diff --git a/.changeset/soft-candles-obey.md b/.changeset/soft-candles-obey.md
new file mode 100644
index 0000000000..006955d16e
--- /dev/null
+++ b/.changeset/soft-candles-obey.md
@@ -0,0 +1,4 @@
+---
+'@finos/legend-extension-dsl-persistence': patch
+'@finos/legend-graph': patch
+---
diff --git a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Persistence.ts b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Persistence.ts
index 8c67ab5af6..6561c27145 100644
--- a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Persistence.ts
+++ b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Persistence.ts
@@ -19,6 +19,7 @@ import type { V1_Persister } from './V1_DSL_Persistence_Persister.js';
 import type { V1_Trigger } from './V1_DSL_Persistence_Trigger.js';
 import {
   V1_PackageableElement,
+  type V1_PackageableElementPointer,
   type V1_PackageableElementVisitor,
 } from '@finos/legend-graph';
 import { type Hashable, hashArray } from '@finos/legend-shared';
@@ -29,7 +30,7 @@ import type { V1_ServiceOutputTarget as V1_ServiceOutputTarget } from './V1_DSL_
 export class V1_Persistence extends V1_PackageableElement implements Hashable {
   documentation!: string;
   trigger!: V1_Trigger;
-  service!: string;
+  service!: V1_PackageableElementPointer;
   persister?: V1_Persister | undefined;
   serviceOutputTargets?: V1_ServiceOutputTarget[] | undefined;
   notifier!: V1_Notifier;
@@ -40,7 +41,7 @@ export class V1_Persistence extends V1_PackageableElement implements Hashable {
       PERSISTENCE_HASH_STRUCTURE.PERSISTENCE,
       this.documentation,
       this.trigger,
-      this.service,
+      this.service.path,
       hashArray(this.serviceOutputTargets ?? []),
       this.persister ?? '',
       this.notifier,
diff --git a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_PersistentTarget.ts b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_PersistentTarget.ts
index 874b2351ef..0d9d22d7ff 100644
--- a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_PersistentTarget.ts
+++ b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_PersistentTarget.ts
@@ -17,6 +17,7 @@
 import { type Hashable, hashArray } from '@finos/legend-shared';
 import { PERSISTENCE_HASH_STRUCTURE } from '../../../../../../../graph/DSL_Persistence_HashUtils.js';
 import type { V1_Temporality } from './V1_DSL_Persistence_Temporality.js';
+import type { V1_PackageableElementPointer } from '@finos/legend-graph';
 
 export abstract class V1_PersistenceTarget implements Hashable {
   abstract get hashCode(): string;
@@ -27,14 +28,14 @@ export class V1_RelationalPersistenceTarget
   implements Hashable
 {
   table!: string;
-  database!: string;
+  database!: V1_PackageableElementPointer;
   temporality!: V1_Temporality;
 
   get hashCode(): string {
     return hashArray([
       PERSISTENCE_HASH_STRUCTURE.RELATIONAL_PERSISTENCE_TARGET,
       this.table,
-      this.database,
+      this.database.path,
       this.temporality,
     ]);
   }
diff --git a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Sink.ts b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Sink.ts
index 2e50d9f683..f154fd1fcc 100644
--- a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Sink.ts
+++ b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/model/packageableElements/persistence/V1_DSL_Persistence_Sink.ts
@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+import type { V1_PackageableElementPointer } from '@finos/legend-graph';
 import { PERSISTENCE_HASH_STRUCTURE } from '../../../../../../../graph/DSL_Persistence_HashUtils.js';
 import { type Hashable, hashArray } from '@finos/legend-shared';
 
@@ -22,23 +23,23 @@ export abstract class V1_Sink implements Hashable {
 }
 
 export class V1_RelationalSink extends V1_Sink implements Hashable {
-  database!: string;
+  database!: V1_PackageableElementPointer;
 
   override get hashCode(): string {
     return hashArray([
       PERSISTENCE_HASH_STRUCTURE.RELATIONAL_SINK,
-      this.database,
+      this.database.path,
     ]);
   }
 }
 
 export class V1_ObjectStorageSink extends V1_Sink implements Hashable {
-  binding!: string;
+  binding!: V1_PackageableElementPointer;
 
   override get hashCode(): string {
     return hashArray([
       PERSISTENCE_HASH_STRUCTURE.OBJECT_STORAGE_SINK,
-      this.binding,
+      this.binding.path,
     ]);
   }
 }
diff --git a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DSL_Persistence_TransformerHelper.ts b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DSL_Persistence_TransformerHelper.ts
index 339fb8ab2f..4c5f039c9a 100644
--- a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DSL_Persistence_TransformerHelper.ts
+++ b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DSL_Persistence_TransformerHelper.ts
@@ -154,6 +154,8 @@ import {
   V1_transformEmbeddedData,
   V1_transformTestAssertion,
   V1_transformAtomicTest,
+  PackageableElementPointerType,
+  V1_PackageableElementPointer,
 } from '@finos/legend-graph';
 import { guaranteeType, UnsupportedOperationError } from '@finos/legend-shared';
 import type { PersistenceTestBatch } from '../../../../../../../graph/metamodel/pure/model/packageableElements/persistence/DSL_Persistence_PersistenceTestBatch.js';
@@ -357,7 +359,10 @@ export const V1_transformRelationalSink = (
   context: V1_GraphTransformerContext,
 ): V1_RelationalSink => {
   const protocol = new V1_RelationalSink();
-  protocol.database = element.database.value.path;
+  protocol.database = new V1_PackageableElementPointer(
+    PackageableElementPointerType.STORE,
+    element.database.value.path,
+  );
   return protocol;
 };
 
