diff --git a/README.md b/README.md
deleted file mode 100644
index 493bb1a..0000000
--- a/README.md
+++ /dev/null
@@ -1,26 +0,0 @@
-Bio2RDF-scripts
-===============
- This Git repository holds all of the RDF converter scripts used to generate Bio2RDF linked data.
-
-Requirements
--------------
-The majority of these scripts were created so as to run on Linux servers. Depending on the script you wish to run you will need:
-
-* PHP5
-* Perl 6
-* Ruby(1.9.3)
-* Java 1.5
-* Bio2RDF API (available from: https://github.com/micheldumontier/php-lib)
-
-The Bio2RDF API should be installed in the root directory of the project tree (i.e bio2rdf-scripts).
-
-Usage
------
-Each script is run independently. See README files inside each script directory.
-
-Contact Us
----------
-For more information visit http://bio2rdf.org or http://dumontierlab.com
-
----
-Licensed under [MIT License](http://en.wikipedia.org/wiki/MIT_License), see [license page](https://github.com/bio2rdf/bio2rdf-scripts/wiki/MIT-License) for details.
diff --git a/bioportal/bioportal.php b/bioportal/bioportal.php
index cece375..a3028ad 100644
--- a/bioportal/bioportal.php
+++ b/bioportal/bioportal.php
@@ -89,8 +89,9 @@ function Run()
 		foreach($ontologies AS $i => $o) {
 			$label = (string) $o->name;
 			$abbv = (string) $o->acronym;
-
-			if(array_search($abbv,$exclude_list) !== FALSE) continue;
+			if(array_search($abbv,$exclude_list) !== FALSE) {
+				continue;
+			}
 			if($include_list[0] != 'all') {
 				// ignore if we don't find it in the include list OR we do find it in the exclude list
 				if( (array_search($abbv,$include_list) === FALSE)
@@ -106,9 +107,7 @@ function Run()
 			if(!isset($ls['hasOntologyLanguage'])) {echo 'insufficient metadata'.PHP_EOL;continue;}
 
 			$format = strtolower($ls['hasOntologyLanguage']);
-/***********/
 			if($format != 'owl' and $format != 'obo') continue;
-
 			echo "Processing ($i/$total) $abbv ... ";
 
 			$version = $ls['version'];
@@ -117,7 +116,6 @@ function Run()
 
 			$rfile = $ls['ontology']['links']['download'];
 
-
 			$lfile = $abbv.".".$format.".gz";
 			if(parent::getParameterValue('download') == 'true') {
 				echo "downloading ... ";
@@ -138,6 +136,7 @@ function Run()
 				if(isset($m[1])) {
 					$filename = $m[1];
 					if(strstr($filename,".zip"))  continue;
+
 				} else {echo "error: no filename".PHP_EOL;continue;}
 
 				$body = substr($ret, $header_size);
@@ -148,6 +147,7 @@ function Run()
 
 				$lz = "compress.zlib://".$idir.$lfile;
 				file_put_contents($lz,$body);
+
 				echo "done".PHP_EOL;
 			}
 
@@ -160,6 +160,11 @@ function Run()
 				// process
 				echo "converting ... ";
 				set_time_limit(0);
+				// let's double check the format
+				$fp = gzopen($idir.$lfile,"r");
+				$l = gzgets($fp);
+				if(strstr($l,"xml")) $format= "owl";
+				gzclose($fp);
 				if($format == 'obo') {
 					$this->OBO2RDF($abbv);
 				} else if($format == 'owl') {
@@ -366,6 +371,7 @@ function OBO2RDF($abbv)
 		if($abbv == "doid") $abbv = "do";
 		$minimal = (parent::getParameterValue('detail') == 'min')?true:false;
 		$minimalp = (parent::getParameterValue('detail') == 'min+')?true:false;
+		$version = parent::getParameterValue("bio2rdf_release");
 
 		$tid = '';
 		$first = true;
@@ -374,7 +380,7 @@ function OBO2RDF($abbv)
 		$min = $buf = '';
 		$ouri = "http://bio2rdf.org/lsr:".$abbv;
 
-		$dataset_uri = $abbv."_resource:bio2rdf.dataset.$abbv.R3";
+		$dataset_uri = $abbv."_resource:bio2rdf.dataset.$abbv.R".$version;
 		parent::setGraphURI($dataset_uri);
 		$buf = parent::triplify($ouri,"rdf:type","owl:Ontology");
 		$graph_uri = '<'.parent::getRegistry()->getFQURI(parent::getGraphURI()).'>';
diff --git a/clinicaltrials/clinicaltrials.php b/clinicaltrials/clinicaltrials.php
index d1fc868..78c74e1 100644
--- a/clinicaltrials/clinicaltrials.php
+++ b/clinicaltrials/clinicaltrials.php
@@ -233,12 +233,11 @@ function parse_dir(){
 	**/
 	function process_file($infile) {
 		$indir = parent::getParameterValue('indir');
-		$xml = new CXML($indir,basename($infile));
+		$xml = new CXML($infile);
 		$this->setCheckPoint('file');
 		while($xml->Parse("clinical_study") == TRUE) {
 			$this->setCheckPoint('record');
 			$this->root = $root = $xml->GetXMLRoot();
-	
 			$this->nct_id = $nct_id = $this->getString("//id_info/nct_id");
 			$this->study_id = $study_id = parent::getNamespace()."$nct_id";
 
@@ -759,7 +758,7 @@ function process_file($infile) {
 						parent::triplifyString($location_uri,parent::getVoc()."status", $this->getString('//status',$location)).
 						parent::triplify($study_id,parent::getVoc()."location",$location_uri).
 						parent::triplify($location_uri, parent::getVoc()."address", $this->makeAddress($address)).
-						parent::triplify($location_uri, parent::getVoc()."contact", $this->makeContact($contact))
+						($contact != null?parent::triplify($location_uri, parent::getVoc()."contact", $this->makeContact($contact)):"")
 					);
 					if($backups) {
 						foreach($backups AS $backup) {
@@ -831,11 +830,13 @@ function process_file($infile) {
 			try{
 				$links = $root->xpath('//link');
 				foreach($links AS $i => $link) {
-					$lid = parent::getRes().md5($this->getString('./url',$link));
+					$url = $this->getString('./url',$link);
+					$url = preg_replace("/>.*$/","",$url);
+					$lid = parent::getRes().md5($url);
 					parent::addRDF(
 						parent::describeIndividual($lid, $this->getString('./description',$link), parent::getVoc()."Link").
 						parent::describeClass(parent::getVoc()."Link","Link").
-						parent::triplify($lid,parent::getVoc()."url",preg_replace("/>$/","",$this->getString('./url',$link))).
+						parent::triplify($lid,parent::getVoc()."url",$url).
 						parent::triplify($study_id,parent::getVoc()."link",$lid)
 					);
 				}
@@ -1166,7 +1167,7 @@ function process_file($infile) {
 						if(!$et) continue;
 						$ev_uri = parent::getVoc().str_replace(" ","-",$ev_label);
 
-						$categories = array_shift($et->xpath('./category_list'));
+						$categories = @array_shift($et->xpath('./category_list'));
 						foreach($categories AS $category) {
 							$major_title = $this->getString('./title', $category);
 							$major_title_uri = parent::getRes().md5($major_title);
@@ -1272,8 +1273,8 @@ public function getDatetimeFromDate($date)
 	
 	public function makeContact($contact)
 	{
-		if($contact == null) return null;
-		$contact_uri = parent::getRes().md5($contact->asXML());		
+		if($contact == null) return '';
+		$contact_uri = parent::getRes().md5($contact->asXML());
 		$contact_type_uri = parent::getVoc()."Contact";
 		$contact_label = trim($this->getString('//first_name',$contact)." ".$this->getString('//last_name', $contact));
 		parent::addRDF(
diff --git a/drugbank/drugbank.php b/drugbank/drugbank.php
index ac7757b..d19c76d 100755
--- a/drugbank/drugbank.php
+++ b/drugbank/drugbank.php
@@ -34,17 +34,17 @@
 class DrugBankParser extends Bio2RDFizer 
 {    
     function __construct($argv) {
-        parent::__construct($argv,"drugbank");
-        parent::addParameter('files', true, 'all|drugbank','all','Files to convert');
-        parent::addParameter('download_url',false,null,'http://www.drugbank.ca/system/downloads/current/');
-        parent::initialize();
+		parent::__construct($argv,"drugbank");
+		parent::addParameter('files', true, 'all|drugbank','all','Files to convert');
+		parent::addParameter('download_url',false,null,'http://www.drugbank.ca/system/downloads/current/');
+		parent::initialize();
     }
     
     function Run()
     {
-        $indir        = parent::getParameterValue('indir');
-        $outdir       = parent::getParameterValue('outdir');
-        $download_url = parent::getParameterValue('download_url');
+		$indir        = parent::getParameterValue('indir');
+		$outdir       = parent::getParameterValue('outdir');
+		$download_url = parent::getParameterValue('download_url');
 
 		if(parent::getParameterValue('files') == 'all') {
 			$files = explode("|",parent::getParameterList('files'));
@@ -52,11 +52,11 @@ function Run()
 		} else {
 			$files = explode("|",parent::getParameterValue('files'));
 		}
-		
+
 		if(parent::getParameterValue("id_list")) {
 			$this->id_list = array_flip(explode(",",parent::getParameterValue('id_list')));
 		}
-		
+
 		$dataset_description = '';
 		foreach($files AS $f) {
 			if($f == 'drugbank') {
@@ -64,7 +64,7 @@ function Run()
 				$lname = 'drugbank';
 			}
 			$fnx = 'parse_'.$f;
-			
+
 			$rfile = parent::getParameterValue('download_url').$file;
 			$lfile = parent::getParameterValue('indir').$file;
 			$cfile = $lname.".".parent::getParameterValue('output_format');
@@ -73,10 +73,11 @@ function Run()
 			if(!file_exists($lfile) || parent::getParameterValue('download') == true) {
 				utils::downloadSingle($rfile,$lfile);
 			}
-			
+
 			// setup the write
 			$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
 			parent::setWriteFile($outdir.$cfile, $gz);
+			echo $outdir.$cfile;
 			if(file_exists($indir.$file)) {
 				// call the parser
 				echo "processing $file ...".PHP_EOL;
@@ -85,65 +86,65 @@ function Run()
 				parent::clear();
 			}
 			parent::getWriteFile()->close();
-			
+
 			// dataset description
 			$ouri = parent::getGraphURI();
 			parent::setGraphURI(parent::getDatasetURI());
-			
+
 			$source_version = parent::getDatasetVersion();
 			$bVersion = parent::getParameterValue('bio2rdf_release');
 			$prefix = parent::getPrefix();
 			$date = date ("Y-m-d\TH:i:sP");
 			// dataset description
 			$source_file = (new DataResource($this))
-				->setURI($rfile)
-				->setTitle("DrugBank ($file)")
-				->setRetrievedDate( date ("Y-m-d\TH:i:sP", filemtime($indir.$file)))
-				->setFormat("application/xml")
-				->setFormat("application/zip")
-				->setPublisher("http://drugbank.ca")
-				->setHomepage("http://drugbank.ca")
-				->setRights("use")
-				->setRights("by-attribution")
-				->setRights("no-commercial")
-				->setLicense("http://www.drugbank.ca/about")
-				->setDataset("http://identifiers.org/drugbank/");
-			
+			->setURI($rfile)
+			->setTitle("DrugBank ($file)")
+			->setRetrievedDate( date ("Y-m-d\TH:i:sP", filemtime($indir.$file)))
+			->setFormat("application/xml")
+			->setFormat("application/zip")
+			->setPublisher("http://drugbank.ca")
+			->setHomepage("http://drugbank.ca")
+			->setRights("use")
+			->setRights("by-attribution")
+			->setRights("no-commercial")
+			->setLicense("http://www.drugbank.ca/about")
+			->setDataset("http://identifiers.org/drugbank/");
+
 			$output_file = (new DataResource($this))
-				->setURI("http://download.bio2rdf.org/release/$bVersion/$prefix/$cfile")
-				->setTitle("Bio2RDF v$bVersion RDF version of $prefix v$source_version")
-				->setSource($source_file->getURI())
-				->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/drugbank/drugbank.php")
-				->setCreateDate($date)
-				->setHomepage("http://download.bio2rdf.org/release/$bVersion/$prefix/$prefix.html")
-				->setPublisher("http://bio2rdf.org")			
-				->setRights("use-share-modify")
-				->setRights("by-attribution")
-				->setRights("restricted-by-source-license")
-				->setLicense("http://creativecommons.org/licenses/by/3.0/")
-				->setDataset(parent::getDatasetURI());
+			->setURI("http://download.bio2rdf.org/release/$bVersion/$prefix/$cfile")
+			->setTitle("Bio2RDF v$bVersion RDF version of $prefix v$source_version")
+			->setSource($source_file->getURI())
+			->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/drugbank/drugbank.php")
+			->setCreateDate($date)
+			->setHomepage("http://download.bio2rdf.org/release/$bVersion/$prefix/$prefix.html")
+			->setPublisher("http://bio2rdf.org")			
+			->setRights("use-share-modify")
+			->setRights("by-attribution")
+			->setRights("restricted-by-source-license")
+			->setLicense("http://creativecommons.org/licenses/by/3.0/")
+			->setDataset(parent::getDatasetURI());
 
 			$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
 			if($gz) $output_file->setFormat("application/gzip");
 			if(strstr(parent::getParameterValue('output_format'),"nt")) $output_file->setFormat("application/n-triples");
 			else $output_file->setFormat("application/n-quads");
-		
+
 			parent::writeToReleaseFile($source_file->toRDF().$output_file->toRDF());
 			parent::setGraphURI($ouri);
 		}
-        parent::closeReleaseFile();
+		parent::closeReleaseFile();
     }
 
