Accession numbers for each entry selected by the HGNC"));
             }
         }
         if (!empty($enzyme_ids)) {
             $enzyme_ids = explode(", ", $enzyme_ids);
             foreach ($enzyme_ids as $enzyme_id) {
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "x-ec", utf8_encode(htmlspecialchars($enzyme_id))) . parent::describeProperty($this->getVoc() . "x-ec", "Enzyme Commission (EC) number", "Enzyme entries have Enzyme Commission (EC) numbers associated with them that indicate the hierarchical functional classes to which they belong"));
             }
         }
         if (!empty($entrez_gene_id)) {
             parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ncbigene", "ncbigene:{$entrez_gene_id}") . parent::describeProperty($this->getVoc() . "x-ncbigene", "NCBI Gene", "NCBI Gene provides curated sequence and descriptive information about genetic loci including official nomenclature, synonyms, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites"));
         }
         if (!empty($ensembl_gene_id)) {
             parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ensembl", "ensembl:{$ensembl_gene_id}") . parent::describeProperty($this->getVoc() . "x-ensembl", "Ensembl Gene"));
         }
         if (!empty($mouse_genome_database_id)) {
             if (strpos($mouse_genome_database_id, "MGI:") !== FALSE) {
                 $mouse_genome_database_id = substr($mouse_genome_database_id, 4);
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-mgi", "mgi:{$mouse_genome_database_id}") . parent::describeProperty($this->getVoc() . "x-mgi", "MGI entry"));
             }
         }
         if (!empty($specialist_database_links)) {
             $specialist_database_links = explode(", ", $specialist_database_links);
             foreach ($specialist_database_links as $specialist_database_link) {
                 preg_match('/href="(\\S+)"/', $specialist_database_link, $matches);
                 if (!empty($matches[1])) {
                     parent::AddRDF(parent::QQuadO_URL($id_res, $this->getVoc() . "xref", $matches[1]) . parent::describeProperty($this->getVoc() . "xref", "Specialist database references."));
                 }
             }
         }
         if (!empty($pubmed_ids)) {
             $pubmed_ids = explode(", ", $pubmed_ids);
             foreach ($pubmed_ids as $pubmed_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-pubmed", "pubmed:" . trim($pubmed_id)) . parent::describeProperty($this->getVoc() . "x-pubmed", "NCBI PubMed entry", "Identifier that links to published articles relevant to the entry in the NCBI's PubMed database."));
             }
         }
         if (!empty($refseq_ids)) {
             $refseq_ids = explode(", ", $refseq_ids);
             foreach ($refseq_ids as $refseq_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-refseq", "refseq:" . trim($refseq_id)) . parent::describeProperty($this->getVoc() . "x-refseq", "NCBI Refseq entry", "The Reference Sequence (RefSeq) identifier for that entry, provided by the NCBI. As we do not aim to curate all variants of a gene only one selected RefSeq is displayed per gene report. RefSeq aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. RefSeq identifiers are designed to provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses. In the HTML results page this ID links to the RefSeq page for that entry."));
             }
         }
         if (!empty($gene_family_tag)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "gene-family-tag", utf8_encode(htmlspecialchars($gene_family_tag))) . parent::describeProperty($this->getVoc() . "gene-family-tag", "Gene Family Tag", "Tag used to designate a gene family or group the gene has been assigned to, according to either sequence similarity or information from publications, specialist advisors for that family or other databases. Families/groups may be either structural or functional, therefore a gene may belong to more than one family/group. These tags are used to generate gene family or grouping specific pages at genenames.org and do not necessarily reflect an official nomenclature. Each gene family has an associated gene family tag and gene family description. If a particular gene is a member of more than one gene family, the tags and the descriptions will be shown in the same order."));
         }
         if (!empty($gene_family_description)) {
             $gene_family_description = str_replace("\"", "", $gene_family_description);
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "gene-family-description", utf8_encode(htmlspecialchars($gene_family_description))) . parent::describeProperty($this->getVoc() . "gene-family-description", "gene family name", "Name given to a particular gene family. The gene family description has an associated gene family tag. Gene families are used to group genes according to either sequence similarity or information from publications, specialist advisors for that family or other databases. Families/groups may be either structural or functional, therefore a gene may belong to more than one family/group."));