@@ -366,7 +371,10 @@ export const V1_transformObjectStorageSink = (
   context: V1_GraphTransformerContext,
 ): V1_ObjectStorageSink => {
   const protocol = new V1_ObjectStorageSink();
-  protocol.binding = element.binding.value.path;
+  protocol.binding = new V1_PackageableElementPointer(
+    PackageableElementPointerType.BINDING,
+    element.binding.value.path,
+  );
   return protocol;
 };
 
@@ -963,7 +971,11 @@ export const V1_transformPersistenceTarget = (
 ): V1_PersistenceTarget => {
   if (element instanceof RelationalPersistenceTarget) {
     const protocol = new V1_RelationalPersistenceTarget();
-    protocol.database = element.database;
+    protocol.database = new V1_PackageableElementPointer(
+      PackageableElementPointerType.STORE,
+      element.database,
+    );
+
     protocol.table = element.table;
     protocol.temporality = V1_transformTemporality(
       element.temporality,
@@ -1252,7 +1264,10 @@ export const V1_transformPersistence = (
   protocol.documentation = element.documentation;
   protocol.notifier = V1_transformNotifier(element.notifier, context);
   protocol.persister = V1_transformPersister(element.persister, context);
-  protocol.service = element.service.valueForSerialization ?? '';
+  protocol.service = new V1_PackageableElementPointer(
+    PackageableElementPointerType.SERVICE,
+    element.service.valueForSerialization ?? '',
+  );
   protocol.serviceOutputTargets = V1_transformServiceOutputTargets(
     element.serviceOutputTargets,
     context,
diff --git a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_DSL_Persistence_BuilderHelper.ts b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_DSL_Persistence_BuilderHelper.ts
index 28f1a90e71..c6bb09e611 100644
--- a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_DSL_Persistence_BuilderHelper.ts
+++ b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_DSL_Persistence_BuilderHelper.ts
@@ -368,7 +368,7 @@ export const V1_buildRelationalSink = (
 ): RelationalSink => {
   const sink = new RelationalSink();
   sink.database = context.resolveElement(
-    protocol.database,
+    protocol.database.path,
     false,
   ) as PackageableElementImplicitReference<Database>;
   return sink;
@@ -380,7 +380,7 @@ export const V1_buildObjectStorageSink = (
 ): ObjectStorageSink => {
   const sink = new ObjectStorageSink();
   sink.binding = context.resolveElement(
-    protocol.binding,
+    protocol.binding.path,
     false,
   ) as PackageableElementImplicitReference<Binding>;
   return sink;
@@ -1164,7 +1164,7 @@ export const V1_buildPersistenceTarget = (
 ): PersistenceTarget => {
   if (protocol instanceof V1_RelationalPersistenceTarget) {
     const persistentTarget = new RelationalPersistenceTarget();
-    persistentTarget.database = protocol.database;
+    persistentTarget.database = protocol.database.path;
     persistentTarget.table = protocol.table;
     persistentTarget.temporality = V1_buildTemporality(
       protocol.temporality,
@@ -1222,7 +1222,7 @@ export const V1_buildPersistence = (
   );
   persistence.notifier = V1_buildNotifier(protocol.notifier, context);
   persistence.persister = V1_buildPersister(protocol.persister, context);
-  persistence.service = context.resolveService(protocol.service);
+  persistence.service = context.resolveService(protocol.service.path);
   persistence.serviceOutputTargets = V1_buildServiceOutputTargets(
     protocol.serviceOutputTargets,
     context,
diff --git a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/V1_DSL_Persistence_ProtocolHelper.ts b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/V1_DSL_Persistence_ProtocolHelper.ts
index 404156eefb..4b1e07aa32 100644
--- a/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/V1_DSL_Persistence_ProtocolHelper.ts
+++ b/packages/legend-extension-dsl-persistence/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/V1_DSL_Persistence_ProtocolHelper.ts
@@ -92,6 +92,9 @@ import {
   V1_externalFormatDataModelSchema,
   V1_serializeAtomicTest,
   V1_deserializeAtomicTest,
+  V1_packageableElementPointerModelSchema,
+  V1_serializePackageableElementPointer,
+  PackageableElementPointerType,
 } from '@finos/legend-graph';
 import {
   type PlainObject,
@@ -777,7 +780,14 @@ const V1_relationalSinkModelSchema = (
 ): ModelSchema<V1_RelationalSink> =>
   createModelSchema(V1_RelationalSink, {
     _type: usingConstantValueSchema(V1_SinkType.RELATIONAL_SINK),
-    database: primitive(),
+    database: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.STORE,
+        ),
+    ),
   });
 
 const V1_objectStorageSinkModelSchema = (
@@ -785,7 +795,14 @@ const V1_objectStorageSinkModelSchema = (
 ): ModelSchema<V1_ObjectStorageSink> =>
   createModelSchema(V1_ObjectStorageSink, {
     _type: usingConstantValueSchema(V1_SinkType.OBJECT_STORAGE_SINK),
-    binding: primitive(),
+    binding: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.BINDING,
+        ),
+    ),
   });
 