 
-    function parse_drugbank($ldir,$infile)
-    {		
-		$xml = new CXML($ldir,$infile);
+	function parse_drugbank($ldir,$infile)
+	{
+		$xml = new CXML($ldir.$infile);
 		while($xml->parse("drug") == TRUE) {
 			if(isset($this->id_list) and count($this->id_list) == 0) break;
 			$this->parseDrugEntry($xml);
 		}
 		unset($xml);
-    }
+	}
 	
 	    
     function NSMap($source)
@@ -179,122 +180,126 @@ function NSMap($source)
                 return strtolower($source);
         }
     }
-    
-    function parsePartnerEntry($did, &$x,$type)
-    {
-        $id = (string)$x->id;
-        $pid = "drugbank:".$id;
-	$lid = parent::getRes().substr($did,strpos($did,":")+1)."_".$id; // local pivot to keep the action between the drug and target
-        $name = (string) $x->name;
-	$parent = parent::getVoc().ucfirst(str_replace(" ","-",$type));
-        parent::addRDF(
-		parent::describeIndividual($pid,$name,$parent).
-		parent::describeClass($parent,ucfirst($type)).
-		parent::triplify($did,parent::getVoc().$type,$pid).
-		parent::describeIndividual($lid,"$did to $pid relation",parent::getVoc().ucfirst("$type-Relation")).
-		parent::describeClass(parent::getVoc().ucfirst("$type-Relation"), ucfirst("$type Relation")).
-		parent::triplify($lid,parent::getVoc()."drug",$did).
-		parent::triplify($lid,parent::getVoc().$type,$pid)
-        );
-
-        // iterate over all the child nodes
-        foreach($x->children() AS $k => $v) {
-            // get the direct values
-             if(!$v->children()) {
-                // special cases
-                if($k == "references") { // for local pivot
-                    $a = preg_match_all("/pubmed\/([0-9]+)/",$v,$m);
-                    if(isset($m[1])) {
-                        foreach($m[1] AS $pmid) {
-                            parent::addRDF(
-                                parent::triplify($lid,parent::getVoc()."reference","pubmed:".$pmid)
-                            );
-                        }
-                    }
-                } else if($v != '') {
-			if($k == 'known-action') {  // for local pivot
-				parent::addRDF(
-					parent::triplifyString($lid,parent::getVoc().$k,(string)$v)
-				);
-			} else {
-				parent::addRDF(
-					parent::triplifyString($pid,parent::getVoc().$k,(string)$v)
-				);
-			}
-                }
-
-            } else {
-                // work with nested elements
-		$found = false;
-		$list_name = $k;
-		$item_name = substr($k,0,-1);
-		foreach($v->children() AS $k2 => $v2) {
-			if($k2 == "organism") {
-				// extract the ncbi id
-				$taxid = $v2->attributes()->{'ncbi-taxonomy-id'};
-				$label = $v2;
+	
+	function parsePartnerEntry($did, $pid, $x)
+	{
+		$debug = false;
+		if(!isset($x->polypeptide)) {
+			return;
+		}
+		$partner = $x->polypeptide;
+		
+		foreach($partner->children() AS $k1 => $v1) {
+			// get the direct values
+			$tv1 = trim($v1);
+			$nc  = count($v1->children());
+			
+			if($debug) echo "tv1 $nc $k1 $tv1".PHP_EOL;
+			if($nc == 0) {
+				if($debug) echo "k1 $k1 $v1".PHP_EOL;
 				parent::addRDF(
-					parent::triplify($pid, parent::getVoc()."x-taxonomy", "taxonomy:$taxid").
-					parent::triplifyString("taxonomy:$taxid","rdfs:label",$label)
+					parent::triplifyString($pid,parent::getVoc().$k1,(string)$v1)
 				);
-				continue;
-			}
-
-			if(!$v2->children()) {
-				// echo "not nested $k2".PHP_EOL;
-				if($k2 == "action") {
-					$aid = str_replace(array(" ","/"),"-",$v2);
+				
+				if($k1 == "organism") {
+					$taxid = $v1->attributes()->{'ncbi-taxonomy-id'};
 					parent::addRDF(
-						parent::describeIndividual($lid,$v2,parent::getVoc()."Action").
-						parent::describeClass(parent::getVoc()."Action","Action").
-						parent::triplify($lid,parent::getVoc()."action",parent::getVoc().$aid)
+						parent::triplify($pid, parent::getVoc()."x-taxonomy", "taxonomy:$taxid")
 					);
-				} else {
-					// default handler
+				}
+				continue;
+			} 
+
+			foreach($v1->children() AS $k2 => $v2) {
+				$tv2 = trim($v2);
+				$nc  = count($v2->children());
+				
+				if($debug) echo "tv2 $nc $k2 $tv2".PHP_EOL;
+				if($nc == 0) {
+					if($debug) echo "k2 $k2 $v2".PHP_EOL;
 					parent::addRDF(
-						parent::triplifyString($pid, parent::getVoc().$k2, "".$v2)
+						parent::triplifyString($pid,parent::getVoc().$k2,(string)$v2)
 					);
+					continue;
 				}
-			} else { // nested elements
-				// echo "nested $k2".PHP_EOL;
-				foreach($v2->children() AS $k3 => $v3) {
-					// echo " ".$k3.PHP_EOL;
-					if(!$v3->children()) {
+				
+				if($k2 == 'external-identifier') {
+					$ns = $this->NSMap($v2->resource);
+					$id = (string) $v2->identifier;
+					$id = str_replace(array("HGNC:","GNC:"),"",$id);
+					parent::addRDF(
+						parent::triplify($pid, parent::getVoc()."x-$ns","$ns:$id")
+					);
+					if($ns == "uniprot") {
 						parent::addRDF(
-							parent::triplifyString($pid,parent::getVoc().$k3, "".$v3)
+							parent::triplify("$ns:$id","skos:exactMatch","http://purl.uniprot.org/uniprot/$id")
 						);
-					} else {
-						foreach($v3 AS $k4 => $v4) {
-							if($k3 == 'external-identifier') {
-								$ns = $this->NSMap($v3->resource);
-								$id = (string) $v3->identifier;
-								$id = str_replace(array("HGNC:","GNC:"),"",$id);
-								parent::addRDF(
-									parent::triplify($pid, parent::getVoc()."x-$ns","$ns:$id")
-								);
-							} else if($k3 == 'pfam') {
-								parent::addRDF(
-									parent::triplify($pid, parent::getVoc()."x-pfam","pfam:"."".$v3->identifier)
-								);
-							} else if($k3 == "go-classifier") {
-								parent::addRDF(
-									parent::triplifyString($pid, parent::getVoc()."go-".$v3->category, $v3->description)
-								);
-							} else {
-								trigger_error("no handler for $k3",E_USER_WARNING);
-/*								parent::addRDF(
-									parent::triplifyString($pid, parent::getVoc().$k3, $v4)
-								);
-*/
-							}
-						 }
 					}
+				} else if($k2 == 'pfam') {
+					parent::addRDF(
+						parent::triplify($pid, parent::getVoc()."x-pfam","pfam:"."".$v2->identifier)
+					);
+				} else if($k2 == "go-classifier") {
+					parent::addRDF(
+						parent::triplifyString($pid, parent::getVoc()."go-".$v2->category, $v2->description)
+					);
+				} else {
+					trigger_error("no handler for $k2",E_USER_WARNING);
+	/*					parent::addRDF(
+							parent::triplifyString($pid, parent::getVoc().$k3, $v4)
+						);
+	*/
 				}
 			}
-		} // foreach
-            }
-         }
-    }
+		}
+	}
+ 
+	
+    function parsePartnerRelation($did, &$x,$type)
+    {	
+		$id = (string)$x->id;
+		$pid = "drugbank:".$id;
+		$lid = parent::getRes().substr($did,strpos($did,":")+1)."_".$id; // local pivot to keep the action between the drug and target
+		$parent = parent::getVoc().ucfirst(str_replace(" ","-",$type));
+		$name = (string) $x->name;
+		$knownaction = (string) $x->{'known-action'};
+		$knownaction = $knownaction=="unknown"?'':$knownaction;
+
+		parent::addRDF(
+			parent::describeIndividual($pid,$name,$parent).
+			parent::describeClass($parent,ucfirst($type)).
+			parent::triplify($did,parent::getVoc().$type,$pid).
+			parent::describeIndividual($lid,"$did to $pid relation",parent::getVoc().ucfirst("$type-Relation")).
+			parent::describeClass(parent::getVoc().ucfirst("$type-Relation"), ucfirst("$type Relation")).
+			parent::triplify($lid,parent::getVoc()."drug",$did).
+			parent::triplify($lid,parent::getVoc().$type,$pid).
+			parent::triplifyString($lid, parent::getVoc()."known-action", $knownaction)
+		);
+		
+		// the main elements for the relation are actions, known-action, references, 
+		foreach($x->actions AS $actions => $action) {
+			if(!trim($action)) continue;
+			$aid = str_replace(array(" ","/"),"-",$action->action);
+			$auri = parent::getVoc().$aid;
+			parent::addRDF(
+				parent::describeIndividual($auri,$action->action,parent::getVoc()."Action").
+				parent::describeClass(parent::getVoc()."Action","Action").
+				parent::triplify($lid,parent::getVoc()."action",$auri)
+			);	
+		}
+		if(isset($x->references)) {
+			foreach( explode("\n",$x->references) AS $ref) {
+				preg_match_all("/pubmed\/([0-9]+)/",$ref,$m);
+				foreach($m[1] AS $pmid) {
+					parent::addRDF(
+						parent::triplify($lid,parent::getVoc()."reference","pubmed:".$pmid)
+					);
+				}
+			}
+		}
+		
+		$this->parsePartnerEntry($did, $pid, $x);
+	}
 
     /**
     * @description check if a type has already been defined and add appropriate RDF
@@ -315,393 +320,399 @@ function typify($id,$tid,$subclass,$label)
 
     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 $dbid.PHP_EOL;
-	if(isset($x->description) && $x->description != '') {
-		$description = trim((string)$x->description);
-        }
+		$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]);
+		}
 
-        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)
-        );
+		echo "Processing $dbid".PHP_EOL;
+		if(isset($x->description) && $x->description != '') {
+			$description = trim((string)$x->description);
+		}
 
-	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'})
+			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)
 		);
-	}
- 
-	$literals = array(
-		"indication",
-		"pharmacology",
-		"mechanism-of-action",
-		"toxicity",
-		"biotransformation",
-		"absorption",
-		"half-life",
-		"protein-binding",
-		"route-of-elimination",
-		"volume-of-distribution",
-		"clearance"
-	);
-
-	foreach($literals AS $l) {
-		if(isset($x->$l) and $x->$l != '') {
-			$lid = parent::getRes().md5($l.$x->$l);
+
+		foreach($x->{'drugbank-id'} AS $id) {
 			parent::addRDF(
-				parent::describeIndividual($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)
+				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");
+		$this->AddList($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", $cid)
-			);
+		if(isset($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');
+		$this->addLinkedResource($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");
+		// taxonomy
+		$this->AddText($x,$did,"taxonomy","kingdom",parent::getVoc()."kingdom");
 
-        // substructures
-        $this->AddText($x,$did,"taxonomy","substructures",parent::getVoc()."substructure", "substructure");
+		// substructures
+		$this->AddText($x,$did,"taxonomy","substructures",parent::getVoc()."substructure", "substructure");
 
-        // synonyms
-        $this->AddCategory($x,$did,"synonyms","synonym",parent::getVoc()."synonym");
+		// synonyms
+		$this->AddCategory($x,$did,"synonyms","synonym",parent::getVoc()."synonym");
 
-        // brand names
-        $this->AddCategory($x,$did,"brands","brand",parent::getVoc()."brand");
+		// 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:".$s->{'inchikey'})
-			);
+		// salt
+		if(isset($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);
+		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($did,parent::getVoc()."packager",$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","".$item->url[0])
+						parent::triplify($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]) 
 					);
-				}
-                    }
-                 }
-             }
-         }
-     }     
-
-//      // 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)
-			);
+					$a = explode(" + ",$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)
+						);
+					}
+				}
+			}
 		}
-	}
 
-     // 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 ".$dosage->route. " route";
+		// packagers
+		// <packagers><packager><name>Cardinal Health</name><url>http://www.cardinal.com</url></packager>
+		if(isset($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::describeIndividual($id,$label,parent::getVoc()."Dosage").
-			parent::describeClass(parent::getVoc()."Dosage","Dosage").
-			parent::triplify($did, parent::getVoc()."dosage", $id)
-		);
+						parent::addRDF(
+							parent::triplify($did,parent::getVoc()."packager",$pid)
+						);
+						if(!isset($defined[$pid])) {
+							$defined[$pid] = '';
+							parent::addRDF(
+								parent::describe($pid,"".$item->name[0])
+							);
 
-		$rid = parent::getVoc().md5($dosage->route);
-		$this->typify($id,$rid,"Route","".$dosage->route);
+							if(strstr($item->url,"http://") && $item->url != "http://BASF Corp."){
+								parent::addRDF(
+									$this->triplify($pid,"rdfs:seeAlso","".$item->url[0])
+								);
+							}
+						}
+					}
+				}
+			}
+		}     
 
-		$fid =  parent::getVoc().md5($dosage->form);
-		$this->typify($id,$fid,"Form","".$dosage->form);
+		// manufacturers
+		$this->AddText($x,$did,"manufacturers","manufacturer",parent::getVoc()."manufacturer"); // @TODO RESOURCE
 
-		if($dosage->strength != '') {
-			parent::addRDF(
-				parent::triplifyString($id, parent::getVoc()."strength", $dosage->strength)
-			);
+		// prices
+		if(isset($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)
+				);
+			}
 		}
-         }
-     }
-
-    // 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 ".$property->source);
+
+		// dosages <dosages><dosage><form>Powder, for solution</form><route>Intravenous</route><strength></strength></dosage>
+		if(isset($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($dosage->strength != '') {
 					parent::addRDF(
-						parent::describeIndividual($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)
+						parent::triplifyString($id, parent::getVoc()."strength", $dosage->strength)
 					);
-
-					// Source
-					if(isset($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)
-							);
-						}
-					 }       
-				 }
-			 }
+				}
+			}
 		}
-     } 
+
+		// 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;
+		// 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","".$patent->expires)
-             );
+				parent::addRDF(
+					parent::triplify($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);
-         }
-     }
+				$cid = parent::getRes().md5($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) {  
-					$this->parsePartnerEntry($did,$item,$partner);
-					parent::writeRDFBufferToWriteFile();
+		// 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")
-                 );
-             }
-         }
-     }
-     // <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();
-    }
+		// 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")
+						);
+					}
+				}
+			}
+		}
 