         }
         if (!empty($record_type)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "record-type", utf8_encode(htmlspecialchars($record_type))));
         }
         if (!empty($primary_ids)) {
             $primary_ids = explode(", ", $primary_ids);
             foreach ($primary_ids as $primary_id) {
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "primary-id", utf8_encode(htmlspecialchars($primary_id))) . parent::describeProperty($this->getVoc() . "primary-id", "primary identifier"));
             }
         }
         if (!empty($secondary_ids)) {
             $secondary_ids = explode(", ", $secondary_ids);
             foreach ($secondary_ids as $secondary_id) {
                 parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "secondary-id", utf8_encode(htmlspecialchars($secondary_id))) . parent::describeProperty($this->getVoc() . "secondary-id", "secondary identifier"));
             }
         }
         if (!empty($ccd_ids)) {
             $ccd_ids = explode(", ", $ccd_ids);
             foreach ($ccd_ids as $ccd_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ccds", "ccds:" . trim($ccd_id)) . parent::describeProperty($this->getVoc() . "x-ccds", "consensus CDS entry", "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations."));
             }
         }
         if (!empty($vega_ids)) {
             $vega_ids = explode(", ", $vega_ids);
             foreach ($vega_ids as $vega_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-vega", "vega:" . trim($vega_id)) . parent::describeProperty($this->getVoc() . "x-vega", "VEGA gene entry"));
             }
         }
         if (!empty($locus_specific_databases)) {
             parent::AddRDF(parent::triplifyString($id_res, $this->getVoc() . "locus-specific-xref", utf8_encode(htmlspecialchars($locus_specific_databases))) . parent::describeProperty($this->getVoc() . "locus-specific-xref", "locus specific xref", "This contains a list of links to databases or database entries pertinent to the gene"));
         }
         if (!empty($entrez_gene_id_mappeddatasuppliedbyNCBI)) {
             $entrez_gene_id_mappeddatasuppliedbyNCBI = explode(", ", $entrez_gene_id_mappeddatasuppliedbyNCBI);
             foreach ($entrez_gene_id_mappeddatasuppliedbyNCBI as $gene_id) {
                 if (strstr($gene_id, ":") !== FALSE) {
                     $a = explode(":", $gene_id);
                     $gene_id = $a[1];
                 }
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ncbigene", "ncbigene:" . trim($gene_id)) . parent::describeProperty($this->getVoc() . "x-ncbigene", "NCBI Gene entry"));
             }
         }
         if (!empty($omim_id_mappeddatasuppliedbyNCBI)) {
             $omim_id_mappeddatasuppliedbyNCBI = explode(", ", $omim_id_mappeddatasuppliedbyNCBI);
             foreach ($omim_id_mappeddatasuppliedbyNCBI as $omim_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-omim", "omim:" . trim($omim_id)) . parent::describeProperty($this->getVoc() . "x-omim", "OMIM entry", "Identifier provided by Online Mendelian Inheritance in Man (OMIM) at the NCBI. This database is described as a catalog of human genes and genetic disorders containing textual information and links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere. In the HTML results page this ID links to the OMIM page for that entry."));
             }
         }
         if (!empty($refseq_mappeddatasuppliedbyNCBI)) {
             $refseq_mappeddatasuppliedbyNCBI = explode(", ", $refseq_mappeddatasuppliedbyNCBI);
             foreach ($refseq_mappeddatasuppliedbyNCBI as $refseq_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-refseq", "refseq:" . trim($refseq_id)) . parent::describeProperty($this->getVoc() . "x-refseq", "NCBI Refseq entry", "The Reference Sequence (RefSeq) identifier for that entry, provided by the NCBI. As we do not aim to curate all variants of a gene only one selected RefSeq is displayed per gene report. RefSeq aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. RefSeq identifiers are designed to provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses. In the HTML results page this ID links to the RefSeq page for that entry."));
             }
         }
         if (!empty($uniprot_id_mappeddatasuppliedbyUniProt)) {
             $uniprot_id_mappeddatasuppliedbyUniProt = explode(", ", $uniprot_id_mappeddatasuppliedbyUniProt);
             foreach ($uniprot_id_mappeddatasuppliedbyUniProt as $uniprot_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-uniprot", "uniprot:" . trim($uniprot_id)) . parent::describeProperty($this->getVoc() . "x-uniprot", "Uniprot entry", "The UniProt identifier, provided by the EBI. The UniProt Protein Knowledgebase is described as a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and high level of integration with other databases. In the HTML results page this ID links to the UniProt page for that entry."));
             }
         }
         if (!empty($ensembl_id_mappeddatasuppliedbyEnsembl)) {