 export const V1_serializeSink = (
@@ -1599,7 +1616,14 @@ export const V1_relationalPersistenceTargetModelSchema = (
     _type: usingConstantValueSchema(
       V1_PersistentTargetType.RELATIONAL_PERSISTENCE_TARGET,
     ),
-    database: primitive(),
+    database: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.STORE,
+        ),
+    ),
     table: primitive(),
     temporality: custom(
       (val) => V1_serializeTemporality(val, plugins),
@@ -2134,7 +2158,14 @@ export const V1_persistenceModelSchema = (
       (val) => V1_serializePersister(val, plugins),
       (val) => V1_deserializePersister(val, plugins),
     ),
-    service: primitive(),
+    service: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.SERVICE,
+        ),
+    ),
     serviceOutputTargets: optionalCustomList(
       (val: V1_ServiceOutputTarget) =>
         V1_serializeServiceOutputTarget(val, plugins),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Class.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Class.ts
index 250053cde3..44625b111f 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Class.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Class.ts
@@ -20,6 +20,7 @@ import type { V1_Property } from '../../../model/packageableElements/domain/V1_P
 import type { V1_StereotypePtr } from '../../../model/packageableElements/domain/V1_StereotypePtr.js';
 import {
   type V1_PackageableElementVisitor,
+  type V1_PackageableElementPointer,
   V1_PackageableElement,
 } from '../../../model/packageableElements/V1_PackageableElement.js';
 import type { V1_TaggedValue } from '../../../model/packageableElements/domain/V1_TaggedValue.js';
@@ -27,7 +28,7 @@ import type { V1_Constraint } from '../../../model/packageableElements/domain/V1
 import type { V1_DerivedProperty } from './V1_DerivedProperty.js';
 
 export class V1_Class extends V1_PackageableElement implements Hashable {
-  superTypes: string[] = [];
+  superTypes: V1_PackageableElementPointer[] = [];
   properties: V1_Property[] = [];
   derivedProperties: V1_DerivedProperty[] = [];
   stereotypes: V1_StereotypePtr[] = [];
@@ -40,7 +41,7 @@ export class V1_Class extends V1_PackageableElement implements Hashable {
       this.path,
       hashArray(this.properties),
       hashArray(this.derivedProperties),
-      hashArray(this.superTypes),
+      hashArray(this.superTypes.map((e) => e.path)),
       hashArray(this.constraints),
       hashArray(this.stereotypes),
       hashArray(this.taggedValues),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Profile.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Profile.ts
index cc0cffeef6..2eeb64d33f 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Profile.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/domain/V1_Profile.ts
@@ -21,16 +21,31 @@ import {
   V1_PackageableElement,
 } from '../../../model/packageableElements/V1_PackageableElement.js';
 
+export class V1_ProfileStereotype {
+  value!: string;
+
+  constructor(value: string) {
+    this.value = value;
+  }
+}
+
+export class V1_ProfileTag {
+  value!: string;
+  constructor(value: string) {
+    this.value = value;
+  }
+}
+
 export class V1_Profile extends V1_PackageableElement implements Hashable {
-  stereotypes: string[] = [];
-  tags: string[] = [];
+  stereotypes: V1_ProfileStereotype[] = [];
+  tags: V1_ProfileTag[] = [];
 
   override get hashCode(): string {
     return hashArray([
       CORE_HASH_STRUCTURE.PROFILE,
       this.path,
-      hashArray(this.stereotypes),
-      hashArray(this.tags),
+      hashArray(this.stereotypes.map((e) => e.value)),
+      hashArray(this.tags.map((e) => e.value)),
     ]);
   }
 
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_AssociationMapping.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_AssociationMapping.ts
index 3553934f22..019fafe12a 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_AssociationMapping.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_AssociationMapping.ts
@@ -16,16 +16,17 @@
 
 import { hashArray, type Hashable } from '@finos/legend-shared';
 import { CORE_HASH_STRUCTURE } from '../../../../../../../graph/Core_HashUtils.js';
+import type { V1_PackageableElementPointer } from '../V1_PackageableElement.js';
 
 export abstract class V1_AssociationMapping implements Hashable {
   id?: string | undefined;
-  association!: string;
+  association!: V1_PackageableElementPointer;
   stores: string[] = [];
 
   get hashCode(): string {
     return hashArray([
       CORE_HASH_STRUCTURE.ASSOCIATION_IMPLEMENTATION,
-      this.association,
+      this.association.path,
       this.id ?? '',
       hashArray(this.stores),
     ]);
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_EnumerationMapping.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_EnumerationMapping.ts
index 2a2cd2ad1f..a90ec6becf 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_EnumerationMapping.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_EnumerationMapping.ts
@@ -24,10 +24,11 @@ import {
   type V1_EnumValueMapping,
   V1_getEnumValueMappingSourceValueType,
 } from '../../../model/packageableElements/mapping/V1_EnumValueMapping.js';
+import type { V1_PackageableElementPointer } from '../V1_PackageableElement.js';
 
 export class V1_EnumerationMapping implements Hashable {
   id?: string | undefined;
-  enumeration!: string;
+  enumeration!: V1_PackageableElementPointer;
   /**
    * NOTE: the order is important, during deserialization, we want sourceType to be already available
    * @deprecated since v1_11_0
@@ -41,7 +42,7 @@ export class V1_EnumerationMapping implements Hashable {
     return hashArray([
       CORE_HASH_STRUCTURE.ENUMERATION_MAPPING,
       this.id ?? '',
-      this.enumeration,
+      this.enumeration.path,
       // NOTE: older protocol formats have information about source type so we have to account for those,
       // otherwise, we don't need to account for the source type in hash computation
       // If there is no enum value mapping, ignore the source type since it's synthetic and used by the editor
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_MappingStoreTestData.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_MappingStoreTestData.ts
index c67b290289..ab9d6c3ea7 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_MappingStoreTestData.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/mapping/V1_MappingStoreTestData.ts
@@ -17,15 +17,16 @@
 import { hashArray, type Hashable } from '@finos/legend-shared';
 import { CORE_HASH_STRUCTURE } from '../../../../../../../graph/Core_HashUtils.js';
 import type { V1_EmbeddedData } from '../../data/V1_EmbeddedData.js';
+import type { V1_PackageableElementPointer } from '../V1_PackageableElement.js';
 