-    function AddLinkedResource(&$x, $id, $list_name,$item_name,$ns)
-    {
-        if(isset($x->$list_name)) {
-            foreach($x->$list_name AS $item) {
-                if(isset($item->$item_name) && ($item->$item_name != '')) {
-			if($item_name == "atc-code") {
-				$l = $ns.":".$item->$item_name->attributes()->code;
-			} else {
-				$l = $ns.":".$item->$item_name;
+		// 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")
+						);
+					}
+
+				}
 			}
-			$this->addRDF($this->triplify($id,parent::getVoc()."x-$ns",trim($l)));
-                }
-            }
-        }
-    }
+		}
+		// <external-links>
+		if(isset($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();
+	}
 
-    function AddText(&$x, $id, $list_name,$item_name,$predicate, $list_item_name = null)
-    {
-        if(isset($x->$list_name)) {
-            foreach($x->$list_name AS $item) {
-                if(isset($item->$item_name) && ($item->$item_name != '')) { 
-                    $l = $item->$item_name;
-                    if(isset($l->$list_item_name)) {
-                        foreach($l->$list_item_name AS $k) {
-				$kid = parent::getRes().md5($k);
-				$this->addRDF(
-					$this->describeIndividual($kid,"$item_name for $id",parent::getVoc().ucfirst($item_name)).
-					$this->describeClass(parent::getVoc().ucfirst($item_name),$item_name).
-					$this->triplifyString($kid,"rdf:value",$k).
-					$this->triplify($id,$predicate,$kid)
-				);
-                        }
-                    } else {
+	function AddLinkedResource(&$x, $id, $list_name,$item_name,$ns)
+	{
+		if(isset($x->$list_name)) {
+			foreach($x->$list_name AS $item) {
+				if(isset($item->$item_name) && ($item->$item_name != '')) {
+					if($item_name == "atc-code") {
+						$l = $ns.":".$item->$item_name->attributes()->code;
+					} else {
+						$l = $ns.":".$item->$item_name;
+					}
+					$this->addRDF($this->triplify($id,parent::getVoc()."x-$ns",trim($l)));
+				}
+			}
+		}
+	}
+
+	function AddText(&$x, $id, $list_name,$item_name,$predicate, $list_item_name = null)
+	{
+		if(isset($x->$list_name)) {
+			foreach($x->$list_name AS $item) {
+				if(isset($item->$item_name) && ($item->$item_name != '')) { 
+					$l = $item->$item_name;
+					if(isset($l->$list_item_name)) {
+						foreach($l->$list_item_name AS $k) {
+							$kid = parent::getRes().md5($k);
+							$this->addRDF(
+								$this->describeIndividual($kid,"$item_name for $id",parent::getVoc().ucfirst($item_name)).
+								$this->describeClass(parent::getVoc().ucfirst($item_name),$item_name).
+								$this->triplifyString($kid,"rdf:value",$k).
+								$this->triplify($id,$predicate,$kid)
+							);
+						}
+					} else {
 						$kid = parent::getRes().md5($l);
-                        $this->addRDF(
+						$this->addRDF(
 							$this->describeIndividual($kid,"$item_name for $id",parent::getVoc().ucfirst($item_name)).
 							$this->describeClass(parent::getVoc().ucfirst($item_name),$item_name).
 							$this->triplifyString($kid,"rdf:value",$l).
 							$this->triplify($id,$predicate,$kid)
 						);
-                    }
-                }
-            }
-        }
-    }
+					}
+				}
+			}
+		}
+	}
 	
 	function AddCategory(&$x, $id, $list_name, $item_name, $predicate, $list_item_name = null) 
 	{
@@ -709,60 +720,57 @@ function AddCategory(&$x, $id, $list_name, $item_name, $predicate, $list_item_na
 			foreach($x->$list_name AS $item) {
 				if(isset($item->$item_name) && ($item->$item_name != '')) { 
 					$l = $item->$item_name;
-					if(isset($l->$list_item_name)) {
-						foreach($l->$list_item_name AS $k) {
-							$kid = parent::getVoc().ucfirst(str_replace(" ","-",$k));
-							$this->addRDF(
-								$this->describeIndividual($kid,ucfirst($k),parent::getVoc().ucfirst($item_name)).
-								$this->describeClass(parent::getVoc().ucfirst($item_name),ucfirst($item_name)).
-								$this->triplify($id,$predicate,$kid)
-							);
-						}
-					} else {
-						if($item_name == "synonym") {
-							$kid = parent::getvoc().md5($l);
-						} else {
-							$kid = parent::getVoc().ucfirst(str_replace(" ","-",$l));
-						}
+					$att = ($l->attributes()); 
+					foreach($l AS $key => $item_value) {
+						$kid = parent::getvoc().md5($item_value);
 						$this->addRDF(
-							$this->describeIndividual($kid,ucfirst($l),parent::getVoc().ucfirst($item_name)).
-							$this->describeClass(parent::getVoc().ucfirst($item_name),ucfirst($item_name)).
+							$this->describeIndividual($kid,"".$item_value,parent::getVoc().ucfirst($item_name)).
+							$this->describeClass(parent::getVoc().ucfirst($item_name),ucfirst("".$item_name)).
 							$this->triplify($id,$predicate,$kid)
 						);
-						foreach($l->attributes() AS $ka => $va) {
+						foreach($att AS $ka => $va) {
 							parent::addRDF(
-								$this->triplifyString($kid, parent::getVoc().$ka, $va)
+								$this->triplifyString($kid, parent::getVoc().$ka, "".$va)
 							);
 						}
 					}
+					$kid = parent::getvoc().md5($l->asXML());
+					foreach($l->children() AS $k2 => $v2) {
+						$this->addRDF(
+							$this->describeIndividual($kid,($k2=="name"?$v2:$predicate),parent::getVoc().ucfirst($k2)).
+							$this->describeClass(parent::getVoc().ucfirst($k2),ucfirst("".$v2)).
+							$this->triplifyString($kid, parent::getVoc().$k2, $v2).
+							$this->triplify($id, $predicate, $kid)
+						);
+					}
 				}
 			}
 		}
 	}
-	
+
 	function AddList(&$x, $id, $list_name, $item_name, $predicate, $list_item_name = null)
-{
-	if(isset($x->$list_name)) {
-		foreach($x->$list_name->$item_name AS $k => $item) {
-			if(isset($item->$item_name)) {
-				foreach($item->$item_name AS $k => $v) {
-					$mylist[] = ''.$v;
-				}
-			} else $mylist[] = ''.$item;
+	{
+		if(isset($x->$list_name)) {
+			foreach($x->$list_name->$item_name AS $k => $item) {
+				if(isset($item->$item_name)) {
+					foreach($item->$item_name AS $k => $v) {
+						$mylist[] = ''.$v;
+					}
+				} else $mylist[] = ''.$item;
+			}
 		}
-	}
-	if(isset($mylist)) {
-		foreach($mylist AS $item) {
-			$label = ''.$item;
-			$kid = parent::getVoc().ucfirst(str_replace(" ","-",$label)); // generate a new identifier for the list item
-			$this->addRDF(
-				$this->describeIndividual($kid,$label,parent::getVoc().ucfirst($item_name)).
-				$this->describeClass(parent::getVoc().ucfirst($item_name),ucfirst($item_name)).
-				$this->triplify($id,$predicate,$kid)
-			);
+		if(isset($mylist)) {
+			foreach($mylist AS $item) {
+				$label = ''.$item;
+				$kid = parent::getVoc().ucfirst(str_replace(" ","-",$label)); // generate a new identifier for the list item
+				$this->addRDF(
+					$this->describeIndividual($kid,$label,parent::getVoc().ucfirst($item_name)).
+					$this->describeClass(parent::getVoc().ucfirst($item_name),ucfirst($item_name)).
+					$this->triplify($id,$predicate,$kid)
+				);
+			}
 		}
 	}
-}
 
 } // end class
 
diff --git a/goa/goa.php b/goa/goa.php
index 1c5a067..9d3f6d6 100644
--- a/goa/goa.php
+++ b/goa/goa.php
@@ -36,7 +36,8 @@ class GOAParser extends Bio2RDFizer
 {
 	function __construct($argv) {
 		parent::__construct($argv,"goa");
-		parent::addParameter('files',true,'all|arabidopsis|chicken|cow|dicty|dog|fly|human|mouse|pdb|pig|rat|uniprot|worm|yeast|zebrafish','all','all or comma-separated list of files to process');
+//		parent::addParameter('files',true,'all|arabidopsis|chicken|cow|dicty|dog|fly|human|mouse|pdb|pig|rat|uniprot|worm|yeast|zebrafish','all','all or comma-separated list of files to process');
+		parent::addParameter('files',true,'all|arabidopsis|chicken|cow|dicty|dog|fly|human|mouse|pig|rat|worm|yeast|zebrafish','all','all or comma-separated list of files to process');
 		parent::addParameter('download_url',false,null,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/');		
 		parent::initialize();
 	}
@@ -161,9 +162,13 @@ function process($file){
 
 			//entity id
 			$eid = $this->getdbURI($db,$id);
+if(!$eid) {
+print_r($fields);
+continue;
+}
 			parent::addRDF(
 				parent::describeIndividual($eid,$label,parent::getVoc()."GO-Annotation").
-				parent::describeClass(parent::getVoc()."GO-Annotation","GO Annotation").
+ 				parent::describeClass(parent::getVoc()."GO-Annotation","GO Annotation").
 				parent::triplifyString($eid,parent::getVoc()."symbol",$symbol)
 			);
 			parent::addRDF(
@@ -261,6 +266,8 @@ function getdbURI($db_id, $db_object_id){
 		} else if ($db_id == "PDB"){
 			$split_object = explode("_", $db_object_id);
 			$returnMe = "pdb:".$split_object[0]."/chain_".$split_object[1];
+		} else {
+			$returnMe = $db_id.":".$db_object_id;
 		}
 		return $returnMe;
 	}
diff --git a/hgnc/hgnc.php b/hgnc/hgnc.php
index 94ab10d..164bcf5 100755
--- a/hgnc/hgnc.php
+++ b/hgnc/hgnc.php
@@ -117,11 +117,13 @@ function Run(){
 	function process(){
 		$header = $this->GetReadFile()->Read(200000);
 		$header_arr = explode("\t", $header);
-
-		if (count($header_arr) != 40)
+		$n = 41;
+		$c = count($header_arr);
+		if ($c != $n)
 		{
 			echo PHP_EOL;
-			trigger_error ("Header format is different than expected, please update the script",E_USER_ERROR);
+			print_r($header_arr);
+			trigger_error ("Expected $n columns, found $c . please update the script",E_USER_ERROR);
 			exit;
 		}
 
@@ -164,9 +166,10 @@ function process(){
 			$refseq_mappeddatasuppliedbyNCBI = $fields[34];
 			$uniprot_id_mappeddatasuppliedbyUniProt = $fields[35];
 			$ensembl_id_mappeddatasuppliedbyEnsembl = $fields[36];
-			$ucsc_id_mappeddatasuppliedbyUCSC = $fields[37];
-			$mouse_genome_database_id_mappeddatasuppliedbyMGI = $fields[38];
-			$rat_genome_database_id_mappeddatasuppliedbyRGD = $fields[39];
+			$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;
@@ -464,6 +467,15 @@ function process(){
 				}
 			}
 
+			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 $ucsc_id) {
diff --git a/irefindex/irefindex.php b/irefindex/irefindex.php
index d5a7ceb..d6d1c0d 100644
--- a/irefindex/irefindex.php
+++ b/irefindex/irefindex.php
@@ -33,8 +33,8 @@ class irefindexParser extends Bio2RDFizer
 {
 	function __construct($argv) { //
 		parent::__construct($argv,"irefindex");
-		parent::addParameter('files',true,'all|10090|10116|4932|559292|562|6239|7227|9606|A','all','all or comma-separated list of files to process');
-		parent::addParameter('version',false,'08122013|03022013|10182011','08122013','dated version of files to download');
+		parent::addParameter('files',true,'all|10090|10116|4932|559292|562|6239|7227|9606','all','all or comma-separated list of files to process');
+		parent::addParameter('version',false,'07042015|08122013|03022013|10182011','07042015','dated version of files to download');
 		parent::addParameter('download_url',false,null,'http://irefindex.org/download/irefindex/data/current/psi_mitab/MITAB2.6/');
 		parent::initialize();
 	}
@@ -55,9 +55,8 @@ function Run()
 
 		foreach($files AS $file) {
 			$download = parent::getParameterValue('download');
-
-			$base_file = ucfirst($file).".mitab.".parent::getParameterValue("version").".txt";
-			$zip_file  = $base_file.".zip";
+			$version = parent::getParameterValue("version");
+			$zip_file  = ucfirst($file).".mitab.".$version.".txt.zip";
 			$lfile = $ldir.$zip_file;
 
 			$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
@@ -82,9 +81,14 @@ function Run()
 				trigger_error("Unable to open $lfile");
 				exit;
 			}
+			if($zin->numFiles != 1) {
+				trigger_error("Found more than one file ... using first file");
+			}
+			$f = $zin->statIndex(0);
+			$base_file = $f['name'];
 			if(($fp = $zin->getStream($base_file)) === FALSE) {
-					trigger_error("Unable to get $base_file in ziparchive $lfile");
-					return FALSE;
+				trigger_error("Unable to get $base_file in ziparchive $lfile");
+				return FALSE;
 			}
 			parent::setReadFile($lfile);
 			parent::getReadFile()->setFilePointer($fp);
diff --git a/kegg/kegg.php b/kegg/kegg.php
index 4bf7e0a..db6dcf6 100644
--- a/kegg/kegg.php
+++ b/kegg/kegg.php
@@ -230,6 +230,7 @@ function process($db)
 				parent::describeIndividual($uri,$name,parent::getVoc().ucfirst($db)).
 				parent::describeClass(parent::getVoc().ucfirst($db),"KEGG $db").
 				parent::triplifyString($uri,parent::getVoc()."internal-id",$nsid)
+				// http://www.kegg.jp/entry/
 			);
 