             $ensembl_id_mappeddatasuppliedbyEnsembl = explode(", ", $ensembl_id_mappeddatasuppliedbyEnsembl);
             foreach ($ensembl_id_mappeddatasuppliedbyEnsembl as $ensembl_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ensembl", "ensembl:" . trim($refseq_id)) . parent::describeProperty($this->getVoc() . "x-ensembl", "Ensembl entry", "The Ensembl ID is derived from the current build of the Ensembl database and provided by the Ensembl team."));
             }
         }
         if (!empty($ucsc_id_mappeddatasuppliedbyVega)) {
             $ucsc_id_mappeddatasuppliedbyVega = explode(", ", $ucsc_id_mappeddatasuppliedbyVega);
             foreach ($ucsc_id_mappeddatasuppliedbyVega as $vega_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-vega", "vega:" . trim($vega_id)) . parent::describeProperty($this->getVoc() . "x-vega", "Vega entry"));
             }
         }
         if (!empty($ucsc_id_mappeddatasuppliedbyUCSC)) {
             $ucsc_id_mappeddatasuppliedbyUCSC = explode(", ", $ucsc_id_mappeddatasuppliedbyUCSC);
             foreach ($ucsc_id_mappeddatasuppliedbyUCSC as $ucsc_id) {
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-ucsc", "ucsc:" . trim($ucsc_id)) . parent::describeProperty($this->getVoc() . "x-ucsc", "UCSC entry"));
             }
         }
         if (!empty($mouse_genome_database_id_mappeddatasuppliedbyMGI)) {
             $mouse_genome_database_id_mappeddatasuppliedbyMGI = explode(", ", $mouse_genome_database_id_mappeddatasuppliedbyMGI);
             foreach ($mouse_genome_database_id_mappeddatasuppliedbyMGI as $mgi_id) {
                 if (strpos($mgi_id, "MGI:") !== FALSE) {
                     $mgi_id = substr($mgi_id, 4);
                 }
                 parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-mgi", "mgi:" . trim($mgi_id)) . parent::describeProperty($this->getVoc() . "x-mgi", "MGI entry"));
             }
         }
         if (!empty($rat_genome_database_id_mappeddatasuppliedbyRGD)) {
             $rat_genome_database_id_mappeddatasuppliedbyRGD = explode(", ", trim($rat_genome_database_id_mappeddatasuppliedbyRGD));
             foreach ($rat_genome_database_id_mappeddatasuppliedbyRGD as $rgd_id) {
                 $rgd_id = trim($rgd_id);
                 if (!empty($rgd_id)) {
                     parent::AddRDF(parent::triplify($id_res, $this->getVoc() . "x-rgd", trim($rgd_id)) . parent::describeProperty($this->getVoc() . "x-rgd", "RGD entry"));
                 }
             }
         }
         //write RDF to file
         $this->WriteRDFBufferToWriteFile();
     }
     //while
 }
Ejemplo n.º 22
0
 function process()
 {
     $gb_record_str = "";
     while ($aLine = $this->getReadFile()->Read(4096)) {
         preg_match("/^\\/\\/\$/", $aLine, $matches);
         if (count($matches)) {
             //now remove the header if it is there
             $gb_record_str = $this->removeHeader($gb_record_str);
             $sectionsRaw = $this->parseGenbankRaw($gb_record_str);
             /**
              * SECTIONS being parsed:
              * locus, definition, accession, version, keywords, segment, source, reference, features
              */
             //get locus section(s)
             $locus = $this->retrieveSections("LOCUS", $sectionsRaw);
             $parsed_locus_arr = $this->parseLocus($locus);
             //get the definition section
             $definition = $this->retrieveSections("DEFINITION", $sectionsRaw);
             $parsed_definition_arr = $this->parseDefinition($definition);
             //get the accession
             $accessions = $this->retrieveSections("ACCESSION", $sectionsRaw);
             $parsed_accession_arr = $this->parseAccession($accessions);
             //get the version
             $versions = $this->retrieveSections("VERSION", $sectionsRaw);
             $parsed_version_arr = $this->parseVersion($versions);
             //get the keywords
             $keywords = $this->retrieveSections("KEYWORDS", $sectionsRaw);
             $parsed_keyword_arr = $this->parseKeywords($keywords);
             //may not be any segment section
             $segments = $this->retrieveSections("SEGMENT", $sectionsRaw);
             if (!empty($segments)) {
                 $parsed_segments_arr = $this->parseSegment($segments);
             }
             $features = $this->retrieveSections("FEATURES", $sectionsRaw);
             $parsed_features_arr = $this->parseFeatures($features);
             //get the source section
             $source = $this->retrieveSections("SOURCE", $sectionsRaw);
             $parsed_source_arr = $this->parseSource($source);
             $contig = $this->retrieveSections("CONTIG", $sectionsRaw);
             if (!empty($contig)) {
                 $parsed_contig_arr = $this->parseContig($contig);
             }
             //get the reference section
             $references = $this->retrieveSections("REFERENCE", $sectionsRaw);
             $parsed_refs_arr = $this->parseReferences($references);