 export class V1_MappingStoreTestData implements Hashable {
-  store!: string;
+  store!: V1_PackageableElementPointer;
   data!: V1_EmbeddedData;
 
   get hashCode(): string {
     return hashArray([
       CORE_HASH_STRUCTURE.STORE_TEST_DATA,
-      this.store,
+      this.store.path,
       this.data,
     ]);
   }
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/V1_Store.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/V1_Store.ts
index 73efb3d6e7..7f9ec3b643 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/V1_Store.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/V1_Store.ts
@@ -15,11 +15,14 @@
  */
 
 import type { Hashable } from '@finos/legend-shared';
-import { V1_PackageableElement } from '../../../model/packageableElements/V1_PackageableElement.js';
+import {
+  V1_PackageableElement,
+  type V1_PackageableElementPointer,
+} from '../../../model/packageableElements/V1_PackageableElement.js';
 
 export abstract class V1_Store
   extends V1_PackageableElement
   implements Hashable
 {
-  includedStores: string[] = [];
+  includedStores: V1_PackageableElementPointer[] = [];
 }
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/flatData/model/V1_FlatData.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/flatData/model/V1_FlatData.ts
index 5418c8c1c2..adeab08c18 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/flatData/model/V1_FlatData.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/flatData/model/V1_FlatData.ts
@@ -27,7 +27,7 @@ export class V1_FlatData extends V1_Store implements Hashable {
     return hashArray([
       CORE_HASH_STRUCTURE.FLAT_DATA,
       this.path,
-      hashArray(this.includedStores),
+      hashArray(this.includedStores.map((e) => e.path)),
       hashArray(this.sections),
     ]);
   }
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/relational/model/V1_Database.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/relational/model/V1_Database.ts
index 570a88c7df..5254522799 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/relational/model/V1_Database.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/model/packageableElements/store/relational/model/V1_Database.ts
@@ -33,7 +33,7 @@ export class V1_Database extends V1_Store implements Hashable {
     return hashArray([
       CORE_HASH_STRUCTURE.DATABASE,
       this.path,
-      hashArray(this.includedStores),
+      hashArray(this.includedStores.map((e) => e.path)),
       hashArray(this.schemas),
       hashArray(this.joins),
       hashArray(this.filters),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DatabaseTransformer.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DatabaseTransformer.ts
index d6a5df2b41..b9eb457f82 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DatabaseTransformer.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DatabaseTransformer.ts
@@ -48,6 +48,7 @@ import {
   RelationalOperationElementWithJoin,
   extractLine,
 } from '../../../../../../../graph/metamodel/pure/packageableElements/store/relational/model/RelationalOperationElement.js';
+import { PackageableElementPointerType } from '../../../../../../../graph/MetaModelConst.js';
 import type { Table } from '../../../../../../../graph/metamodel/pure/packageableElements/store/relational/model/Table.js';
 import type { Column } from '../../../../../../../graph/metamodel/pure/packageableElements/store/relational/model/Column.js';
 import type { Filter } from '../../../../../../../graph/metamodel/pure/packageableElements/store/relational/model/Filter.js';
@@ -107,6 +108,7 @@ import { V1_FilterMapping } from '../../../model/packageableElements/store/relat
 import { V1_FilterPointer } from '../../../model/packageableElements/store/relational/mapping/V1_FilterPointer.js';
 import type { TablePtr } from '../../../../../../../graph/metamodel/pure/packageableElements/service/TablePtr.js';
 import { V1_transformStereotype } from './V1_DomainTransformer.js';
+import { V1_PackageableElementPointer } from '../../../model/packageableElements/V1_PackageableElement.js';
 
 const transformRelationalDataType = (
   type: RelationalDataType,
@@ -429,7 +431,11 @@ export const V1_transformDatabase = (
     V1_transformStereotype(stereotype),
   );
   database.includedStores = element.includes.map(
-    (store) => store.valueForSerialization ?? '',
+    (store) =>
+      new V1_PackageableElementPointer(
+        PackageableElementPointerType.STORE,
+        store.valueForSerialization ?? '',
+      ),
   );
   return database;
 };
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DomainTransformer.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DomainTransformer.ts
index 35225bfcd4..6be74a31e7 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DomainTransformer.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_DomainTransformer.ts
@@ -29,7 +29,11 @@ import type { Class } from '../../../../../../../graph/metamodel/pure/packageabl
 import type { Association } from '../../../../../../../graph/metamodel/pure/packageableElements/domain/Association.js';
 import type { ConcreteFunctionDefinition } from '../../../../../../../graph/metamodel/pure/packageableElements/function/ConcreteFunctionDefinition.js';
 import type { Property } from '../../../../../../../graph/metamodel/pure/packageableElements/domain/Property.js';
-import { V1_Profile } from '../../../model/packageableElements/domain/V1_Profile.js';
+import {
+  V1_Profile,
+  V1_ProfileStereotype,
+  V1_ProfileTag,
+} from '../../../model/packageableElements/domain/V1_Profile.js';
 import { V1_StereotypePtr } from '../../../model/packageableElements/domain/V1_StereotypePtr.js';
 import {
   V1_initPackageableElement,
@@ -73,6 +77,7 @@ import { V1_transformTestAssertion } from './V1_TestTransformer.js';
 import { V1_DefaultValue } from '../../../model/packageableElements/domain/V1_DefaultValue.js';
 import { PackageableElementPointerType } from '../../../../../../../graph/MetaModelConst.js';
 import { V1_createGenericTypeWithElementPath } from '../../../helpers/V1_DomainHelper.js';
+import { V1_PackageableElementPointer } from '../../../model/packageableElements/V1_PackageableElement.js';
 