 			// now get the entries for each
@@ -248,6 +249,23 @@ function process($db)
 			echo "parsing $nsid ... ";
 			$this->parseEntry($lfile);
 			parent::writeRDFBufferToWriteFile();
+			
+			if($db === "pathway") {
+					$ko = str_replace("map","ko",$id);
+					$lfile = $ldir.$id.".kgml";
+					$rfile = "http://www.kegg.jp/kegg-bin/download?entry=".$ko."&format=kgml";
+					if(!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
+						echo "downloading KGML for $nsid ";
+						$ret = utils::downloadSingle($rfile,$lfile);
+						if($ret === false) {
+							echo "unable to download ".$nsid." ... skipping".PHP_EOL;
+							continue;
+						}
+						echo "done. ";
+					}
+					$this->parseKGML($lfile);
+					parent::writeRDFBufferToWriteFile();
+			}
 			echo "done!".PHP_EOL;
 		}
 	}
@@ -719,6 +737,99 @@ function parseEntry($lfile)
 		fclose($fp);
 	}
 	
+	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::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;				
+	}
 }
 
 
diff --git a/lsr/lsr.php b/lsr/lsr.php
index 19d8f48..df8fb93 100644
--- a/lsr/lsr.php
+++ b/lsr/lsr.php
@@ -47,7 +47,7 @@ function run()
 		$ifile = "registry.csv";
 		$lfile = $idir.$ifile;
 		if(!file_exists($lfile) or parent::getParameterValue("download") == "true") {
-			echo "Downloading regsitry";
+			echo "Downloading registry";
 			utils::downloadSingle($rfile,$lfile);
 			echo "done".PHP_EOL;
 		}
@@ -109,17 +109,11 @@ function parse()
 			if(!isset($r['preferredPrefix'])) continue;
 			$dataset = $r['preferredPrefix'];
 			$id = $this->getNamespace().$r['preferredPrefix'];
-			
+
 			parent::addRDF( 
-				parent::QQuad($id,"rdf:type","dcat:Dataset").
-				parent::QQuad($id,"rdf:type","lsr:Dataset").
-				parent::QQuadL($id,"dc:title",$r['title']).
-				parent::QQuadL($id,"dc:description",$r['description']).
-				parent::QQuadL($id,"rdfs:label", $r['title']." [".$id."]").
-				parent::QQuadL($id,"dc:identifier",$id).
-				parent::QQuadL($id,"bio2rdf:identifier", $r['preferredPrefix']).
-				parent::QQuadL($id,"bio2rdf:namespace", "lsr")
-//				parent::describeIndividual($id,$r['title'],"dcat:Dataset",$r['title'],$r['description'])
+				parent::describeIndividual($id,$r['title'],"lsr_vocabulary:Dataset",$r['title'],$r['description']).
+				parent::describeClass("lsr_vocabulary:Dataset","LSR Dataset").
+				parent::triplify($id,"rdf:type","dctypes:Dataset")
 			);
 			parent::addRDF(
 				parent::triplifyString($id,"idot:preferredPrefix",$r['preferredPrefix'])
@@ -130,25 +124,27 @@ function parse()
 					if(trim($syn) == '') continue;
 					$syn = $this->getRegistry()->normalizePrefix(preg_replace("/\([^\)]+/","",$syn));
 					parent::addRDF(
-						parent::QQuadL($id,"idot:alternativePrefix",$syn)
+						parent::triplifyString($id,"idot:alternativePrefix",$syn)
 					);
 				}
 			}
 			if($r['providerURI']) {
-				parent::QQuad($id,"void:uriRegexPattern",$r['providerURI']);
+				parent::triplifyString($id,"void:uriRegexPattern",$r['providerURI'], "xsd:anyUri");
 			}
 			if($r['alternateURI']) {
 				foreach( explode(",",$r['alternateURI']) AS $alt_uri) {
-					parent::addRDF(
-						parent::QQuad($id,"void:uriRegexPattern",$alt_uri)
-					);
+					if(trim($alt_uri) != '') {
+						parent::addRDF(
+							parent::triplifyString($id,"void:uriRegexPattern",$alt_uri, "xsd:anyUri")
+						);
+					}
 				}
 			}
 			if($r['miriam']) {
 				foreach(explode(",",$r['miriam']) AS $miriam) {
 					$miriam_id = str_replace("MIR:","",$miriam);
 					parent::addRDF(
-						parent::QQuad($id,$this->getVoc()."x-miriam","miriam:$miriam_id").
+						parent::triplify($id,$this->getVoc()."x-miriam","miriam:$miriam_id").
 						parent::triplify("miriam:$miriam_id","bio2rdf_vocabulary:url",'http://identifiers.org/'.$dataset)
 					);
 				}
@@ -157,7 +153,7 @@ function parse()
 				foreach(explode(",",$r['biodbcore']) AS $biodbcore_id) {
 					$biodbcore = "biodbcore:$biodbcore_id";
 					parent::addRDF(
-						parent::QQuad($id,$this->getVoc()."x-biodbcore",$biodbcore).
+						parent::triplify($id,$this->getVoc()."x-biodbcore",$biodbcore).
 						parent::triplify($biodbcore,"bio2rdf_vocabulary:url","http://www.biosharing.org/$biodbcore_id")
 					);
 				}
@@ -165,44 +161,44 @@ function parse()
 			if($r['bioportal']) {
 				foreach(explode(",",$r['bioportal']) AS $bioportal) {
 					parent::addRDF(
-						parent::QQuad($id,$this->getVoc()."x-bioportal","bioportal:".$bioportal)
+						parent::triplify($id,$this->getVoc()."x-bioportal","bioportal:".$bioportal)
 					);
 				}
 			}
 			if($r['datahub']) {
 				parent::addRDF(
-					parent::QQuad($id,$this->getVoc()."x-datahub","datahub:".$r['datahub'])
+					parent::triplify($id,$this->getVoc()."x-datahub","datahub:".$r['datahub'])
 				);
 			}
 			if($r['pubmed']) {
 				foreach(explode(",",$r['pubmed']) AS $pubmed) {
 					parent::addRDF(
-						parent::QQuad($id,"cito:citesAsAuthority","pubmed:".$pubmed).
-						parent::QQuad("pubmed:".$pubmed, "rdf:type", "pubmed_vocabulary:Resource")
+						parent::triplify($id,"cito:citesAsAuthority","pubmed:".$pubmed)
+//						parent::triplify("pubmed:".$pubmed, "rdf:type", "pubmed_vocabulary:Resource")
 					);
 				}
 			}
 			if($r['abbreviation']) {
 				parent::addRDF(
-					parent::QQuadL($id,"dc:alternative",$r['abbreviation'])
+					parent::triplifyString($id,"dc:alternative",$r['abbreviation'])
 				);
 			}
 			if($r['organization']) {
 				$pid = parent::getRes().md5($r['organization']);
 				parent::addRDF(
-					parent::QQuad($id,"dc:publisher", $pid).
-					parent::QQuadL($pid, "dc:title", $r['organization'])
+					parent::triplify($id,"dc:publisher", $pid).
+					parent::triplifyString($pid, "dc:title", $r['organization'])
 				);
 			}
 			if($r['type']) {
 				parent::addRDF(
-					parent::QQuadL($id,$this->getVoc()."type",$r['type'])
+					parent::triplifyString($id,$this->getVoc()."type",$r['type'])
 				);
 			}
 			foreach( explode(",",$r['keywords']) AS $keyword) {
 				if($keyword) {
 					parent::addRDF(
-						parent::QQuadL($id,"dcat:keyword",$keyword)
+						parent::triplifyString($id,"dcat:keyword",$keyword)
 					);
 				}
 			}
@@ -210,38 +206,38 @@ function parse()
 				&& $r['homepage'] !== 'dead'
 				&& $r['homepage'] !== 'unavailable') {
 				parent::addRDF(
-					parent::QQuad($id,"foaf:page",$r['homepage'])
+					parent::triplify($id,"foaf:page",$r['homepage'])
 				);
 			}
 			if($r['license']) {
 				parent::addRDF(
-					parent::QQuad($id,"dc:license",$r['license'])
+					parent::triplify($id,"dc:license",$r['license'])
 				);
 			}
 			if($r['licenseText']) {
 				parent::addRDF(
-					parent::QQuadL($id,$this->getVoc()."license-text",$r['licenseText'])
+					parent::triplifyString($id,$this->getVoc()."license-text",$r['licenseText'])
 				);
 			}
 			foreach(explode(",",$r['rights']) AS $right) {
 				if($right) {
 					parent::addRDF(
-						parent::QQuadL($id,"dc:rights",$right)
+						parent::triplifyString($id,"dc:rights",$right)
 					);
 				}
 			}
 			parent::addRDF(
-				parent::QQuadL($id,"idot:identifierPattern",$r['id_regex'])
+				parent::triplifyString($id,"idot:identifierPattern",$r['id_regex'])
 			);
 			parent::addRDF(
-				parent::QQuadL($id,"idot:exampleIdentifier",$r['example_id'])
+				parent::triplifyString($id,"idot:exampleIdentifier",$r['example_id'])
 			);
 			if($r['html_template']
 				&& $r['html_template'] !== 'unavailable'
 				&& $r['html_template'] !== 'N/A') {
 
 				parent::addRDF(
-					parent::QQuadL($id,"idot:accessPattern",$r['html_template'])
+					parent::triplifyString($id,"idot:accessPattern",$r['html_template'])
 				);
 			}
 
diff --git a/mgi/mgi.php b/mgi/mgi.php
index 2be4e83..bbb1359 100644
--- a/mgi/mgi.php
+++ b/mgi/mgi.php
@@ -403,7 +403,7 @@ function MGI_Geno_Disease()
 			if(!$allele) {echo "ignoring ".$a[0].PHP_EOL;continue;}
 
 			$alleles = explode("|",strtolower($a[2]));
-
+			$genotype = $a[0];
 			$diseases = explode(",",$a[7]);
 			foreach($diseases AS $d) {
 				$disease = "omim:$d";
@@ -413,6 +413,7 @@ function MGI_Geno_Disease()
 					parent::addRDF(
 						parent::describeIndividual($id, $label, $this->getVoc()."Allele-Disease-Association").
 						parent::describeClass($this->getVoc()."Allele-Disease-Association","MGI Allele-Disease Association").
+						parent::triplifyString($id,$this->getVoc()."genotype-string",$genotype).
 						parent::triplify($id,$this->getVoc()."allele",$allele).
 						parent::triplify($id,$this->getVoc()."disease",$disease)
 					);
@@ -450,6 +451,7 @@ function MGI_Geno_NotDisease()
 				continue;
 			}
 			