             $gb_res = "gi:" . $parsed_version_arr['gi'];
             $gb_label = utf8_encode(htmlspecialchars($parsed_definition_arr[0]));
             parent::AddRDF(parent::describeIndividual($gb_res, $gb_label, $this->getVoc() . "genbank-record") . parent::triplifyString($gb_res, $this->getVoc() . 'sequence-length', $parsed_locus_arr[0]['sequence_length']) . parent::triplifyString($gb_res, $this->getVoc() . 'strandedness', $parsed_locus_arr[0]['strandedness']) . parent::triplify($gb_res, "rdf:type", $this->getRes() . $parsed_locus_arr[0]['mol_type']) . parent::triplifyString($gb_res, $this->getVoc() . 'chromosome-shape', $parsed_locus_arr[0]['chromosome_shape']) . parent::triplifyString($gb_res, $this->getVoc() . 'division-name', $parsed_locus_arr[0]['division_name']) . parent::triplifyString($gb_res, $this->getVoc() . 'date-of-entry', $parsed_locus_arr[0]['date']) . parent::triplifyString($gb_res, $this->getVoc() . 'source', utf8_encode($parsed_source_arr[0])) . parent::QQuadO_URL($gb_res, $this->getVoc() . 'fasta-seq', 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?sendto=on&db=nucest&dopt=fasta&val=' . $parsed_version_arr['gi']));
             foreach ($parsed_features_arr as $aFeature) {
                 //getFeatures
                 $type = $aFeature['type'];
                 $feat_desc = $this->getFeatures($type);
                 $label = preg_replace('/\\s\\s*/', ' ', $feat_desc['definition']);
                 $comment = null;
                 $value = $aFeature['value'];
                 $value_arr = explode("/", $value);
                 $location = preg_replace('/\\n/', '', $value_arr[0]);
                 $class_id = parent::getVoc() . md5($type);
                 $feat_res = parent::getRes() . md5($type . $location . $gb_res);
                 $feat_label = utf8_encode($type . " " . $location . " for " . $gb_res);
                 if (isset($feat_desc['comment'])) {
                     $comment = $feat_desc['comment'];
                     $comment = preg_replace('/\\s\\s*/', ' ', $comment);
                     $label .= " " . $comment;
                 }
                 parent::AddRDF(parent::describeClass($class_id, $label, parent::getVoc() . "Feature") . parent::describeIndividual($feat_res, $feat_label, $class_id) . parent::triplify($gb_res, $this->getVoc() . "has-feature", $feat_res));
                 foreach ($value_arr as $aL) {
                     //check if aL has an equals in it
                     $p = "/(\\S+)\\=(.*)/";
                     preg_match($p, $aL, $m);
                     if (count($m)) {
                         if ($m[1] == "db_xref") {
                             parent::AddRDF(parent::triplify($feat_res, "rdfs:seeAlso", str_replace("\"", "", $m[2])));
                         } else {
                             parent::AddRDF(parent::triplifyString($feat_res, $this->getVoc() . $m[1], utf8_encode(str_replace("\"", "", $m[2]))));
                         }
                     }
                 }
             }
             foreach ($parsed_accession_arr[0] as $acc) {
                 parent::AddRDF(parent::triplifyString($gb_res, $this->getVoc() . "accession", $acc));
             }
             if (isset($parsed_version_arr['versioned_accession'])) {
                 parent::AddRDF(parent::triplifyString($gb_res, $this->getVoc() . "versioned-accession", $parsed_version_arr['versioned_accession']));
             }
             if (isset($parsed_contig_arr)) {
                 foreach ($parsed_contig_arr as $aContig) {
                     parent::AddRDF(parent::triplifyString($gb_res, $this->getVoc() . "contig", parent::safeLiteral($aContig)));
                 }
             }
             foreach ($parsed_keyword_arr as $akw) {
                 parent::AddRDF(parent::triplifyString($gb_res, $this->getVoc() . "keyword", $akw));
             }
             if (isset($parsed_segments_arr)) {
                 foreach ($parsed_segments_arr as $aSeg) {
                     parent::AddRDF(parent::triplifyString($gb_res, $this->getVoc() . "segment-number", $aSeg['segment_number']) . parent::triplifyString($gb_res, $this->getVoc() . "total-segments", $aSeg['total_segments']));
                 }
             }
             foreach ($parsed_refs_arr as $aRef) {
                 $r = rand();
                 $ref_res = $this->getRes() . md5($r);
                 $ref_label = "reference for " . $gb_res;
                 if (isset($aRef['TITLE'])) {
                     parent::AddRDF(parent::describeIndividual($ref_res, $ref_label, $this->getVoc() . "reference") . parent::triplifyString($ref_res, $this->getVoc() . "title", $aRef['TITLE']));
                 }
                 if (isset($aRef['PUBMED'])) {
                     parent::AddRDF(parent::triplify($ref_res, $this->getVoc() . "x-pubmed", 'pubmed:' . $aRef['PUBMED']));
                 }
                 if (isset($aRef['AUTHORS'])) {
                     parent::AddRDF(parent::triplifyString($ref_res, $this->getVoc() . "authors", $aRef['AUTHORS']));