 export const V1_createRawGenericTypeWithElementPath = (
   path: string,
@@ -87,8 +92,10 @@ export const V1_createRawGenericTypeWithElementPath = (
 export const V1_transformProfile = (element: Profile): V1_Profile => {
   const profile = new V1_Profile();
   V1_initPackageableElement(profile, element);
-  profile.stereotypes = element.p_stereotypes.map((s) => s.value);
-  profile.tags = element.p_tags.map((t) => t.value);
+  profile.stereotypes = element.p_stereotypes.map(
+    (s) => new V1_ProfileStereotype(s.value),
+  );
+  profile.tags = element.p_tags.map((t) => new V1_ProfileTag(t.value));
   return profile;
 };
 
@@ -238,7 +245,11 @@ export const V1_transformClass = (
   _class.stereotypes = element.stereotypes.map(V1_transformStereotype);
   _class.taggedValues = element.taggedValues.map(V1_transformTaggedValue);
   _class.superTypes = element.generalizations.map(
-    (e) => e.ownerReference.valueForSerialization ?? '',
+    (e) =>
+      new V1_PackageableElementPointer(
+        PackageableElementPointerType.CLASS,
+        e.ownerReference.valueForSerialization ?? '',
+      ),
   );
   _class.derivedProperties = element.derivedProperties.map((dp) =>
     transformDerivedProperty(dp, context),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_MappingTransformer.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_MappingTransformer.ts
index 61fc193827..a77eb9e6c9 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_MappingTransformer.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/from/V1_MappingTransformer.ts
@@ -174,6 +174,7 @@ import { INTERNAL__UnknownPropertyMapping } from '../../../../../../../graph/met
 import { V1_INTERNAL__UnknownPropertyMapping } from '../../../model/packageableElements/mapping/V1_INTERNAL__UnknownPropertyMapping.js';
 import type { INTERNAL__UnknownSetImplementation } from '../../../../../../../graph/metamodel/pure/packageableElements/mapping/INTERNAL__UnknownSetImplementation.js';
 import { V1_INTERNAL__UnknownClassMapping } from '../../../model/packageableElements/mapping/V1_INTERNAL__UnknownClassMapping.js';
+import { V1_PackageableElementPointer } from '../../../model/packageableElements/V1_PackageableElement.js';
 
 export const V1_transformPropertyReference = (
   element: PropertyReference,
@@ -245,8 +246,10 @@ const transformEnumerationMapping = (
   enumerationMapping.enumValueMappings = element.enumValueMappings
     .filter((e) => !isStubbed_EnumValueMapping(e))
     .map(transformEnumValueMapping);
-  enumerationMapping.enumeration =
-    element.enumeration.valueForSerialization ?? '';
+  enumerationMapping.enumeration = new V1_PackageableElementPointer(
+    PackageableElementPointerType.ENUMERATION,
+    element.enumeration.valueForSerialization ?? '',
+  );
   enumerationMapping.id = mappingElementIdSerializer(element.id);
   return enumerationMapping;
 };
@@ -358,7 +361,10 @@ const transformMappingStoreTestData = (
 ): V1_MappingStoreTestData => {
   const testData = new V1_MappingStoreTestData();
   testData.data = V1_transformEmbeddedData(element.data, context);
-  testData.store = element.store.valueForSerialization ?? '';
+  testData.store = new V1_PackageableElementPointer(
+    PackageableElementPointerType.STORE,
+    element.store.valueForSerialization ?? '',
+  );
   return testData;
 };
 