+			$genotype = $a[0];
 			$alleles = explode("|",strtolower($a[2]));
 			$diseases = explode(",",$a[7]);
 			foreach($diseases AS $d) {
@@ -462,6 +464,7 @@ function MGI_Geno_NotDisease()
 						parent::describeIndividual($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")
 					);
diff --git a/miriam/miriam.php b/miriam/miriam.php
new file mode 100644
index 0000000..31bd80d
--- /dev/null
+++ b/miriam/miriam.php
@@ -0,0 +1,232 @@
+<?php
+/**
+Copyright (C) 2012 Michel Dumontier
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+*/
+
+require_once(__DIR__.'/../../php-lib/bio2rdfapi.php');
+require_once(__DIR__.'/../../php-lib/xmlapi.php');
+
+/**
+ * MIRIAM DB RDFizer
+ * @version 1.0 
+ * @author Michel Dumontier
+ * @description http://www.ebi.ac.uk/miriam/
+*/
+class MIRIAMParser extends Bio2RDFizer 
+{	
+	private $version = null;
+	
+	function __construct($argv) {
+		parent::__construct($argv,"miriam");
+		parent::addParameter('files',true,'all','all','files to process');
+		parent::addParameter('download_url',false,null,'http://www.ebi.ac.uk/miriam/main/export/xml/');
+		parent::addParameter('overwrite',false,'true|false','false','overwrite existing files with download option');
+		parent::initialize();
+	}
+	
+	function Run()
+	{	
+		echo "processing miriam database";
+	
+		// directory shortcuts
+		$ldir = $this->getParameterValue('indir');
+		$odir = $this->getParameterValue('outdir');
+		
+		// download and set the read file
+		$file = 'miriam.xml';
+		$rfile = $this->getParameterValue("download_url");
+		$lfile = $ldir.$file;
+		if(!file_exists($lfile) || $this->getParameterValue("download") == "true") {
+			utils::downloadSingle($rfile,$lfile);
+		}
+		
+		parent::setReadFile($lfile);
+
+		// set the write file
+		$outfile = "miriam.".parent::getParameterValue('output_format');
+		$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
+		parent::setWriteFile(parent::getParameterValue("outdir").$outfile,$gz);		
+		$this->parse();
+		parent::WriteRDFBufferToWriteFile();
+		$this->getWriteFile()->Close();
+				
+		return true;
+	}	
+	
+	function parse()
+	{
+		// convert into json
+		$lfile = parent::getReadFile()->getFileName();
+		$xml = simplexml_load_file($lfile);
+		$json = json_encode($xml);
+		$db = json_decode($json,TRUE);
+		
+		// miriam metadata
+		// $attributes = $db['@attributes'];
+		foreach($db['datatype'] AS $item) {
+			$this->parseItem($item);
+		}
+	}
+	
+	function parseItem($item)
+	{
+		$id = $item['@attributes']['id'];
+		$label = $item['name'];
+		
+		parent::addRDF(
+			parent::describeIndividual($id, $item['name'], parent::getVoc()."Entry").
+			parent::describeClass(parent::getVoc()."Entry","MIRIAM database entry").
+			parent::triplifyString($id, parent::getVoc()."namespace", $item['namespace'])
+		);
+		
+		if(isset($item['@attributes'])) {
+			foreach($item['@attributes'] AS $k => $v) {
+				parent::addRDF(
+					parent::triplifyString($id, parent::getVoc().$k, $v)
+				);
+			}
+		}
+		if(isset($item['comment'])) parent::addRDF(parent::triplifyString($id, parent::getVoc()."comment", $item['comment']));
+		if(isset($item['definition'])) parent::addRDF(parent::triplifyString($id, parent::getVoc()."definition", $item['definition']));
+		if(isset($item['synonyms'])) {
+			$mylist = null;
+			if(is_array($item['synonyms']['synonym'])) $mylist = $item['synonyms']['synonym'];
+			else $mylist[] = $item['synonyms']['synonym'];
+			foreach($mylist AS $myitem) {
+				parent::addRDF(
+					parent::triplifyString($id, "skos:altLabel", $myitem)
+				);
+			}
+		}
+
+		if(isset($item['uris'])) {
+			foreach($item['uris']['uri'] AS $uri) {
+				parent::addRDF(
+					parent::triplifyString($id, parent::getVoc()."uri", $uri)
+				);
+			}
+		}
+		if(isset($item['resources'])) {		
+			$mylist = null;
+			if(!isset($item['resources']['resource']['dataEntry'])) $mylist = $item['resources']['resource'];
+			else $mylist[] = $item['resources']['resource'];
+			foreach($mylist AS $myitem) {
+				$rid = $myitem['@attributes']['id'];
+				parent::addRDF(
+					parent::describeIndividual($rid, $myitem['dataInfo'], parent::getVoc()."Resource").
+					parent::describeClass(parent::getVoc()."Resource", "MIRIAM Resource").
+					parent::triplify($rid, parent::getVoc()."url", $myitem['dataResource']).
+					parent::triplifyString($rid, parent::getVoc()."urlTemplate", $myitem['dataEntry']).
+					parent::triplifyString($rid, parent::getVoc()."organization", is_array($myitem['dataInstitution'])?"":$myitem['dataInstitution']).
+					parent::triplifyString($rid, parent::getVoc()."location", is_array($myitem['dataLocation'])?"":$myitem['dataLocation']).
+					parent::triplify($id, parent::getVoc()."resource", $rid)
+				);
+			}
+		}
+		if(isset($item['tags'])) {
+			$i = $item['tags']['tag'];
+			$mylist = null;
+			if(!is_array($i)) $mylist[] = $i;
+			else $mylist = $i;
+			foreach($mylist AS $myitem) {
+				parent::addRDF(
+					parent::triplifyString($id, parent::getvoc()."tag", $myitem)
+				);
+		}}
+
+		if(isset($item['documentations'])) {
+			$i = $item['documentations']['documentation'];
+			$mylist = null;
+			if(!is_array($i)) $mylist[] = $i;
+			else $mylist = $i;
+			foreach($mylist AS $myitem) {
+				if(strstr($myitem, "pubmed")) $uri = "pubmed:".substr($myitem, strrpos($myitem, ":")+1);
+				else if(strstr($myitem, "doi")) $uri = "http://dx.doi.org/".substr($myitem, strpos($myitem, "doi:"));
+				else $uri = $myitem;
+
+				parent::addRDF(
+					parent::triplify($id, parent::getvoc()."documentation", $uri)
+				);
+		}}
+		
+		if(isset($item['restrictions'])) {
+			$mylist = null;
+			if(!isset($item['restrictions']['restriction']['statement'])) $mylist = $item['restrictions']['restriction'];
+			else $mylist[] = $item['restrictions']['restriction'];			
+			foreach($mylist AS $i => $myitem) {
+				$rid = parent::getRes().str_replace(":","",$id)."_".($i+1);
+				$a = $myitem['@attributes'];
+				$rid_type = parent::getVoc().'restriction_type_'.$a['type'];
+
+				parent::addRDF(
+					parent::describeIndividual($rid, $a['desc'], parent::getVoc()."Restriction").
+					parent::describeClass(parent::getVoc()."Restriction", "Resource Restriction").
+					parent::triplify($rid, "rdf:type", $rid_type).
+					parent::describeClass($rid_type, $a['desc'], parent::getVoc()."Restriction").
+					parent::triplifyString($rid, "dct:description", $myitem['statement']).
+					parent::triplify($rid, "foaf:page", isset($myitem['link'])?$myitem['link']:"").
+					parent::triplify($id, parent::getVoc()."restriction", $rid)
+				);
+		}}
+		
+		/*
+		<annotation>
+			<format name="SBML">
+				<elements>
+					<element>reaction</element>
+					<element>event</element>
+					<element>rule</element>
+					<element>species</element>
+				</elements>
+			</format>
+		*/
+		if(isset($item['annotation'])) {
+			$mylist = null;
+			if(!isset($item['annotation']['format']['elements'])) $mylist = $item['annotation']['format'];
+			else $mylist[] = $item['annotation']['format'];	
+			foreach($mylist AS $i => $myitem) {
+				$name = $myitem['@attributes']['name'];
+				$myid = str_replace("MIR:",parent::getRes(), $id)."_annotation_".($i+1)."_".urlencode($name);
+				parent::addRDF(
+					parent::describeIndividual($myid, "$label used by $name", parent::getVoc()."ValueSet").
+					parent::describeClass(parent::getVoc()."ValueSet", "MIRIAM Value Set").
+					parent::triplifyString($myid, parent::getVoc()."used-in", $name).
+					parent::triplify($myid, parent::getVoc()."uses", $id)
+				);
+				
+				$b = $myitem['elements']['element'];
+				$mylist2 = null;
+				if(!is_array($b)) $mylist2[] = $b;
+				else $mylist2 = $b;
+				foreach($mylist2 AS $i => $e) {
+					parent::addRDF(
+						parent::triplifyString($myid, parent::getVoc()."used-for", $e)
+					);
+				}
+			}
+			
+		}
+
+	}
+
+}
+
+?>
diff --git a/omim/omim.php b/omim/omim.php
index d938f6a..89d68c1 100644
--- a/omim/omim.php
+++ b/omim/omim.php
@@ -34,7 +34,8 @@ function __construct($argv) {
 		parent::__construct($argv, 'omim');
 		parent::addParameter('files',true,null,'all|omim#','entries to process: comma-separated list or hyphen-separated range');
 		parent::addParameter('omim_api_url',false,null,'http://api.omim.org/api/entry?include=all&format=json');
-		parent::addParameter('omim_api_key',false,null,'D43076A680B921682DA253BEFE05DE998957B3FC');
+		parent::addParameter('omim_api_key',false,null);
+		parent::addParameter('omim_api_key_file',false,null,'omim.key','A file containing your omim KEY');
 		parent::initialize();
 	}
 	
@@ -43,6 +44,19 @@ function Run()
 		// directory shortcuts
 		$ldir = parent::getParameterValue('indir');
 		$odir = parent::getParameterValue('outdir');
+		if(parent::getParameterValue('omim_api_key') == '') {
+			$key_file = parent::getParameterValue('omim_api_key_file');
+			if(file_exists($key_file)) {
+				$key = trim(file_get_contents($key_file));
+				if($key) {
+					parent::setParameterValue('omim_api_key', $key);
+				} else {
+					trigger_error("No API key found in the specified omim key file $key_file",E_USER_WARNING);						
+				}
+			} else {	
+				trigger_error("No OMIM key has been provided either by commmand line or in the expected omim key file $key_file",E_USER_WARNING);	
+			}
+		}
 
 		// get the list of mim2gene entries
 		$entries = $this->GetListOfEntries($ldir);
@@ -88,7 +102,8 @@ function Run()
 		$total = count($entries);
 		foreach($entries AS $omim_id => $type) {
 			echo "processing ".(++$i)." of $total - omim# ";
-			$download_file = $ldir.$omim_id.".json";
+			$download_file = $ldir.$omim_id.".json.gz";
+			$gzfile = "compress.zlib://$download_file";
 			// download if the file doesn't exist or we are told to
 			if(!file_exists($download_file) || parent::getParameterValue('download') == true) {
 				// download using the api
@@ -101,7 +116,7 @@ function Run()
 			}
 			
 			// load entry, parse and write to file
-			$entry = json_decode(file_get_contents($download_file), true);
+			$entry = json_decode(file_get_contents($gzfile), true);
 			$omim_id = trim((string)$entry["omim"]["entryList"][0]["entry"]['mimNumber']);
 			echo $omim_id;
 			$this->ParseEntry($entry,$type);
@@ -184,8 +199,9 @@ function getListOfEntries($ldir)
 			}
 				
 			// download
+			ftp_pasv($ftp, true);
 			echo "Downloading $file ...";
-			if(ftp_get($ftp, $ldir.$file, 'omim/'.$file, FTP_BINARY) === FALSE) {
+			if(ftp_get($ftp, $ldir.$file, 'OMIM/'.$file, FTP_BINARY) === FALSE) {
 				trigger_error("Error in downloading $file");
 				continue;
 			}
@@ -480,7 +496,11 @@ function ParseEntry($obj, $type)
 			foreach($o['phenotypeMapList'] AS $i => $phenotypeMap) {
 				$phenotypeMap = $phenotypeMap['phenotypeMap'];
 				$pm_uri = parent::getRes().$omim_id."_pm_".($i+1);
-				parent::addRDF(parent::triplify($omim_uri, parent::getVoc()."phenotype-map", $pm_uri));
+				parent::addRDF(
+					parent::describeIndividual($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"))) {
@@ -488,7 +508,7 @@ function ParseEntry($obj, $type)
 					} else if($k == "geneSymbols") {
 						$l = explode(", ",$phenotypeMap[$k]);
 						foreach($l AS $gene) {
-							parent::addRDF(parent::triplify($pm_uri, parent::getVoc().$k, "hgnc.symbol:".$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[$k]);
@@ -519,7 +539,8 @@ function ParseEntry($obj, $type)
 		// external ids
 		if(isset($o['externalLinks'])) {		
 			foreach($o['externalLinks'] AS $k => $id) {
-
+				if($id === false) continue;
+				
 				$ns = '';
 				switch($k) {
 					case 'approvedGeneSymbols':        $ns = 'symbol';break;
@@ -544,10 +565,12 @@ function ParseEntry($obj, $type)
 					case 'icd9cmIDs':                  $ns = 'icd9';break;
 					case 'umlsIDs':                    $ns = 'umls';break;
 					case 'wormbaseIDs':                $ns = 'wormbase';break;
-					case 'diseaseOntologyIDs':	   $ns = 'do';break;
+					
+					case 'diseaseOntologyIDs':	   		$ns = 'do';break;
 					
 					// specifically ignorning
 					case 'geneTests':
+					case 'cmgGene':
 					case 'geneticAllianceIDs':  // #
 					case 'nextGxDx':
 					case 'nbkIDs': // NBK1207;;Alport Syndrome and Thin Basement Membrane Nephropathy
@@ -560,7 +583,11 @@ function ParseEntry($obj, $type)
 					case 'coriellDiseases': 
 					case 'clinicalDiseaseIDs':        
 					case 'possumSyndromes':
+					case 'keggPathways':
+					case 'gtr':
+					case 'gwasCatalog':
 					case 'mgiHumanDisease':
+					case 'wormbaseDO':
 					case 'dermAtlas':                  // true/false
 						break;
 					
@@ -571,11 +598,15 @@ function ParseEntry($obj, $type)
 				$ids = explode(",",$id);
 				foreach($ids AS $id) {
 					if($ns) {
-						$b = explode(";;",$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)); 
+						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)); 
+								}
 							}
 						}
 					}
diff --git a/pharmgkb/pharmgkb.php b/pharmgkb/pharmgkb.php
index 37666e7..117323a 100644
--- a/pharmgkb/pharmgkb.php
+++ b/pharmgkb/pharmgkb.php
@@ -145,9 +145,10 @@ function run()
 				exit;
 			}
 			$zipentries = array();
-			if($file == "annotations")
-				$zipentries = array('clinical_ann.tsv','clinical_ann_metadata.tsv','var_drug_ann.tsv','var_pheno_ann.tsv','var_fa_ann.tsv','study_parameters.tsv'); 
-			else if($file == "pathways") {
+			if($file == "annotations") {
+				// exclude: 'clinical_ann.tsv','study_parameters.tsv'
+				$zipentries = array('clinical_ann_metadata.tsv','var_drug_ann.tsv','var_pheno_ann.tsv','var_fa_ann.tsv'); 
+			} else if($file == "pathways") {
 				for( $i = 0; $i < $zin->numFiles; $i++ ){ 
 					$stat = $zin->statIndex( $i ); 
 					$entry = $stat['name'];
@@ -182,8 +183,7 @@ function run()
 				$this->GetReadFile()->SetFilePointer($fp);
 
 				if($file == "annotations") {
-					if($zipentry == "clinical_ann_metadata.tsv") $fnx = "clinical_ann_metadata";
-					else $fnx = 'annotations';
+					$fnx = substr($zipentry,0,strpos($zipentry,".tsv"));
 					echo "processing $zipentry..";
 				} else if($file == 'pathways') {
 					$fnx = 'pathways';
@@ -357,6 +357,7 @@ function genes()
 					
 					$url = false;
 					$x = $this->MapXrefs($xref, $url, $ns, $id2);
+					$ns = str_replace(' ','',$ns);
 					if($url == true) {
 						parent::addRDF(
 							parent::QQuadO_URL($id, parent::getVoc()."x-$ns", $x)
@@ -398,9 +399,16 @@ function MapXrefs($xref, &$url = false, &$ns = null, &$id = null)
 			"refseqrna" => "refseq",
 			"ucscgenomebrowser" => "refseq",
 			"uniprotkb" => "uniprot",
-			'genecard'=>'genecards'
+			'genecard'=>'genecards',
+			'ucscgenomebrowser' => 'refseq',
+			'refseqrna' => 'refseq',
+			'refseqprotein' => 'refseq',
+			'refseqdna' => 'refseq',
+			'comparativetoxicogenomicsdatabase' => 'ctd',
+			'humancycgene' => 'humancyc'
 		);
 		$this->getRegistry()->ParseQName($xref,$ns,$id);
+		$ns = str_replace(array('"',' '),'',$ns);
 		if(isset($xrefs[$ns])) {
 			$ns = $xrefs[$ns];
 		}
@@ -496,10 +504,13 @@ function drugs()
 			if(trim($a[6])) {
 				// Cross References	
 				// drugBank:DB00789,keggDrug:D01707,pubChemCompound:55466,pubChemSubstance:192903,url:http://en.wikipedia.org/wiki/Gadopentetate_dimeglumine
-				$b = explode(',',trim($a[6]));
+				$b = explode(',',trim(str_replace('"','',$a[6])));
 				foreach($b as $c) {
 					$this->getRegistry()->parseQName($c,$ns,$id1);
-					$ns = str_replace(array('keggcompound','keggdrug','drugbank','uniprotkb'), array('kegg','kegg','drugbank', 'uniprot'), strtolower($ns));
+					$ns = str_replace(array('"',' '),'',$ns);
+					$ns = str_replace(array('keggcompound','keggdrug','drugbank','uniprotkb','clinicaltrials.gov','drugsproductdatabase(dpd)','nationaldrugcodedirectory','therapeutictargetsdatabase','fdadruglabelatdailymed'), 
+						array('kegg','kegg','drugbank', 'uniprot','clinicaltrials','dpd','ndc','ttd','dailymed'), 
+						strtolower(str_replace('"','',$ns)));
 					if($ns == "url") {
 						parent::addRDF(
 							parent::QQuadO_URL($id, "rdfs:seeAlso", $id)
@@ -553,7 +564,7 @@ function diseases()
 
 	  while($l = $this->GetReadFile()->Read(10000)) {
 		$a = explode("\t",$l);
-			
+
 		$id = parent::getNamespace().$a[0];
 		$label = str_replace("'", "\\\'", $a[1]);
 