                 }
                 parent::AddRDF(parent::triplify($gb_res, $this->getVoc() . "reference", $ref_res) . parent::triplifyString($ref_res, $this->getVoc() . "coordinates", $aRef['COORDINATES']) . parent::triplifyString($ref_res, $this->getVoc() . "citation", $aRef['JOURNAL']));
             }
             $gb_record_str = "";
             $this->WriteRDFBufferToWriteFile();
             continue;
         }
         preg_match("/^\n\$/", $aLine, $matches);
         if (count($matches) == 0) {
             $gb_record_str .= $aLine;
         }
     }
     //while
 }
Ejemplo n.º 23
0
 private function geneinfo()
 {
     $i = 1;
     $header = $this->GetReadFile()->Read(200000);
     while ($aLine = $this->GetReadFile()->Read(200000)) {
         if ($i++ % 1000 == 0) {
             parent::clear();
         }
         $a = $splitLine = explode("\t", $aLine);
         if (count($splitLine) == 15) {
             $taxid = "taxon:" . trim($splitLine[0]);
             if (isset($this->taxids) and !isset($this->taxids[trim($splitLine[0])])) {
                 continue;
             }
             $aGeneId = trim($splitLine[1]);
             $geneid = "ncbigene:" . trim($splitLine[1]);
             $symbol = addslashes(stripslashes(trim($splitLine[2])));
             $symbolid = "symbol:{$symbol}";
             $locusTag = trim($splitLine[3]);
             $symbols_arr = explode("|", $splitLine[4]);
             $dbxrefs_arr = explode("|", $splitLine[5]);
             $chromosome = trim($splitLine[6]);
             $map_location = trim($splitLine[7]);
             $description = addslashes(stripslashes(trim($splitLine[8])));
             $type_of_gene = trim($splitLine[9]);
             $symbol_authority = addslashes(stripslashes(trim($splitLine[10])));
             $symbol_auth_full_name = addslashes(stripslashes(trim($splitLine[11])));
             $nomenclature_status = addslashes(stripslashes(trim($splitLine[12])));
             $other_designations = addslashes(stripslashes(trim($splitLine[13])));
             $mod_date = date_parse(trim($splitLine[14]));
             //check for a valid symbol
             if ($symbol != "NEWENTRY") {
                 $this->AddRDF(parent::describeIndividual($geneid, "{$description} ({$symbolid}, {$taxid})", $this->getVoc() . "Gene") . parent::triplify($geneid, $this->getVoc() . "x-taxonomy", $taxid) . parent::triplifyString($geneid, $this->getVoc() . "symbol", $symbol) . parent::triplifyString($geneid, $this->getVoc() . "locus", addslashes(stripslashes($locusTag))) . parent::describeClass($this->getVoc() . "Gene", "NCBI Gene gene"));
                 if ($type_of_gene != '-') {
                     $this->AddRDF(parent::triplify($geneid, "rdf:type", $this->getVoc() . ucfirst($type_of_gene) . "-Gene") . parent::describeClass($this->getVoc() . ucfirst($type_of_gene) . "-Gene", ucfirst($type_of_gene) . " Gene"));
                 }
                 //symbol synonyms
                 foreach ($symbols_arr as $s) {
                     if ($s != "-") {
                         $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "symbol-synonym", addslashes(stripslashes($s))));
                     }
                 }
                 //dbxrefs
                 foreach ($dbxrefs_arr as $dbx) {
                     if ($dbx != "-") {
                         $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "dbxref", $dbx));
                     }
                 }
                 //chromosome
                 if ($chromosome != "-") {
                     $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "chromosome", $chromosome));
                 }
                 //map location
                 if ($map_location != "-") {
                     $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "map-location", $map_location));
                 }
                 //description
                 if ($description != "-") {
                     $this->AddRDF(parent::triplifyString($geneid, "dc:description", $description));
                 }
                 //nomenclature authority
                 if ($symbol_authority != "-") {
                     $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "nomenclature-authority", $symbol_authority));
                     if ($symbol_auth_full_name != "-") {
                         $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "nomenclature-authority-fullname", $symbol_auth_full_name));
                     }
                 }
                 //nomenclature status
                 if ($nomenclature_status != "-") {
                     $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "nomenclature-status", $nomenclature_status));
                 }
                 //other designations
                 if ($other_designations != "-") {
                     foreach (explode("|", $other_designations) as $d) {
                         $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "other-designation", $d));
                     }