@@ -1307,8 +1313,10 @@ const transformRelationalAssociationImplementation = (
   relationalMapping.stores = element.stores.map(
     (store) => store.valueForSerialization ?? '',
   );
-  relationalMapping.association =
-    element.association.valueForSerialization ?? '';
+  relationalMapping.association = new V1_PackageableElementPointer(
+    PackageableElementPointerType.ASSOCIATION,
+    element.association.valueForSerialization ?? '',
+  );
   relationalMapping.propertyMappings = transformClassMappingPropertyMappings(
     element.propertyMappings,
     true,
@@ -1326,8 +1334,10 @@ const transformFlatDataAssociationImplementation = (
   flatDataAssociationMapping.stores = element.stores.map(
     (store) => store.valueForSerialization ?? '',
   );
-  flatDataAssociationMapping.association =
-    element.association.valueForSerialization ?? '';
+  flatDataAssociationMapping.association = new V1_PackageableElementPointer(
+    PackageableElementPointerType.ASSOCIATION,
+    element.association.valueForSerialization ?? '',
+  );
   flatDataAssociationMapping.propertyMappings =
     transformClassMappingPropertyMappings(
       element.propertyMappings,
@@ -1346,7 +1356,10 @@ const transformXStorelAssociationImplementation = (
   xStoreMapping.stores = element.stores.map(
     (store) => store.valueForSerialization ?? '',
   );
-  xStoreMapping.association = element.association.valueForSerialization ?? '';
+  xStoreMapping.association = new V1_PackageableElementPointer(
+    PackageableElementPointerType.ASSOCIATION,
+    element.association.valueForSerialization ?? '',
+  );
   xStoreMapping.propertyMappings = transformClassMappingPropertyMappings(
     element.propertyMappings,
     false,
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementSecondPassBuilder.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementSecondPassBuilder.ts
index 17531d06ca..550d99ad94 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementSecondPassBuilder.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementSecondPassBuilder.ts
@@ -240,7 +240,8 @@ export class V1_ElementSecondPassBuilder
       V1_buildFullPath(element.package, element.name),
     );
     const uniqueStereotypes = new Set<string>();
-    profile.p_stereotypes = element.stereotypes.map((stereotype) => {
+    profile.p_stereotypes = element.stereotypes.map((stereotypeV) => {
+      const stereotype = stereotypeV.value;
       if (uniqueStereotypes.has(stereotype)) {
         const message = `Found duplicated stereotype '${stereotype}' in profile '${element.path}'`;
         /**
@@ -258,7 +259,8 @@ export class V1_ElementSecondPassBuilder
       return new Stereotype(profile, stereotype);
     });
     const uniqueTags = new Set<string>();
-    profile.p_tags = element.tags.map((tag) => {
+    profile.p_tags = element.tags.map((tagV) => {
+      const tag = tagV.value;
       if (uniqueTags.has(tag)) {
         const message = `Found duplicated tag '${tag}' in profile '${element.path}'`;
         /**
@@ -408,7 +410,7 @@ export class V1_ElementSecondPassBuilder
       V1_buildFullPath(element.package, element.name),
     );
     database.includes = element.includedStores.map((includedStore) =>
-      this.context.resolveDatabase(includedStore),
+      this.context.resolveDatabase(includedStore.path),
     );
     database.schemas = element.schemas.map((schema) =>
       V1_buildSchema(schema, database, this.context),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementThirdPassBuilder.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementThirdPassBuilder.ts
index 5f838b3e95..e70841c042 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementThirdPassBuilder.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/V1_ElementThirdPassBuilder.ts
@@ -132,7 +132,8 @@ export class V1_ElementThirdPassBuilder
     const _class = this.context.currentSubGraph.getOwnClass(
       V1_buildFullPath(element.package, element.name),
     );
-    element.superTypes.forEach((type) => {
+    element.superTypes.forEach((pointer) => {
+      const type = pointer.path;
       // supertype `Any` will not be processed
       if (type !== CORE_PURE_PATH.ANY) {
         try {
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_AssociationMappingHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_AssociationMappingHelper.ts
index 9cefb02284..8d2c864a01 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_AssociationMappingHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_AssociationMappingHelper.ts
@@ -55,7 +55,7 @@ const buildRelationalAssociationMapping = (
   ]
     .map((m) => m.classMappings)
     .flat();
-  const association = context.resolveAssociation(element.association);
+  const association = context.resolveAssociation(element.association.path);
   const relationalAssociationImplementation =
     new RelationalAssociationImplementation(
       getInferredAssociationMappingId(association.value, element),
@@ -92,7 +92,7 @@ const buildFlatDataAssociationMapping = (
   ]
     .map((m) => m.classMappings)
     .flat();
-  const association = context.resolveAssociation(element.association);
+  const association = context.resolveAssociation(element.association.path);
   const flatDataAssociationImplementation =
     new FlatDataAssociationImplementation(
       getInferredAssociationMappingId(association.value, element),
@@ -129,7 +129,7 @@ const buildXStoreAssociationMapping = (
   ]
     .map((m) => m.classMappings)
     .flat();
-  const association = context.resolveAssociation(element.association);
+  const association = context.resolveAssociation(element.association.path);
   const xStoreAssociationImplementation = new XStoreAssociationImplementation(
     getInferredAssociationMappingId(association.value, element),
     parentMapping,
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_MappingBuilderHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_MappingBuilderHelper.ts
index 5bd476d53c..413360a259 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_MappingBuilderHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureGraph/to/helpers/V1_MappingBuilderHelper.ts
@@ -154,11 +154,11 @@ export const V1_buildEnumerationMapping = (
   parentMapping: Mapping,
 ): EnumerationMapping => {
   assertNonEmptyString(
-    srcEnumerationMapping.enumeration,
+    srcEnumerationMapping.enumeration.path,
     `Enumeration mapping 'enumeration' field is missing or empty`,
   );
   const targetEnumeration = context.resolveEnumeration(
-    srcEnumerationMapping.enumeration,
+    srcEnumerationMapping.enumeration.path,
   );
   const possibleSourceTypes = new Set(
     srcEnumerationMapping.enumValueMappings.flatMap((enumValueMapping) =>
@@ -246,12 +246,12 @@ const buildMappingStoreTestData = (
   context: V1_GraphBuilderContext,
 ): StoreTestData => {
   const mappingStoreTestData = new StoreTestData();
-  if (element.store === ModelStore.NAME) {
+  if (element.store.path === ModelStore.NAME) {
     mappingStoreTestData.store = PackageableElementExplicitReference.create(
       ModelStore.INSTANCE,
     );
   } else {
-    mappingStoreTestData.store = context.resolveStore(element.store);
+    mappingStoreTestData.store = context.resolveStore(element.store.path);
   }
   mappingStoreTestData.data = V1_buildEmbeddedData(element.data, context);
   return mappingStoreTestData;
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_CoreSerializationHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_CoreSerializationHelper.ts
index c4b123a65e..4e6867b686 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_CoreSerializationHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_CoreSerializationHelper.ts
@@ -14,10 +14,12 @@
  * limitations under the License.
  */
 
