Bio2RDF v5 release preparation

MIT-LICENSE.txt

@@ -0,0 +1,21 @@
+Copyright 2014 Bio2RDF project team and other contributors
+http://bio2rdf.org
+
+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.

README.md

@@ -0,0 +1,10 @@
+Bio2RDF-scripts
+===============
+ This Git repository holds all of the RDF converter scripts used to generate Bio2RDF linked data.
+
+Requirements
+-------------
+See the [wiki](https://github.com/bio2rdf/bio2rdf-scripts/wiki) for details. 
+
+---
+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.

bioportal/bioportal.php

@@ -36,7 +36,7 @@ function __construct($argv) {
 		parent::__construct($argv,'bioportal');
 		parent::addParameter('files',true,null,'all','all or comma-separated list of ontology short names to process');
 		parent::addParameter('download_url',false,null,'http://data.bioontology.org/');
-		parent::addParameter('exclude',false,null,"AURA",'ontologies to exclude - use acronyms');
+		parent::addParameter('exclude',false,null,"AURA,HOOM",'ontologies to exclude - use acronyms');
 		parent::addParameter('continue_from',false,null,"",'the ontology abbreviation to restart from');
 		parent::addParameter('ncbo_api_key',false,null,null,'BioPortal API key (please use your own)');
 		parent::addParameter('ncbo_api_key_file',false,null,'ncbo.api.key','BioPortal API key file');
@@ -123,7 +123,6 @@ function Run()
 			if(isset($ls['description'])) $description = $ls['description'];
 
 			$rfile = $ls['ontology']['links']['download'];
-
 			$lfile = $abbv.".".$format.".gz";
 			if(!file_exists($idir.$lfile) or parent::getParameterValue('download') == 'true') {
 				echo "downloading ... ";
@@ -134,7 +133,7 @@ function Run()
 				$ret = curl_setopt($ch, CURLOPT_HEADER,         1);
 				$ret = curl_setopt($ch, CURLOPT_FOLLOWLOCATION, 1);
 				$ret = curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
-				$ret = curl_setopt($ch, CURLOPT_TIMEOUT,        300);
+				$ret = curl_setopt($ch, CURLOPT_TIMEOUT,        600);
 				$ret = curl_exec($ch);
 				if(!$ret) {echo "no content";continue;}
 
@@ -167,12 +166,13 @@ 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') {
@@ -182,6 +182,7 @@ function Run()
 				} else {
 					echo "no processor for $label (format $format)".PHP_EOL;
 				}
+
 				if(!file_exists($odir.$ofile)) { echo "no output".PHP_EOL;continue;}
 				parent::getWriteFile()->close();
 				parent::clear();
@@ -366,7 +367,7 @@ public function TriplifyMap($a, $prefix)
 
 		} else {
 			parent::addRDF(
-				parent::triplifyString($s_uri,$p_uri,$a['o'],(($a['o_datatype'] == '')?null:$a['o_datatype']),(($a['o_lang'] == '')?null:$a['o_lang']))
+				parent::triplifyString($s_uri,$p_uri,addslashes($a['o']),(($a['o_datatype'] == '')?null:$a['o_datatype']),(($a['o_lang'] == '')?null:$a['o_lang']))
 			);			
 		}
 
@@ -394,7 +395,7 @@ function OBO2RDF($abbv)
 		$graph_uri = '<'.parent::getRegistry()->getFQURI(parent::getGraphURI()).'>';
 		$bid = 1;
 
-		while($l = parent::getReadFile()->read()) {
+		while(FALSE !== ($l = parent::getReadFile()->read())) {
 			$lt = trim($l);
 			if(strlen($lt) == 0) continue;
 			if($lt[0] == '!') continue;
@@ -461,6 +462,7 @@ function OBO2RDF($abbv)
 					else {$ns = strtolower($c[0]);$id=$c[1];}
 					$id = str_replace( array("(",")"), array("_",""), $id);
 					$tid = $ns.":".$id;
+					echo $tid.PHP_EOL;
 				} else if($a[0] == "name") {
 					$buf .= parent::describeClass($tid,addslashes(stripslashes($a[1])));
 				} else if($a[0] == "is_a") {
@@ -483,7 +485,8 @@ function OBO2RDF($abbv)
 					$buf .= $t;
 					$is_deprecated = true;
 				} else if($a[0] == "id") {	
-					parent::getRegistry()->parseQName($a[1],$ns,$id);					
+					parent::getRegistry()->parseQName($a[1],$ns,$id);
+					if(trim($ns) == '') $ns = "unspecified";			
 					$tid = "$ns:$id";
 //					$buf .= parent::describeClass($tid,null,"owl:Class");
 //					$buf .= parent::triplify($tid,"rdfs:isDefinedBy",$ouri);					
@@ -610,6 +613,7 @@ function OBO2RDF($abbv)
 				} else if($a[0] == "is_a") {
 					// do subclassing
 					parent::getRegistry()->parseQName($a[1],$ns,$id);
+					if(trim($ns) == '') $ns = "unspecified";
 					$t = parent::triplify($tid,"rdfs:subClassOf","$ns:$id");
 					$buf .= $t;
 					$min .= $t;
@@ -657,17 +661,19 @@ function OBO2RDF($abbv)
 					$c = explode(" ",$a[1]);
 					if(count($c) == 1) { // just a class	
 						parent::getRegistry()->parseQName($c[0],$ns,$id);
+						if(trim($ns) == '') $ns = "unspecified";
 						$relationship .= parent::getRegistry()->getFQURI("$ns:$id");
 						$buf .= parent::triplify($tid,"rdfs:subClassOf","$ns:$id");
 