                 }
                 //modification date
                 if ($mod_date != "-") {
                     $this->AddRDF(parent::triplifyString($geneid, $this->getVoc() . "modification-date", $mod_date["year"] . "-" . $mod_date["month"] . "-" . $mod_date["day"]));
                 }
             }
         }
         parent::writeRDFBufferToWriteFile();
     }
     // while
 }
Ejemplo n.º 24
0
 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", $p_value));
         parent::writeRDFBufferToWriteFile();
     }
     //while
 }
Ejemplo n.º 25
0
 /**
  *	Convert pubchem substance XML record to RDF
  **/
 function parse_substance_record(&$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)));
         }
     }
 }
Ejemplo n.º 26
0
 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();
     }
 }
Ejemplo n.º 27
0
 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'], $c));
                 }
             }
         }
         parent::WriteRDFBufferToWriteFile();
     }
     return TRUE;
 }
Ejemplo n.º 28
0
 /**
  * add an RDF representation of the incoming param to the model.
  * @$qual_record_arr is an assoc array with the contents of one qualifier record
  */
 private function makeQualifierRecordRDF($qual_record_arr)
 {
     //get the UI of the qualifier record
     $qr_ui = $qual_record_arr["UI"][0];
     $qr_res = $this->getNamespace() . $qr_ui;
     $qr_label = $qual_record_arr['SH'][0];
     parent::AddRDF(parent::describeIndividual($qr_res, $qr_label, $this->getVoc() . "Qualifier-Descriptor", $qr_label) . parent::describeClass($this->getVoc() . "Qualifier-Descriptor", "MeSH Qualifier Descriptor"));
     //now get the descriptor_data_elements
     $qde = $this->getQualifierDataElements();
     //iterate over the properties
     foreach ($qual_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 $anAn) {
                         parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde["AN"], $anAn) . parent::describeProperty($this->getVoc() . $qde["AN"], "Relationship between a qualifier record and its annotation"));
                     }
                     //foreach
                 }
                 //foreach
             }
             //if
             if ($k == "DA") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['DA'], $this->formatDate($vv), "xsd:date") . parent::describeProperty($this->getVoc() . $qde['DA'], "Relationship between a qualifier record and its date of entry"));
                 }
             }
             //if
             if ($k == "DQ") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['DQ'], $this->formatDate($vv), "xsd:date") . parent::describeProperty($this->getVoc() . $qde['DQ'], "Relationship between a qualifier record and its date qualifier established"));
                 }
             }
             //if
             if ($k == "GM") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['GM'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['GM'], "Relationship between a qualifier record and its grateful med note"));
                 }
             }
             if ($k == "HN") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['HN'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['HN'], "Relationship between a qualifier record and its history note"));
                 }
             }
             if ($k == "HN") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['HN'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['HN'], "Relationship between a qualifier record and its history note"));
                 }
             }
             if ($k == "MED") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['MED'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['MED'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "M94") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['M94'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M94'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "M90") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['M90'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M90'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "M85") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['M85'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M85'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "M80") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['M80'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M80'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "M75") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['M75'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M75'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "M66") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['M66'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['M66'], "Relationship between a qualifier record and its backfile postings"));
                 }
             }
             if ($k == "MR") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['MR'], $this->formatDate($vv), "xsd:date") . parent::describeProperty($this->getVoc() . $qde['MR'], "Relationship between a qualifier record and its major revision date"));
