add predicate omopconceptid to active ingredient graph

Author: Richard Boyce

linkedSPLs/LinkedSPLs-activeMoiety/createActiveMoietySubInRDF.py

@@ -29,18 +29,19 @@
 DRUGBANK_BIO2RDF = "http://bio2rdf.org/drugbank:"
 NDFRT_BASE = "http://purl.bioontology.org/ontology/NDFRT/"
 DRON_BASE = "http://purl.obolibrary.org/obo/"
-#OHDSI_BASE = "http://purl.org/net/ohdsi#"
+OHDSI_BASE = "http://purl.org/net/ohdsi#"
 
 
 class DictItem:
 
-    def __init__(self, pt, db_uri1, db_uri2, rxcui, chebi, nui, dron, nameAndRole):
+    def __init__(self, pt, db_uri1, db_uri2, rxcui, chebi, nui, dron, omopid, nameAndRole):
         self.pt = str(pt)
         self.db_uri1 = str(db_uri1)
         self.db_uri2 = str(db_uri2)
         self.rxcui = str(rxcui)
         self.chebi = str(chebi)
         self.dron = str(dron)
+        self.omopid = str(omopid)
 
         if nui and nameAndRole:
             self.drugClass = Set([str(nui)+'|'+str(nameAndRole)])
@@ -56,7 +57,7 @@ def __init__(self, pt, db_uri1, db_uri2, rxcui, chebi, nui, dron, nameAndRole):
 for item in data_set:
 
     if item["unii"] not in dict_moieties:
-        moiety = DictItem(item["pt"], item["db_uri1"], item["db_uri2"], item["rxcui"], item["chebi"], item["nui"], item["dron"] ,item["nameAndRole"])
+        moiety = DictItem(item["pt"], item["db_uri1"], item["db_uri2"], item["rxcui"], item["chebi"], item["nui"], item["dron"], item["omopid"] ,item["nameAndRole"])
         dict_moieties[item["unii"]]=moiety
 
     else:
@@ -72,7 +73,8 @@ def __init__(self, pt, db_uri1, db_uri2, rxcui, chebi, nui, dron, nameAndRole):
             dict_moieties[item["unii"]].dron = item["dron"] 
         if not dict_moieties[item["unii"]].chebi:
             dict_moieties[item["unii"]].chebi = item["chebi"]  
-        #print item['nui']+'|'+item['nameAndRole']
+        if not dict_moieties[item["unii"]].omopid:
+            dict_moieties[item["unii"]].omopid = item["omopid"]  
 
         if item['nui'] and item['nameAndRole']:
             if dict_moieties[item["unii"]].drugClass:
@@ -159,8 +161,8 @@ def __init__(self, pt, db_uri1, db_uri2, rxcui, chebi, nui, dron, nameAndRole):
     if v.dron:
         graph.add((URIRef(ACTIVEMOIETY_BASE + str(k)), linkedspls_vocabulary["DrOnId"], URIRef(DRON_BASE + v.dron)))
 
-   # if v.omopid:
-   #    graph.add((URIRef(ACTIVEMOIETY_BASE + str(k)), linkedspls_vocabulary["OMOPConceptId"], Literal(OHDSI_BASE + str(int(float(v.omopid))))))
+    if v.omopid:
+       graph.add((URIRef(ACTIVEMOIETY_BASE + str(k)), linkedspls_vocabulary["OMOPConceptId"], Literal(OHDSI_BASE + str((v.omopid)))))