@@ -586,19 +597,23 @@ function diseases()
 		parent::addRDF(
 			parent::triplify($id, "owl:sameAs", $sameID)
 		);
-		if(isset($a[4]) && trim($a[4]) != '') {	 
-			$d = preg_match_all('/[,]?([^\:]+):([A-Za-z0-9]+)\(([^\)]+)\)/',$a[4],$m, PREG_SET_ORDER);
-			foreach($m AS $n) {
-				if(isset($n[1]) && isset($n[2]) && !strstr($n[1]," ")) {
-					$n[1] = str_replace("),","",strtolower($n[1]));
-					$id2 = $n[1].':'.$n[2];
-					parent::addRDF(
-						parent::triplify($id, "pharmgkb_vocabulary:x-".$n[1], $id2)
-					);
-					if(isset($n[3]) && $n[2] != $n[3]){
+		if(isset($a[4]) && trim($a[4]) != '') {
+			$xrefs = explode('","', $a[4]);
+			foreach($xrefs AS $xref) {
+				$xref = str_replace('"','',$xref);
+				$d = preg_match_all('/[,]?([^\:]+):([A-Za-z0-9]+)\(([^\)]+)\)/',$xref,$m, PREG_SET_ORDER);
+				foreach($m AS $n) {
+					if(isset($n[1]) && isset($n[2]) && !strstr($n[1]," ")) {
+						$n[1] = str_replace("),","",strtolower($n[1]));
+						$id2 = $n[1].':'.$n[2];
 						parent::addRDF(
-							parent::triplifyString($id2, "rdfs:label", str_replace(array("\'", "\""),array("\\\'", ""),$n[3]))
+							parent::triplify($id, "pharmgkb_vocabulary:x-".$n[1], $id2)
 						);
+						if(isset($n[3]) && $n[2] != $n[3]){
+							parent::addRDF(
+								parent::triplifyString($id2, "rdfs:label", str_replace(array("\'", "\""),array("\\\'", ""),$n[3]))
+							);
+						}
 					}
 				}
 			}
@@ -607,155 +622,6 @@ function diseases()
 	  }
 	}
 
-	/*
-	0 Position on hg18
-	1 RSID
-	2 Name(s)	
-	3 Genes
-	4 Feature
-	5 Evidence
-	6 Annotation	
-	7 Drugs	
-	8 Drug Classes	
-	9 Diseases	
-	10 Curation Level	
-	11 PharmGKB Accession ID
-	*/
-	function annotations()
-	{ 
-		$hash = ''; // md5 hash list
-		$h = explode("\t",$this->GetReadFile()->Read(100000)); // first line is header
-		if(count($h) != 12) {
-			trigger_error("Change in number of columns for variant annotations file",E_USER_ERROR);
-			return FALSE;
-		}
-	
-		while($l = $this->GetReadFile()->Read(10000)) {
-			$a = explode("\t",$l);
-			$id = parent::getNamespace().$a[11];
-			$label = "variant annotation for ".$a[1];
-			parent::addRDF(
-				parent::describeIndividual($id, $label, parent::getVoc()."Variant-Annotation").
-				parent::describeClass(parent::getVoc()."Variant-Annotation", "PharmGKB Variant Annotation").
-				parent::triplify($id, parent::getVoc()."variant", "dbsnp:".$a[1]).
-				parent::describeProperty(parent::getVoc()."variant", "Relationship between a PharmGKB entity and a variant")
-			);
-
-			if($a[2] != ''){
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."variant_description", addslashes($a[2])).
-					parent::describeProperty(parent::getVoc()."variant_description", "Relationship between a PharmGKB variant annotation and a description")
-				);
-			}
-
-			if($a[3] != '' && $a[3] != '-') {
-				$genes = explode(", ",$a[3]);
-				foreach($genes AS $gene) {
-					$gene = str_replace("@","",$gene);
-					parent::addRDF(
-						parent::triplify($id, parent::getVoc()."gene", parent::getNamespace().$gene)
-					);
-				}
-				parent::addRDF(
-					parent::describeProperty(parent::getVoc()."gene", "Relationship between a PharmGKB variant annotation and a gene")
-				);
-			}
-		
-			if($a[4] != '') {
-				$features = explode(", ",$a[4]);
-				array_unique($features);
-				foreach($features AS $feature) {
-					$z = md5($feature); 
-					parent::addRDF(
-						parent::describeIndividual(parent::getRes().$z, $feature, parent::getVoc()."Feature").
-						parent::triplify($id, parent::getVoc()."feature", parent::getRes().$z)
-					); 
-				}
-				parent::addRDF(
-					parent::describeClass(parent::getVoc()."Feature", "PharmGKB variant annotation feature").
-					parent::describeProperty(parent::getVoc()."feature", "Relationship between a PharmGKB variant annotation and a feature")
-				);
-			}
-			if($a[5] != '') {
-				//PubMed ID:19060906; Web Resource:http://www.genome.gov/gwastudies/
-				$evds = explode("; ",$a[5]);
-				foreach($evds AS $evd) {
-					$b = explode(":",$evd);
-					$key = $b[0];
-					array_shift($b);
-					$value = implode(":",$b);
-					if($key == "PubMed ID"){
-						parent::addRDF(
-							parent::triplify($id, parent::getVoc()."article", "pubmed:".$value).
-							parent::describeProperty(parent::getVoc()."article", "Relationship between a PharmGKB entity and a PubMed article identifier")
-						);
-					} else if($key == "Web Resource"){
-						parent::addRDF(
-							parent::QQuadO_URL($id, parent::getVoc()."url", $value).
-							parent::describeProperty(parent::getVoc()."url", "Relationship between a PharmGKB entity and a web resource")
-						);
-					}
-				}
-			}
-			if($a[6] != '') { //annotation
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."description", str_replace("'", "\\\'", $a[6])).
-					parent::describeProperty(parent::getVoc()."description", "Relationship between a PharmGKB entity and its description")
-				);
-			}
-			if($a[7] != '') { //drugs
-				$drugs = explode("; ",$a[7]);
-				foreach($drugs AS $drug) {
-					$find = array_search($drug, $drug_names_array);
-					if($find != FALSE){
-						parent::addRDF(
-							parent::triplify($id, parent::getVoc()."drug", $find)
-						);
-					} else {
-						$z = md5($drug); 
-						parent::addRDF(
-							parent::describeIndividual(parent::getRes().$z, $drug, parent::getVoc()."Drug").
-							parent::triplify($id, parent::getVoc()."drug", parent::getRes().$z)
-						);
-					}
-				}
-				parent::addRDF(
-					parent::describeProperty(parent::getVoc()."drug", "Relationship between a PharmGKB variant annotation and a drug")
-				);
-			}
-
-			if($a[8] != '') {
-				$diseases = explode("; ",$a[8]);
-				foreach($diseases AS $disease) {
-					$disease = str_replace("'", "\\\'", $disease);
-					$find = array_search($disease, $disease_names_array);
-
-					if($find != FALSE){
-						parent::addRDF(
-							parent::triplify($id, parent::getVoc()."disease", $find)
-						);
-					} else {
-						$z = md5($disease); 
-						parent::addRDF(
-							parent::describeIndividual(parent::getRes().$z, $disease, parent::getVoc()."Disease").
-							parent::triplify($id, parent::getVoc()."disease", parent::getRes().$z)
-						);
-					}
-				}
-				parent::addRDF(
-					parent::describeProperty(parent::getVoc()."disease", "Relationship between a PharmGKB variant annotation and a disease")
-				);
-			}
-			if(trim($a[9]) != '') {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."curation_status", trim($a[9])).
-					parent::describeProperty(parent::getVoc()."curation_status", "Relationship between a PharmGKB entity and its curation status")
-				);
-			}	
-		}
-		parent::WriteRDFBufferToWriteFile();
-	}
-
 	/*
 	0 Entity1_id        - PA267, rs5186, Haplotype for PA121
 	1 Entity1_name  
@@ -877,6 +743,10 @@ function rsid()
 		$z = 0;
 		$this->GetReadFile()->Read();
 		$this->GetReadFile()->Read();
+		parent::addRDF(
+			parent::describeClass(parent::getVoc()."Variation", "PharmGKB Variation")
+		);
+
 		while($l = $this->GetReadFile()->Read()) {
 			if($z % 10000 == 0) {
 				parent::writeRDFBufferToWriteFile();
@@ -885,10 +755,8 @@ function rsid()
 			$rsid = "dbsnp:".$a[0];
 			$genes = explode(";",$a[1]);
 			parent::addRDF(
-				parent::describeIndividual($rsid, $rsid, parent::getVoc()."Variation").
-				parent::describeClass(parent::getVoc()."Variation", "PharmGKB Variation")
+				parent::describeIndividual($rsid, $rsid, parent::getVoc()."Variation")
 			);
-			$this->AddRDF($this->QQuad($rsid,"void:inDataset",$this->GetDatasetURI()));
 			foreach($genes AS $gene) {
 				parent::addRDF(
 					parent::triplify($rsid, parent::getVoc()."gene", parent::getNamespace().$gene)
@@ -899,83 +767,71 @@ function rsid()
 
 	function clinical_ann_metadata()
 	{
-		$this->GetReadFile()->Read();
-		while($l = $this->GetReadFile()->Read(20000)) {
+		$header = array("Clinical Annotation Id","Location","Gene","Level of Evidence","Clinical Annotation Types","Genotype-Phenotype IDs","Annotation Text","Variant Annotations IDs","Variant Annotations","PMIDs","Evidence Count","Related Drugs","Related Diseases","Race");
+		$this_header = explode("\t",$this->GetReadFile()->Read());
+		if(count($this_header) != count($header)) {
+			trigger_error("Change in the number of columns. Expected ".count($header).", but found ".count($this_header),E_USER_ERROR);
+			return (-1);
+		}
+		while($l = $this->GetReadFile()->Read(200000)) {
 			$a = explode("\t",$l);
-			$rsid = "dbsnp:$a[1]";
-			$label = "clinical annotation for $rsid";
-			// [0] => Clinical Annotation Id
 			$id = parent::getNamespace().$a[0];
+			$label = "clinical annotation for ".$a[1];
+			// [0] => Clinical Annotation Id
 			parent::addRDF(
 				parent::describeIndividual($id, $label, parent::getVoc()."Clinical-Annotation").
 				parent::describeClass(parent::getVoc()."Clinical-Annotation", "PharmGKB Clinical Annotation")
 			);
 			