                 }
             }
             //if
             if ($k == "MS") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['MS'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['MS'], "Relationship between a qualifier record and its MeSH scope note"));
                 }
             }
             if ($k == "OL") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['OL'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['OL'], "Relationship between a qualifier record and its online note"));
                 }
             }
             if ($k == "QA") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['QA'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['QA'], "Relationship between a qualifier record and its toplical qualifier abbreviation"));
                 }
             }
             if ($k == "QE") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['QE'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['QE'], "Relationship between a qualifier record and its qualifier entry version"));
                 }
             }
             if ($k == "QS") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['QS'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['QS'], "Relationship between a qualifier record and its qualifier sort version"));
                 }
             }
             if ($k == "QT") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['QT'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['QT'], "Relationship between a qualifier record and its qualifier type"));
                 }
             }
             if ($k == "QX") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['QX'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['QX'], "Relationship between a qualifier record and its qualifier cross reference"));
                 }
             }
             if ($k == "RECTYPE") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['RECTYPE'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['RECTYPE'], "Relationship between a qualifier record and its record type"));
                 }
             }
             if ($k == "SH") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['SH'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['SH'], "Relationship between a qualifier record and its subheading"));
                 }
             }
             if ($k == "TN") {
                 foreach ($v as $kv => $vv) {
                     parent::AddRDF(parent::triplifyString($qr_res, $this->getVoc() . $qde['TN'], utf8_encode(htmlspecialchars($vv))) . parent::describeProperty($this->getVoc() . $qde['TN'], "Relationship between a qualifier record and its tree node allowed"));
                 }
             }
         } else {
             trigger_error("Please add key to qualifier record map: " . $k . PHP_EOL, E_USER_ERROR);
         }
         //else
         $this->WriteRDFBufferToWriteFile();
     }
     //foreach
     $this->WriteRDFBufferToWriteFile();
 }
Ejemplo n.º 29
0
 function Parse($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})"));
         }
     }
 }
Ejemplo n.º 30
0
 private function gene_xrefs()
 {
     while ($aLine = $this->getReadFile()->Read(4096)) {
         $tLine = explode("\t", $aLine);
         if (!$this->startsWith($tLine[0], "#")) {
             $chromosome = null;
             $cosmid = array();
             $start_coord = null;
             $gene_symbol = null;
             $end_coord = null;
             $strand = array();
             $gene_location = array();
             $ensembl_id = array();
             $gene_id = null;
             $ipi_ids = array();
             $uniprotkb_ids = array();
             $uniprot_tre = array();
             $ensembl_peptide_id = array();
             $refseq_ids = array();
             $tair_ids = array();
             $hinv_ids = array();
             $unigene_ids = array();
             $ccds_ids = array();
             $refseq_gis = array();
             $vega_genes = array();
             $vega_peptides = array();
             if (count(isset($tLine[0]))) {
                 @($chr_arr = readIdentifiers($tLine[0]));
                 if ($chr_arr[0] != "Un") {
                     $chromosome = $chr_arr[0];
                 }
             }
             if (count(isset($tLine[1]))) {
                 @($cosmid = readIdentifiers($tLine[1]));
             }
             if (count(isset($tLine[2]))) {
                 @($start_coord_t = readIdentifiers($tLine[2]));
                 if (count($start_coord_t) == 1) {
                     $start_coord = $start_coord_t[0];
                 }
             }
             if (count(isset($tLine[3]))) {
                 @($end_coord_t = readIdentifiers($tLine[3]));
                 if (count($end_coord_t) == 1) {
                     $end_coord = $end_coord_t[0];
                 }
             }
             if (count(isset($tLine[4]))) {
                 @($strand = readIdentifiers($tLine[4]));
             }