 					} else if(count($c) == 2) { // an expression						
 						parent::getRegistry()->parseQName($c[0],$pred_ns,$pred_id);
 						parent::getRegistry()->parseQName($c[1],$obj_ns,$obj_id);
+						if(trim($obj_ns) == '') $obj_ns = "unspecified";
 
 						$relationship .= '_:b'.$bid.' <'.parent::getRegistry()->getFQURI('owl:onProperty').'> <'.parent::getRegistry()->getFQURI("obo_vocabulary:".$pred_id).">  $graph_uri .".PHP_EOL;
 						$relationship .= '_:b'.$bid.' <'.parent::getRegistry()->getFQURI('owl:someValuesFrom').'> <'.parent::getRegistry()->getFQURI("$obj_ns:$obj_id")."> $graph_uri .".PHP_EOL;
 
-						$buf .= parent::triplify($tid,"obo_vocabulary:$pred_id","$obj_ns:$obj_id");
+						$buf .= parent::triplify($tid,"obo_vocabulary:$pred_id","$obj_ns:$obj_id"); #@todo this causes problem with OGG-MM
 					}
 				} else {
 					// default handler
@@ -676,7 +682,8 @@ function OBO2RDF($abbv)
 			} else {
 				//header
 				//format-version: 1.0
-				$buf .= parent::triplifyString($ouri,"obo_vocabulary:$a[0]",str_replace( array('"','\:'), array('\"',':'), isset($a[1])?$a[1]:""));
+				$buf .= parent::triplifyString($ouri,"obo_vocabulary:$a[0]",
+					str_replace( array('"','\:'), array('\"',':'), isset($a[1])?$a[1]:""));
 			}
 
 			if($minimal || $minimalp) parent::getWriteFile()->write($min);

chembl/chembl.php

@@ -1017,8 +1017,68 @@ function compounds($connection) {
 				}
 				parent::writeRDFBufferToWriteFile();
 			}
+		}
+		$result->free();
+	}
 
-			$result->free();
+	/*
+	*	parse the assays tables
+	*/
+	function process_assays() {
+
+		$this->set_write_file("assays");
+
+		$allIDs = mysql_query(
+		    "SELECT DISTINCT * FROM assays, assay_type " .
+		    "WHERE assays.assay_type = assay_type.assay_type"
+		);
+
+		$num = mysql_numrows($allIDs);
+
+		while ($row = mysql_fetch_assoc($allIDs)) {
+
+		  $assay = "chembl:assay_".$row['assay_id'];
+		  $this->AddRDF($this->QQuad($assay,"rdf:type","chembl_vocabulary:Assay"));
+
+		  //chembl assay id
+		  $chembl = "chembl:". $row['chembl_id'];
+		  $this->AddRDF($this->QQuadl($assay,"dc:identifier",$row['chembl_id']));
+		  $this->AddRDF($this->QQuad($assay,"owl:equivalentClass",$chembl));
+		  $this->AddRDF($this->QQuad($chembl,"owl:equivalentClass",$assay));
+		  $this->WriteRDFBufferToWriteFile();
+
+		  if ($row['description']) {
+		    # clean up description
+		    $description = $row['description'];
+		    $description = str_replace("\\", "\\\\", $description);
+		    $description = str_replace("\"", "\\\"", $description);
+		    $this->AddRDF($this->QQuadl($assay,"chembl_vocabulary:hasDescription",$description));
+		  }
+
+		  if ($row['doc_id']){
+		  	$this->AddRDF($this->QQuad($assay,"chembl_vocabulary:citesAsDataSource","chembl:reference_".$row['doc_id']));
+		  }
+
+		  $props = mysql_query("SELECT DISTINCT * FROM assay2target WHERE assay_id = " . $row['assay_id']);
+
+		  while ($prop = mysql_fetch_assoc($props)) {		  	  
+		    if ($prop['tid']) {
+		      $target = "chembl:target_".$prop['tid'];
+		      $this->AddRDF($this->QQuad($assay,"chembl_vocabulary:hasTarget",$target));
+
+		      if ($prop['confidence_score']) {
+		        $targetScore = "chembl:tscore_".md5($assay.$prop['tid']);
+		        $this->AddRDF($this->QQuad($assay,"chembl_vocabulary:hasTargetScore",$targetScore));
+		        $this->AddRDF($this->QQuad($targetScore,"chembl_vocabulary:forTarget",$target));
+		        $this->AddRDF($this->QQuadl($targetScore,"rdf:value",$prop['confidence_score']));
+		      }
+		    }
+
+		     $this->WriteRDFBufferToWriteFile();
+
+		  }
+		  $this->AddRDF($this->QQuad($assay,"chembl_vocabulary:hasAssayType","chembl_vocabulary:".$row['assay_desc']));
+		  $this->WriteRDFBufferToWriteFile();
 		}
 	}
 
@@ -1287,4 +1347,5 @@ function protein_families($connection){
 		}
 	}
 }
+
 ?>