-import { primitive, createModelSchema, optional } from 'serializr';
+import { primitive, createModelSchema, optional, deserialize } from 'serializr';
 import {
   SerializationFactory,
+  isString,
   optionalCustomUsingModelSchema,
+  type PlainObject,
 } from '@finos/legend-shared';
 import { V1_Multiplicity } from '../../../model/packageableElements/domain/V1_Multiplicity.js';
 import { V1_PackageableElementPointer } from '../../../model/packageableElements/V1_PackageableElement.js';
@@ -61,3 +63,14 @@ export const V1_multiplicityModelSchema = createModelSchema(V1_Multiplicity, {
   lowerBound: primitive(),
   upperBound: optional(primitive()),
 });
+
+export const V1_serializePackageableElementPointer = (
+  json: PlainObject<V1_PackageableElementPointer> | string,
+  type?: string | undefined,
+): V1_PackageableElementPointer => {
+  // For backward compatible: see https://github.com/finos/legend-engine/pull/2621
+  if (isString(json)) {
+    return new V1_PackageableElementPointer(type, json);
+  }
+  return deserialize(V1_packageableElementPointerModelSchema, json);
+};
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DatabaseSerializationHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DatabaseSerializationHelper.ts
index 55c53a169e..147a2db64a 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DatabaseSerializationHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DatabaseSerializationHelper.ts
@@ -97,6 +97,12 @@ import {
   V1_serializeDatasourceSpecification,
 } from './V1_ConnectionSerializationHelper.js';
 import { V1_stereotypePtrModelSchema } from './V1_DomainSerializationHelper.js';
+import type { V1_PackageableElementPointer } from '../../../model/packageableElements/V1_PackageableElement.js';
+import {
+  V1_packageableElementPointerModelSchema,
+  V1_serializePackageableElementPointer,
+} from './V1_CoreSerializationHelper.js';
+import { PackageableElementPointerType } from '../../../../../../../graph/MetaModelConst.js';
 
 export const V1_DATABASE_ELEMENT_PROTOCOL_TYPE = 'relational';
 
@@ -547,6 +553,9 @@ const V1_setupRelationalDatabaseConnectionModelSchema = (
     postProcessors: customList(
       (value: V1_PostProcessor) => V1_serializePostProcessor(value, plugins),
       (value) => V1_deserializePostProcessor(value, plugins),
+      {
+        INTERNAL__forceReturnEmptyInTest: true,
+      },
     ),
     postProcessorWithParameter: customEquivalentList({
       INTERNAL__forceReturnEmptyInTest: true,
@@ -565,7 +574,17 @@ export const V1_setupDatabaseSerialization = (
 export const V1_databaseModelSchema = createModelSchema(V1_Database, {
   _type: usingConstantValueSchema(V1_DATABASE_ELEMENT_PROTOCOL_TYPE),
   filters: list(usingModelSchema(V1_filterModelSchema)),
-  includedStores: list(primitive()),
+  includedStores: customList(
+    (val: V1_PackageableElementPointer) =>
+      serialize(V1_packageableElementPointerModelSchema, val),
+    (val) =>
+      V1_serializePackageableElementPointer(
+        val,
+        PackageableElementPointerType.STORE,
+      ),
+
+    { INTERNAL__forceReturnEmptyInTest: true },
+  ),
   joins: list(usingModelSchema(V1_joinModelSchema)),
   name: primitive(),
   package: primitive(),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DomainSerializationHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DomainSerializationHelper.ts
index a4c53ddce2..384ae5eca0 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DomainSerializationHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_DomainSerializationHelper.ts
@@ -25,21 +25,28 @@ import {
   type ModelSchema,
   serialize,
   custom,
+  deserialize,
 } from 'serializr';
 import {
-  customEquivalentList,
   customList,
   customListWithSchema,
   optionalCustom,
   usingConstantValueSchema,
   usingModelSchema,
+  isString,
+  type PlainObject,
 } from '@finos/legend-shared';
 import {
   V1_multiplicityModelSchema,
   V1_packageableElementPointerModelSchema,
+  V1_serializePackageableElementPointer,
 } from '../../../transformation/pureProtocol/serializationHelpers/V1_CoreSerializationHelper.js';
 import { V1_Enumeration } from '../../../model/packageableElements/domain/V1_Enumeration.js';
-import { V1_Profile } from '../../../model/packageableElements/domain/V1_Profile.js';
+import {
+  V1_Profile,
+  V1_ProfileStereotype,
+  V1_ProfileTag,
+} from '../../../model/packageableElements/domain/V1_Profile.js';
 import {
   V1_Measure,
   V1_Unit,
@@ -82,6 +89,8 @@ import {
   V1_deserializeGenericType,
   V1_GenericTypeModelSchema,
 } from './V1_TypeSerializationHelper.js';
+import { PackageableElementPointerType } from '../../../../../../../graph/MetaModelConst.js';
+import type { V1_PackageableElementPointer } from '../../../model/packageableElements/V1_PackageableElement.js';
 
 export const V1_CLASS_ELEMENT_PROTOCOL_TYPE = 'class';
 export const V1_PROFILE_ELEMENT_PROTOCOL_TYPE = 'profile';
@@ -118,12 +127,48 @@ export const V1_taggedValueModelSchema = createModelSchema(V1_TaggedValue, {
   value: primitive(),
 });
 
