Implemented Janna's suggestions: now uses has_role from the OBO ontol…

…ogy, the roles Drug from the ChEBI ontology, antibody from the Vaccin Ontology, and the 'type' Cell from the Cell Type ontology
egonw · Apr 12, 2012 · f5e6190 · f5e6190
1 parent 0d11201
commit f5e6190
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/compounds.php b/compounds.php
@@ -43,19 +43,17 @@
       } else if ($chebiRow['molecule_type'] == "Protein") {
         echo triple( $molecule, $RDFS . "subClassOf", $PRO . "PR_000000001" );
       } else if ($chebiRow['molecule_type'] == "Cell") {
-        echo triple( $molecule, $RDFS . "subClassOf", $ONTO . "Cell" );
+        echo triple( $molecule, $RDFS . "subClassOf", $CL . "CL_0000000" );
       } else if ($chebiRow['molecule_type'] == "Oligosaccharide") {
         echo triple( $molecule, $RDFS . "subClassOf", $CHEBI . "CHEBI_50699");
       } else if ($chebiRow['molecule_type'] == "Oligonucleotide") {
         echo triple( $molecule, $RDFS . "subClassOf", $CHEBI . "CHEBI_7754");
       } else if ($chebiRow['molecule_type'] == "Antibody") {
-        echo triple( $molecule, $RDFS . "subClassOf", $ONTO . "Antibody" );
-      } else {
-        echo triple( $molecule, $RDFS . "subClassOf", $ONTO . "Drug" );
+        echo triple( $molecule, $OBO . "has_role", $VO . "VO_0000148" ); // Vaccin Ontology: Antibody
+        echo triple( $molecule, $RDFS . "subClassOf", $PRO . "PR_000000001" );
       }
-    } else {
-      echo triple( $molecule, $RDFS . "subClassOf", $ONTO . "Drug" );
     }
+    echo triple( $molecule, $OBO . "has_role", $CHEBI . "CHEBI_23888" ); // Drug
 
     echo triple( $molecule, $OWL . "equivalentClass", "http://bio2rdf.org/chebi:" . $chebiRow['chebi_id'] );
 

diff --git a/namespaces.php b/namespaces.php
@@ -10,12 +10,15 @@
 $FOAF = "http://xmlns.com/foaf/0.1/";
 $CITO = "http://purl.org/spar/cito/";
 
+$OBO  =  "http://purl.obolibrary.org/obo#";
 $BODO = "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#";
 $CHEM = "http://www.blueobelisk.org/chemistryblogs/";
 $NMR = "http://www.nmrshiftdb.org/onto#";
 $CHEMINF = "http://semanticscience.org/resource/";
 $CHEBI = "http://purl.org/obo/owl/CHEBI#";
-$PRO = "http://purl.obolibrary.org/obo/";
+$PRO = $OBO;
+$VO = $OBO;
+$CL = $OBO;
 
 $ONTO = "http://rdf.farmbio.uu.se/chembl/onto/#";
 $ACT = $rooturi . "activity/";