-			// [1] => RSID
-			parent::addRDF(
-				parent::triplify($id, parent::getVoc()."variant", $rsid).
-				parent::describeProperty(parent::getVoc()."variant", "Relationship between a PharmGKB entity and a variant")
-			);
-			
-			// [2] => Variant Names
-			if($a[2]) { 
-				$names = explode(";",$a[2]);
-				foreach($names AS $name) {
-					parent::addRDF(
-						parent::triplifyString($rsid, parent::getVoc()."variant-name", addslashes(trim($name)))
-					);
-				}
+			// [1] => RSID/allele
+			if(substr($a[1],0,2) == "rs") {
+				$rsid = "dbsnp:$a[1]";
 				parent::addRDF(
-					parent::describeProperty(parent::getVoc()."variant-name", "Relationship between a PharmGKB entity and a variant name")
+					parent::triplify($id, parent::getVoc()."x-dbsnp", $rsid).
+					parent::describeProperty(parent::getVoc()."x-dbsnp", "Relationship between a PharmGKB entity and a dbSNP entry")
 				);
-			}
-			// [3] => Location
-			if($a[3]) { 
-				$chr = substr($a[3],0,strpos($a[3],":"));
+			} else {
+				// some kind of star allele
 				parent::addRDF(
-					parent::triplifyString($rsid, parent::getVoc()."location", $a[3]).
-					parent::triplifyString($rsid, parent::getVoc()."chromosome", $chr).
-					parent::describeProperty(parent::getVoc()."location", "Relationship between a PharmGKB entity and a chromosomal location").
-					parent::describeProperty(parent::getVoc()."chromosome", "Relationship between a PharmGKB entity and a chromosome")
-
+					parent::triplifyString($id, parent::getVoc()."star-allele", $a[1]).
+					parent::describeProperty(parent::getVoc()."star-allele", "Relationship between a PharmGKB entity and a star allele")
 				);
 			}
-			// [4] => Gene
-			if($a[4]){
-				$genes = explode(";",$a[4]);
+			
+			// [2] => Gene
+			if($a[2]){
+				$genes = explode(",",$a[2]);
 				foreach($genes AS $gene) {
 					preg_match("/\(([A-Za-z0-9]+)\)/",$gene,$m);
 					parent::addRDF(
-						parent::triplify($rsid, parent::getVoc()."gene", parent::getNamespace().$m[1]).
+						parent::triplify($id, parent::getVoc()."gene", parent::getNamespace().$m[1]).
 						parent::triplify(parent::getNamespace().$m[1], "rdf:type", parent::getVoc()."Gene")
 					);
 				}
 			}
-
-			// [5] => Evidence Strength
-			if($a[5]) {
+			
+			// [3] => Evidence Level
+			if($a[3]) {
 				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."evidence-strength", $a[5]).
-					parent::describeProperty(parent::getVoc()."evidence-strength", "Relationship between a PharmGKB annotation and its evidence strength")
+					parent::triplifyString($id, parent::getVoc()."evidence-level", $a[3]).
+					parent::describeProperty(parent::getVoc()."evidence-level", "The level of evidence")
 				);
 			}
+
 			// [6] => Clinical Annotation Types
-			if($a[6]) {
-				$types = explode(";",$a[6]);
+			if($a[4]) {
+				$types = explode(";",$a[4]);
 				foreach($types AS $t) {
 					parent::addRDF(
-						parent::triplifyString($id, parent::getVoc()."annotation-type", $t).
-						parent::triplify($id, "rdf:type", parent::getVoc().strtoupper($t)."-Annotation").
-						parent::describeProperty(parent::getVoc()."annotation-type", "Relationship between a PharmGKB annotation and its type").
-						parent::describeClass(parent::getVoc().strtoupper($t)."-Annotation", "$t Annotation")
+						parent::triplifyString($id, parent::getVoc()."annotation-type", strtolower($t))
 					);
 				}
 			}
-			// [7] => Genotype-Phenotypes IDs
-			// [8] => Text
-			if($a[7]) {
-				$gps = explode(";",$a[7]);
-				$gps_texts = explode(";",$a[8]);
+			// [5] => Genotype-Phenotypes IDs
+			// [6] => Text
+			if($a[5]) {
+				$gps = explode(";",$a[5]);
+				$gps_texts = explode(";",$a[6]);
 				foreach($gps AS $i => $gp) {
 					$gp = trim($gp);
 					$gp_text = trim($gps_texts[$i]);
@@ -991,12 +847,12 @@ function clinical_ann_metadata()
 					);
 				}
 			}
-			
-			// [9] => Variant Annotations IDs
-			// [10] => Variant Annotations
-			if($a[9]) {
-				$b = explode(";",$a[9]);
-				$b_texts =  explode(";",$a[10]);
+						
+			// [7] => Variant Annotations IDs
+			// [8] => Variant Annotations
+			if($a[7]) {
+				$b = explode(";",$a[7]);
+				$b_texts =  explode(";",$a[8]);
 				foreach($b AS $i => $variant) {
 					$variant = trim($variant);
 					$variant_text = trim ($b_texts[$i]);
@@ -1006,9 +862,10 @@ function clinical_ann_metadata()
 					);
 				}
 			}
-			// [11] => PMIDs
-			if($a[11]) {
-				$b = explode(";",$a[11]);
+			
+			// [9] => PMIDs
+			if($a[9]) {
+				$b = explode(";",$a[9]);
 				foreach($b AS $i => $pmid) {
 					$pmid = trim($pmid);
 					parent::addRDF(
@@ -1016,58 +873,22 @@ function clinical_ann_metadata()
 					);
 				}
 			}
-			// [12] => Evidence Count
-			if($a[12]) {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."evidence-count", $a[12]).
-					parent::describeProperty(parent::getVoc()."evidence-count", "Relationship between a PharmGKB annotation and an evidence count")
-				);
-			}
-			
-			// [13] => # Cases
-			if($a[13]) {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."cases-count", $a[13]).
-					parent::describeProperty(parent::getVoc()."cases-count", "Relationship between a PharmGKB annotation and a cases count")
-				);
-			}
-			// [14] => # Controlled
-			if($a[14]) {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."controlled-count", $a[14]).
-					parent::describeProperty(parent::getVoc()."controlled-count", "Relationship between a PharmGKB annotation and a controlled count")
-				);
-			}
-			// [15] => Related Genes
-			if($a[15]) {
-				$b = explode(";",$a[15]);
-				foreach($b AS $gene_label) {
-					// find the gene_id from the label
-					$find = array_search($gene_label, $gene_names_array);
-					if($find != FALSE){
-						parent::addRDF(
-							parent::triplify($id, parent::getVoc()."related-gene", $find)
-						);
-					} else {
-						$gene_id = parent::getRes().md5($gene_label);
-						parent::addRDF(
-							parent::describeIndividual($gene_id, $gene_label, parent::getVoc()."Gene").
-							parent::triplify($id, parent::getVoc()."related-gene", $gene_id)
-						);
-					}
-				}
+
+			// [10] => Evidence Count
+			if($a[10]) {
 				parent::addRDF(
-					parent::describeProperty(parent::getVoc()."related-gene", "Relationship between a PharmGKB annotation and a related gene")
+					parent::triplifyString($id, parent::getVoc()."evidence-count", $a[10]).
+					parent::describeProperty(parent::getVoc()."evidence-count", "Relationship between a PharmGKB annotation and its count of evidence")
 				);
 			}
 
-			// [16] => Related Drugs
-			if($a[16]) {
-				$b = explode(";",$a[16]);
+			// [11] => Related Drugs
+			if($a[11]) {
+				$b = explode(";",$a[11]);
 				foreach($b AS $drug_label) {
 					// find the id from the label
-					$find = array_search($drug_label, $drug_names_array);
-					if($find != FALSE){
+					$find = @array_search($drug_label, $this->drug_names_array);
+					if($find !== FALSE and $find !== NULL){
 						parent::addRDF(
 							parent::triplify($id, parent::getVoc()."related-drug", $find)
 						);
@@ -1083,13 +904,13 @@ function clinical_ann_metadata()
 					parent::describeProperty(parent::getVoc()."related-drug", "Relationship between a PharmGKB annotation and a related drug")
 				);
 			}
-			// [17] => Related Diseases
-			if($a[17]) {
-				$b = explode(";",$a[17]);
+			// [12] => Related Diseases
+			if($a[12]) {
+				$b = explode(";",$a[12]);
 				foreach($b AS $disease_label) {
 					// find the id from the label
-					$find = array_search($disease_label, $disease_names_array);
-					if($find != FALSE){
+					$find = @array_search($disease_label, $this->disease_names_array);
+					if($find !== FALSE and $find !== NULL){
 						parent::addRDF(
 							parent::triplify($id, parent::getVoc()."related-disease", $find)
 						);
@@ -1105,41 +926,32 @@ function clinical_ann_metadata()
 					parent::describeProperty(parent::getVoc()."related-disease", "Relationship between a PharmGKB annotation and a related disease")
 				);
 			}
-			// [18] => OMB Races
-			if($a[18]) {
+			// [13] => OMB Races
+			if($a[13]) {
 				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."race", $a[18]).
+					parent::triplifyString($id, parent::getVoc()."race", $a[13]).
 					parent::describeProperty(parent::getVoc()."race", "Relationship between a PharmGKB annotation and a race")
 				);
 			}
-			// [19] => Is Unknown Race
-			if($a[19]) {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."race", (($a[19] == "TRUE")?"race known":"race unknown"))
-				);
-			}
-			// [20] => Is Mixed Population
-			if($a[20]) {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."population-homogeneity", (($a[20] == "TRUE")?"mixed":"homogeneous")).
-					parent::describeProperty(parent::getVoc()."population-homogeneity", "Relationship between a PharmGKB annotation and a population homogeneity")
-				);
-			}
-			// [21] => Custom Race
-			if($a[21]) {
-				parent::addRDF(
-					parent::triplifyString($id, parent::getVoc()."special-source", $a[21]).
-					parent::describeProperty(parent::getVoc()."special-source", "Relationship between a PharmGKB annotation and a special source")
-				);
-			}
 		}
 		parent::writeRDFBufferToWriteFile();
 	}
 
+	function var_drug_ann() {return $this->variant_annotation();}
+	function var_fa_ann() {return $this->variant_annotation();}
+	function var_pheno_ann() {return $this->variant_annotation();}
+
+		
 	function variant_annotation()
 	{
+		$canonical_header = array("Annotation ID","Variant","Gene","Drug","Literature Id","Phenotype Category","Significance","Notes","Sentence","StudyParameters"," Alleles");
+		$header = explode("\t",$this->getReadFile()->read(20000));
+		if(count($header) != count($canonical_header)) {
+			trigger_error("column mismatch! Expected ".count($canonical_header).",but found ".count($header),E_USER_ERROR);
+			return (-1);
+		}
+		
 		$declaration = '';
-		$this->GetReadFile()->Read();
 		while($l = $this->GetReadFile()->Read(20000)) {
 			$a = explode("\t",$l);
 			//[0] => Annotation ID
@@ -1149,18 +961,27 @@ function variant_annotation()
 				parent::describeClass(parent::getVoc()."Variant-Annotation", "PharmGKB Variant Annotation")
 			);
 			
-			//[1] => RSID
-			$rsid = "dbsnp:$a[1]";
-			parent::addRDF(
-				parent::triplify($id, parent::getVoc()."variant", $rsid).
-				parent::describeProperty(parent::getVoc()."variant", "Relationship between a PharmGKB entity and a variant")
-			);
+			// [1] => RSID/allele
+			if(substr($a[1],0,2) == "rs") {
+				$rsid = "dbsnp:$a[1]";
+				parent::addRDF(
+					parent::triplify($id, parent::getVoc()."x-dbsnp", $rsid).
+					parent::describeProperty(parent::getVoc()."x-dbsnp", "Relationship between a PharmGKB entity and a dbSNP entry")
+				);
+			} else {
+				// some kind of star allele
+				parent::addRDF(
+					parent::triplifyString($id, parent::getVoc()."star-allele", $a[1]).
+					parent::describeProperty(parent::getVoc()."star-allele", "Relationship between a PharmGKB entity and a star allele")
+				);
+			}
+
 			//[2] => Gene
 			//CYP3A (PA27114),CYP3A4 (PA130)
 			if($a[2]) {
 				$genes = explode(",",$a[2]);
 				foreach($genes AS $gene) {
-					preg_match("/\(([A-Za-z0-9]+)\)/",$gene,$m);
+					preg_match("/\((PA[A-Za-z0-9]+)\)/",$gene,$m);
 					if(isset($m[1])) {
 						parent::addRDF(
 							parent::triplify($id, parent::getVoc()."gene", parent::getNamespace().$m[1]).
@@ -1174,7 +995,7 @@ function variant_annotation()
 			if($a[3]) {
 				$drugs = explode(",",$a[3]);
 				foreach($drugs AS $drug) {
-					preg_match("/\(([A-Za-z0-9]+)\)/",$drug,$m);
+					preg_match("/\((PA[A-Za-z0-9]+)\)/",$drug,$m);
 					if(isset($m[1])) {
 						parent::addRDF(
 							parent::triplify($id, parent::getVoc()."drug", parent::getNamespace().$m[1]).
@@ -1183,6 +1004,7 @@ function variant_annotation()
 					}
 				}
 			}
+
 			// [4] => Literature Id
 			if($a[4]) {
 				$b = explode(";",$a[4]);
@@ -1195,15 +1017,12 @@ function variant_annotation()
 				}
 			}
 			
-			//[5] => Secondary Category
+			//[5] => Phenotype
 			if($a[5]) {
 				$types = explode(";",$a[5]);
 				foreach($types AS $t) {
 					parent::addRDF(
-						parent::triplifyString($id, parent::getVoc()."annotation-type", $t).
-						parent::triplify($id, "rdf:type", parent::getVoc().strtoupper($t)."-Annotation").
-						parent::describeProperty(parent::getVoc()."annotation-type", "Relationship between a PharmGKB annotation and its type").
-						parent::describeClass(parent::getVoc().strtoupper($t)."-Annotation", "$t Annotation")
+						parent::triplifyString($id, parent::getVoc()."annotation-type", strtolower($t))
 					);
 				}
 			}
@@ -1214,6 +1033,7 @@ function variant_annotation()
 					parent::describeProperty(parent::getVoc()."significant", "Relationship between a PharmGKB annotation and its significance")
 				);
 			}
+
 			// [7] => Notes
 			if($a[7]) {
 				parent::addRDF(
@@ -1237,28 +1057,15 @@ function variant_annotation()
 					$t = parent::getNamespace().trim($sp);
 					parent::addRDF(
 						parent::describeIndividual($t, $sp, parent::getVoc()."Study-Parameter").
-						parent::triplify($id, parent::getVoc()."study-parameter", $t).
-						parent::describeClass(parent::getVoc()."Study-Parameter", "PharmGKB study parameter").
-						parent::describeProperty(parent::getVoc()."study-parameter", "Relationship between a PharmGKB annotation and a study parameter")
+						parent::triplify($id, parent::getVoc()."study-parameter", $t)
 					);
 				}
 			}
-			//[10] => KnowledgeCategories
+			//[10] => Alleles
 			if($a[10]) {
-				$cats = explode(";",$a[10]);
-				foreach($cats AS $cat) {
-					$t = parent::getNamespace().$cat;
-					parent::addRDF(
-						parent::triplify($id, parent::getVoc()."article-category", $t)
-					);
-					if(!isset($declaration[$t])) {
-						$declaration[$t] = '';
-						parent::addRDF(
-							parent::describeIndividual($t, $cat, parent::getVoc()."KnowledgeCategory").
-							parent::describeClass(parent::getVoc()."KnowledgeCategory", "PharmGKB Knowledge Category")
-						);
-					}
-				}
+				parent::addRDF(
+					parent::triplifyString($id, parent::getVoc()."alleles", $a[10])
+				);
 			}	
 		}
 		return TRUE;
diff --git a/runparser.php b/runparser.php
index d07e575..1a7e46a 100644
--- a/runparser.php
+++ b/runparser.php
@@ -34,8 +34,6 @@ public function __construct($argv)
 		$parsers = $this->getParsers();
 		parent::addParameter('parser',true,implode("|",$parsers),null,'bio2rdf parser to run');
 		parent::addParameter('statistics',false,"true|false","false",'generate statistics');
-		parent::addParameter('bio2rdf_release',false,null,"3",'Bio2RDF release number');
-
 
 		if(parent::setParameters($argv,true) === FALSE) {
 			if(parent::getParameterValue('parser') == '') {
diff --git a/sgd/sgd.php b/sgd/sgd.php
index a7c7198..013a325 100644
--- a/sgd/sgd.php
+++ b/sgd/sgd.php
@@ -38,7 +38,7 @@ function __construct($argv) {
 		parent::__construct($argv,"sgd");
 		parent::addParameter('files',true,'all|dbxref|features|domains|protein|goa|goslim|complex|interaction|phenotype|pathways|mapping','all','all or comma-separated list of files to process');
 		parent::addParameter('download_url',false,null,'http://downloads.yeastgenome.org/');
-		parent::addParameter('ncbo_download_dir', false, null, '/data/download/ncbo/', 'directory of ncbo ontologies');
+		parent::addParameter('ncbo_download_dir', false, null, '/data/download/bioportal/', 'directory of bioportal ontologies');
 		parent::addParameter('ncbo_api_key',true,null,null,'your NCBO API key');
 		parent::addParameter('one_file',false,'true|false','true',"whether to produce a single file output");
 		parent::initialize();
@@ -639,7 +639,11 @@ function domains(){
 			"SignalP_GRAM_POSITIVE" => "signalp",
 			"SignalP_GRAM_NEGATIVE" => "signalp",
 			"SignalP_EUK" => "signalp",
-			"TMHMM" => "tmhmm" 
+			"TMHMM" => "tmhmm",
+			"ProDom" => "prodom",
+			"ProSiteProfiles" => "prosite",
+			"ProSitePatterns" => "prosite",
+			"Hamap" => "hamap" 
 		);
 
 		while($l = $this->GetReadFile()->Read(2048)) {
diff --git a/statistics/bio2rdf-individual-page.php b/statistics/bio2rdf-individual-page.php
index a746231..fc6338f 100644
--- a/statistics/bio2rdf-individual-page.php
+++ b/statistics/bio2rdf-individual-page.php
@@ -84,6 +84,7 @@
         while($l = fgets($fp)) {
                 if(!$l or $l[0] == "#" ) continue;
                 $a = explode("\t",$l);
+		if(!isset($a[2])) continue;
                 if($dataset == 'all' or $dataset == trim($a[2])) $list[] = trim($a[2]);
         }
         fclose($fp);
@@ -95,7 +96,7 @@
 		$endpoint  = getEndpointInfo($dataset);
 		$options['port'] = $endpoint['isql'];
 