             if (count(isset($tLine[5]))) {
                 @($gene_location = readIdentifiers($tLine[5]));
             }
             if (count(isset($tLine[6]))) {
                 @($ensembl_id = readIdentifiers($tLine[6]));
             }
             if (count(isset($tLine[8]))) {
                 @($gene_id_t = readIdentifiers($tLine[8]));
                 if (count($gene_id_t) == 2) {
                     $gene_id = $gene_id_t[0];
                     $gene_symbol = $gene_id_t[1];
                 }
             }
             if (count(isset($tLine[9]))) {
                 @($ipi_ids = readIdentifiers($tLine[9]));
             }
             if (count(isset($tLine[10]))) {
                 @($uniprotkb_ids = readIdentifiers($tLine[10]));
             }
             if (count(isset($tLine[11]))) {
                 @($uniprot_tre = readIdentifiers($tLine[11]));
             }
             if (count(isset($tLine[12]))) {
                 @($ensembl_peptide_id = readIdentifiers($tLine[12]));
             }
             if (count(isset($tLine[13]))) {
                 @($refseq_ids = readIdentifiers($tLine[13]));
             }
             if (count(isset($tLine[14]))) {
                 @($tair_ids = readIdentifiers($tLine[14]));
             }
             if (count(isset($tLine[15]))) {
                 @($hinv_ids = readIdentifiers($tLine[15]));
             }
             if (count(isset($tLine[16]))) {
                 @($unigene_ids = readIdentifiers($tLine[16]));
             }
             if (count(isset($tLine[17]))) {
                 @($ccds_ids = readIdentifiers($tLine[17]));
             }
             if (count(isset($tLine[18]))) {
                 @($refseq_gis = readIdentifiers($tLine[18]));
             }
             if (count(isset($tLine[19]))) {
                 @($vega_genes = readIdentifiers($tLine[19]));
             }
             if (count(isset($tLine[20]))) {
                 @($refseq_ids = readIdentifiers($tLine[20]));
             }
             //lets make some RDF
             if (count($gene_id)) {
                 $res = "gene:" . $gene_id;
                 parent::AddRDF(parent::triplifyString($res, $this->getVoc() . "gene-symbol", $gene_symbol) . parent::triplifyString($res, $this->getVoc() . "chromosome", $chromosome) . parent::triplifyString($res, $this->getVoc() . "start-coordinate", $start_coord) . parent::triplifyString($res, $this->getVoc() . "end-coordinate", $end_coord));
             }
             if (count($strand)) {
                 parent::AddRDF(parent::triplifyString($res, $this->getVoc() . "strand", $strand[0]));
             }
             if (count($ensembl_id)) {
                 foreach ($ensembl_id as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-ensembl", "ensembl:" . $x));
                 }
             }
             if (count($gene_location)) {
                 foreach ($gene_location as $x) {
                     parent::AddRDF(parent::triplifyString($res, $this->getVoc() . "gene-location", $x));
                 }
             }
             if (count($ipi_ids)) {
                 foreach ($ipi_ids as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-ipi", "ipi:" . $x));
                 }
             }
             if (count($uniprotkb_ids)) {
                 foreach ($uniprotkb_ids as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-uniprot", "uniprot:" . $x));
                 }
             }
             if (count($uniprotkb_tre)) {
                 foreach ($uniprotkb_tre as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-uniprot", "uniprot:" . $x));
                 }
             }
             if (count($ensembl_peptide_id)) {
                 foreach ($ensembl_peptide_id as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-ensembl", "ensembl:" . $x));
                 }
             }
             if (count($refseq_ids)) {
                 foreach ($refseq_ids as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-refseq", "refseq:" . $x));
                 }
             }
             if (count($tair_ids)) {
                 foreach ($tair_ids as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-tair", "tair:" . $x));
                 }
             }
             if (count($hinv_ids)) {
                 foreach ($hinv_ids as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-hinv", "hinv:" . $x));
                 }
             }
             if (count($unigene_ids)) {
                 foreach ($unigene_ids as $x) {
                     parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-unigene", "unigene:" . $x));
                 }
             }
             if (count($refseq_gis)) {
                 foreach ($refseq_gis as $x) {
                     if (count($x) != 0 && $x != "\n" && $x != "") {
                         parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-refseq", "refseq:" . $x));
                     }
                 }
             }
             $this->WriteRDFBufferToWriteFile();
         }
     }
 }