diff --git a/dataload/linker/src/main/java/LinkerPass1.java b/dataload/linker/src/main/java/LinkerPass1.java
index 67595924..377429c5 100644
--- a/dataload/linker/src/main/java/LinkerPass1.java
+++ b/dataload/linker/src/main/java/LinkerPass1.java
@@ -178,7 +178,8 @@ public static LinkerPass1Result run(String inputJsonFilename) throws IOException
 					if(curieObject.has("value")) {
 						String curieValue = curieObject.get("value").getAsString();
 						if(!curieValue.contains(":")) {
-							curieValue = entry.getValue().definingOntologyIds.iterator().next().toUpperCase() + ":" + curieValue;
+							var definingOntologyId = entry.getValue().definingOntologyIds.iterator().next();
+							curieValue = entry.getValue().ontologyIdToDefinitions.get(definingOntologyId).curie.getAsJsonObject().get("value").getAsString();
 							curieObject.addProperty("value", curieValue);
 							result.iriToDefinitions.put(entry.getKey(), definitions);
 						}
diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
index 73f3b28e..1b2d5b1b 100644
--- a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
+++ b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
@@ -31,6 +31,9 @@ public static void annotateShortForms(OntologyGraph graph) {
 			if(c.uri == null)
 				continue;
 
+			if (preferredPrefix == null || preferredPrefix.isEmpty()) {
+				preferredPrefix = graph.config.get("id").toString().toUpperCase();
+			}
 
 			String shortForm = extractShortForm(graph, ontologyBaseUris, preferredPrefix, c.uri);
 			String curie = shortForm.replaceFirst("_", ":");