-		$options['sparql'] = $entry['sparql'] = "http://localhost:".$endpoint['sparql']."/sparql";
+		$options['sparql'] = $entry['sparql'] = "http://s2.semanticscience.org:".$endpoint['sparql']."/sparql";
 
 		$entry['target.endpoint'] = $entry['sparql'];
 		if($options['target.endpoint']) $entry['target.endpoint'] = $options['target.endpoint']; 
@@ -107,6 +108,7 @@
 		$entry['from'] = "FROM <".$entry['graph'].">";
 		$entry['describe'] = '';
 		$outfile = $options['odir'].$dataset."/$dataset.html";
+		$outfile = $options['odir']."$dataset.html";
 		makeHTML($entry,$outfile);
 		echo "done.".PHP_EOL;
 	}
diff --git a/statistics/endpoint-statistics.php b/statistics/endpoint-statistics.php
index f67d0a0..69ad353 100644
--- a/statistics/endpoint-statistics.php
+++ b/statistics/endpoint-statistics.php
@@ -29,6 +29,7 @@
 */
 
 $fnx = array(
+//	"typePropertyTypeCount"
 	"triples", 
 	"distinctEntities", 
 	"distinctSubjects",
@@ -744,6 +745,15 @@ function addSubjectPropertyObjectCount()
 function addTypePropertyTypeCount()
 {
 	global $options;
+	$sparql = "SELECT ?p 
+".$options['from-graph']." 
+	  { ?s ?p ?o FILTER (!isLiteral(?o)) }
+	  GROUP BY ?p
+";
+	$r = query($sparql);
+	foreach($r AS $c) {
+	$p = $c->p->value;
+
 	$sparql = "SELECT 
 		distinct ?stype (str(?stype_label) AS ?stype_label) (?sn AS ?sn) (?dsn AS ?dsn) 
 		?p (str(?plabel) AS ?plabel) 
@@ -756,6 +766,7 @@ function addTypePropertyTypeCount()
 			?s ?p ?o . 
 			?s a ?stype .
 			?o a ?otype .
+			FILTER(?p = <$p>)
 		}
 		GROUP BY ?p ?stype ?otype 
 	}
@@ -798,6 +809,7 @@ function addTypePropertyTypeCount()
 			Quad("http://bio2rdf.org/bio2rdf.dataset_vocabulary:Dataset-Object-Count", "http://www.w3.org/2000/01/rdf-schema#subClassOf", "http://bio2rdf.org/bio2rdf.dataset_vocabulary:Dataset-Descriptor")
 		);
 	}
+        } // foreach property
 }
 
 function addDatasetPropertyDatasetCount()
diff --git a/taxonomy/taxonomy.php b/taxonomy/taxonomy.php
index e9fcbae..4dbb1b3 100644
--- a/taxonomy/taxonomy.php
+++ b/taxonomy/taxonomy.php
@@ -48,7 +48,7 @@ class TaxonomyParser extends Bio2RDFizer{
 			),
 			"file_url" => "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip"
 		),
-		"gi2taxid_protein" => array(
+/*		"gi2taxid_protein" => array(
 			"filename" => "gi_taxid_prot.zip",
 			"contents" => array(
 				"gi_taxid_prot" => "gi_taxid_prot.dmp",
@@ -62,7 +62,7 @@ class TaxonomyParser extends Bio2RDFizer{
 			),
 			"file_url" => "ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.zip"
 		) 
-	);
+*/	);
 
 	function __construct($argv) {
 		parent::__construct($argv, "taxonomy");
@@ -325,13 +325,20 @@ private function citations()
 				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;
+				$seelalso = parent::triplify($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])).
-				(!isset($a[4])?"":parent::triplify($c, "rdfs:seeAlso", str_replace("lx: DOI ","http://dx.doi.org/", $a[4]))).
-				(!isset($a[5])?"":parent::triplifyString($c, parent::getVoc()."text", str_replace("\"","", $a[5])))
+				$seealso.
+				((isset($a[5]) and $a[5])?parent::triplifyString($c, parent::getVoc()."text", str_replace("\"","", $a[5])):"")
 			);
 			if(isset($a[6])) {
 				$taxids = explode(" ", trim($a[6]));
diff --git a/wormbase/wormbase.php b/wormbase/wormbase.php
index c50e730..023fff2 100644
--- a/wormbase/wormbase.php
+++ b/wormbase/wormbase.php
@@ -35,7 +35,7 @@ class WormbaseParser extends Bio2RDFizer {
 	function __construct($argv) {
 		parent::__construct($argv, "wormbase");
 		parent::addParameter('files', true, 'all|geneIDs|functional_descriptions|gene_associations|gene_interactions|phenotype_associations','all','files to process');
-		parent::addParameter('release', false, null, 'WS243', 'Release version of WormBase');
+		parent::addParameter('release', false, null, 'current', 'Release version of WormBase');
 		parent::addParameter('download_url', false, null,'ftp://ftp.wormbase.org/pub/wormbase/');
 		parent::initialize();
 	}//constructor
@@ -49,12 +49,13 @@ public function run()
 			$files = explode(",",parent::getParameterValue('files'));
 		}
 		$release = parent::getParameterValue('release');
+		$releaseb = "WS249";
 		$remote_files = array(
-			"geneIDs" => "species/c_elegans/annotation/geneIDs/c_elegans.PRJNA13758.".parent::getParameterValue('release').".geneIDs.txt.gz",
-			"functional_descriptions" => "species/c_elegans/annotation/functional_descriptions/c_elegans.PRJNA13758.".parent::getParameterValue('release').".functional_descriptions.txt.gz",
-			"gene_interactions" => "species/c_elegans/annotation/gene_interactions/c_elegans.PRJNA13758.".parent::getParameterValue('release').".gene_interactions.txt.gz",
-			"gene_associations" => "releases/".$release."/ONTOLOGY/gene_association.".parent::getParameterValue('release').".wb",
-			"phenotype_associations" => "releases/".$release."/ONTOLOGY/phenotype_association.".parent::getParameterValue('release').".wb"
+			"geneIDs" => "species/c_elegans/annotation/geneIDs/c_elegans.PRJNA13758.".$release.".geneIDs.txt.gz",
+			"functional_descriptions" => "species/c_elegans/annotation/functional_descriptions/c_elegans.PRJNA13758.".$release.".functional_descriptions.txt.gz",
+			"gene_interactions" => "species/c_elegans/annotation/gene_interactions/c_elegans.PRJNA13758.".$release.".gene_interactions.txt.gz",
+			"gene_associations" => "releases/current-production-release/ONTOLOGY/gene_association.".$releaseb.".wb",
+			"phenotype_associations" => "releases/current-production-release/ONTOLOGY/phenotype_association.".$releaseb.".wb"
 		);
 
 		$local_files = array(
@@ -62,7 +63,7 @@ public function run()
 			"functional_descriptions" => "wormbase.".parent::getParameterValue('release').".functional_descriptions.txt.gz",
 			"gene_interactions" => "wormbase.".parent::getParameterValue('release').".gene_interactions.txt.gz",
 			"gene_associations" => "wormbase.".parent::getParameterValue('release').".gene_association.wb",
-			"phenotype_associations" => "wormbase.".parent::getParameterValue('release')."phenotype_associations.wb"
+			"phenotype_associations" => "wormbase.".parent::getParameterValue('release').".phenotype_associations.wb"
 		);
 
 		$idir = parent::getParameterValue('indir');
@@ -84,7 +85,6 @@ public function run()
 				Utils::DownloadSingle($rfile, $lfile);
 				echo "done!".PHP_EOL;
 			}
-
 			if(strstr($lfile, "gz")){
 				parent::setReadFile($lfile, TRUE);
 			} else {
@@ -155,7 +155,6 @@ function geneIDs()
 			if($l[0] == '#') continue;
 			// taxon, gene id, symbol, cosmid, status
 			$data = explode(",",trim($l));
-
 			if($first) {
 				if(($c = count($data) != 5)) {
 					trigger_error("WormBase function expects 5 fields, found $c!".PHP_EOL, E_USER_WARNING);
@@ -170,7 +169,8 @@ function geneIDs()
 			parent::addRDF(
 				parent::describeIndividual($id, $label, parent::getVoc()."Gene").
 				parent::describeClass(parent::getVoc()."Gene", "Wormbase Gene").
-				parent::triplify($id, parent::getVoc()."taxonomy", "taxonomy:".$data[1]).
+				parent::triplify($id, "rdfs:seeAlso", "http://www.wormbase.org/db/gene/gene?name=".$data[1]).
+				parent::triplify($id, parent::getVoc()."x-taxonomy", "taxonomy:".$data[0]).
 				parent::triplifyString($id, parent::getVoc()."approved-gene-name", $data[2])
 			);
 			#Add cosmid name 
@@ -190,10 +190,11 @@ function functional_descriptions()
 	{
 		while($l = $this->getReadFile()->read(2000000)){
 			if($l[0] == "#") continue;
-			// gene_id public_name molecular_name concise_description provisional_description detailed_description gene_class_description
+			if(strstr($l,"gene_id")) continue;
 
-			$a = explode("\t",rtrim($l));
-			if(count($a) != 7) {trigger_error("Found one row that only has ".count($a)." columns, expecting 7");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]?" (".$a[2].")":"");
@@ -204,7 +205,8 @@ function functional_descriptions()
 				parent::triplifyString($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()."gene-class-description", $a[6])
+				parent::triplifyString($id, parent::getVoc()."automated-description", $a[6]).
+				parent::triplifyString($id, parent::getVoc()."gene-class-description", trim($a[7]))
 			);
 			parent::writeRDFBufferToWriteFile();
 		}
@@ -213,12 +215,15 @@ function functional_descriptions()
 	function gene_associations(){
 		$go_evidence_type = array(
 			'IC'=>'eco:0000001', 
+			'IBA'=>'eco:0000318',
 			'IDA'=>'eco:0000314', 
 			'IEA'=>'eco:0000203', 
 			'IEP'=>'eco:0000008', 
 			'IGI'=>'eco:0000316',
+			'IKR'=>'eco:0000320',
 			'IMP'=>'eco:0000315',
 			'IPI'=>'eco:0000021',
+			'IRD'=>'eco:0000321',
 			'ISM'=>'eco:0000202',
 			'ISO'=>'eco:0000201',
 			'ISS'=>'eco:0000044',
@@ -258,16 +263,17 @@ function gene_associations(){
 				$split_paper = explode(":", $paper);
 				if($split_paper[0] == "PMID"){
 					$paper_id = "pubmed:".$split_paper[1];
+					parent::addRDF(
+						parent::triplify($association_id, parent::getVoc()."x-pubmed", $paper_id)
+					);
 				} elseif($split_paper[0] == "WB_REF"){
 					$paper_id = parent::getNamespace().$split_paper[1];
 					$paper_label = "Wormbase paper ".$split_paper[1];
 					parent::addRDF(
-						parent::describeIndividual($paper_id, $paper_label, parent::getVoc()."Publication") 
+						parent::describeIndividual($paper_id, $paper_label, parent::getVoc()."Publication").
+						parent::triplify($association_id, parent::getVoc()."publication", $paper_id)
 					);
 				}
-				parent::addRDF(
-					parent::triplify($association_id, parent::getVoc()."publication", $paper_id)
-				);
 			}//foreach
 			parent::WriteRDFBufferToWriteFile();
 		}//while
@@ -287,8 +293,7 @@ function phenotype_associations()
  			$not = $data[3];
  			$phenotype = $data[4];
  			$paper = $data[5];
- 			$var_rnai = explode("WB:",$data[7]);
-	
+ 			$variant = explode("|",trim($data[7]));
 			$neg = ($not == "NOT"?"Negative ":"");
 
  			$pa_id = parent::getRes().($z++);
@@ -308,18 +313,17 @@ function phenotype_associations()
  			);
 
 			if(strstr($data[7], "WBVar")){
-				foreach($var_rnai AS $v) {
-					$v = str_replace("|","",$v);
+				foreach($variant AS $v) {
+					if(trim($v) == '') continue;
 		 			parent::addRDF(
-		 				parent::describeIndividual(parent::getNamespace().$v, "Variant of ".$gene, parent::getVoc()."Gene-Variant").
+		 				parent::describeIndividual($v, "Variant of ".$gene, parent::getVoc()."Gene-Variant").
 						parent::describeClass(parent::getVoc()."Gene-Variant","Gene Variant").
-	 					parent::triplify($pa_id, parent::getVoc()."associated-gene-variant", parent::getNamespace().$v)
+	 					parent::triplify($pa_id, parent::getVoc()."associated-gene-variant", $v)
 	 				);
 				}
 	 		} elseif(strstr($data[7], "WBRNAi")){
-				foreach($var_rnai AS $v) {
-					$v = str_replace("|","",$v);
-		 			$var_rnai_id = parent::getNamespace().$v;
+				foreach($variant AS $v) {
+		 			$var_rnai_id = $v;
 			 		$var_rnai_label = "RNAi ".$v;
 			 		$rnai_exp_id = parent::getRes().($z++);
 	 				parent::addRDF(
@@ -332,7 +336,9 @@ function phenotype_associations()
 	 					parent::triplify($pa_id, parent::getVoc()."associated-rnai-knockdown-experiment", $rnai_exp_id)
 	 				);
 				}
-	 		}
+	 		} else {
+//				var_dump($variant);
+			}
 
 			if($neg) {
 	 			parent::addRDF(