+const V1_ProfileStereotypeSchema = createModelSchema(V1_ProfileStereotype, {
+  value: primitive(),
+});
+
+const V1_ProfileTagSchema = createModelSchema(V1_ProfileTag, {
+  value: primitive(),
+});
+
+export const V1_serializeProfileStereotypeSchema = (
+  json: PlainObject<V1_ProfileStereotype> | string,
+): V1_ProfileTag => {
+  if (isString(json)) {
+    return new V1_ProfileStereotype(json);
+  }
+  return deserialize(V1_ProfileStereotypeSchema, json);
+};
+
+export const V1_serializeProfileTagSchema = (
+  json: PlainObject<V1_ProfileTag> | string,
+): V1_ProfileTag => {
+  if (isString(json)) {
+    return new V1_ProfileTag(json);
+  }
+  return deserialize(V1_ProfileTagSchema, json);
+};
+
 export const V1_profileModelSchema = createModelSchema(V1_Profile, {
   _type: usingConstantValueSchema(V1_PROFILE_ELEMENT_PROTOCOL_TYPE),
   name: primitive(),
   package: primitive(),
-  stereotypes: list(primitive()),
-  tags: list(primitive()),
+  stereotypes: customList(
+    (val: V1_ProfileStereotype) => serialize(V1_ProfileStereotypeSchema, val),
+    (val) => V1_serializeProfileStereotypeSchema(val),
+
+    { INTERNAL__forceReturnEmptyInTest: true },
+  ),
+  tags: customList(
+    (val: V1_ProfileTag) => serialize(V1_ProfileTagSchema, val),
+    (val) => V1_serializeProfileTagSchema(val),
+
+    { INTERNAL__forceReturnEmptyInTest: true },
+  ),
 });
 
 // ------------------------------------- Enumeration -------------------------------------
@@ -330,9 +375,17 @@ export const V1_classModelSchema = createModelSchema(V1_Class, {
   stereotypes: customListWithSchema(V1_stereotypePtrModelSchema, {
     INTERNAL__forceReturnEmptyInTest: true,
   }),
-  superTypes: customEquivalentList({
-    INTERNAL__forceReturnEmptyInTest: true,
-  }),
+  superTypes: customList(
+    (val: V1_PackageableElementPointer) =>
+      serialize(V1_packageableElementPointerModelSchema, val),
+    (val) =>
+      V1_serializePackageableElementPointer(
+        val,
+        PackageableElementPointerType.DATA,
+      ),
+
+    { INTERNAL__forceReturnEmptyInTest: true },
+  ),
   taggedValues: customListWithSchema(V1_taggedValueModelSchema, {
     INTERNAL__forceReturnEmptyInTest: true,
   }),
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_MappingSerializationHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_MappingSerializationHelper.ts
index a7e757f79d..bc2e98b048 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_MappingSerializationHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_MappingSerializationHelper.ts
@@ -46,6 +46,7 @@ import {
   ATOMIC_TEST_TYPE,
   PRIMITIVE_TYPE,
   ELEMENT_PATH_DELIMITER,
+  PackageableElementPointerType,
 } from '../../../../../../../graph/MetaModelConst.js';
 import { V1_Mapping } from '../../../model/packageableElements/mapping/V1_Mapping.js';
 import {
@@ -60,6 +61,7 @@ import {
 import {
   V1_multiplicityModelSchema,
   V1_packageableElementPointerModelSchema,
+  V1_serializePackageableElementPointer,
 } from '../../../transformation/pureProtocol/serializationHelpers/V1_CoreSerializationHelper.js';
 import { V1_propertyPointerModelSchema } from './V1_DomainSerializationHelper.js';
 import type { V1_AssociationMapping } from '../../../model/packageableElements/mapping/V1_AssociationMapping.js';
@@ -878,7 +880,14 @@ export const V1_mappingStoreTestDataModelSchema = (
       (val) => V1_serializeEmbeddedDataType(val, plugins),
       (val) => V1_deserializeEmbeddedDataType(val, plugins),
     ),
-    store: primitive(),
+    store: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.STORE,
+        ),
+    ),
   });
 
 export const V1_mappingTestModelSchema = (
@@ -952,7 +961,14 @@ const relationalAssociationMappingModelschema = createModelSchema(
   V1_RelationalAssociationMapping,
   {
     _type: usingConstantValueSchema(V1_AssociationMappingType.RELATIONAL),
-    association: primitive(),
+    association: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.ASSOCIATION,
+        ),
+    ),
     id: optional(primitive()),
     propertyMappings: list(
       custom(
@@ -968,7 +984,14 @@ const flatDataAssociationMappingModelschema = createModelSchema(
   V1_FlatDataAssociationMapping,
   {
     _type: usingConstantValueSchema(V1_AssociationMappingType.FLAT_DATA),
-    association: primitive(),
+    association: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.ASSOCIATION,
+        ),
+    ),
     id: optional(primitive()),
     propertyMappings: list(
       custom(
@@ -984,7 +1007,14 @@ const xStoreAssociationMappingModelschema = createModelSchema(
   V1_XStoreAssociationMapping,
   {
     _type: usingConstantValueSchema(V1_AssociationMappingType.XSTORE),
-    association: primitive(),
+    association: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.ASSOCIATION,
+        ),
+    ),
     id: optional(primitive()),
     propertyMappings: list(
       custom(
@@ -1167,7 +1197,14 @@ const V1_enumerationMappingModelSchema = createModelSchema(
           ),
       ),
     ),
-    enumeration: primitive(),
+    enumeration: custom(
+      (val) => serialize(V1_packageableElementPointerModelSchema, val),
+      (val) =>
+        V1_serializePackageableElementPointer(
+          val,
+          PackageableElementPointerType.ENUMERATION,
+        ),
+    ),
     id: optional(primitive()),
   },
 );
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_RawValueSpecificationSerializationHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_RawValueSpecificationSerializationHelper.ts
index 27056ebda9..a4c679cad5 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_RawValueSpecificationSerializationHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_RawValueSpecificationSerializationHelper.ts
@@ -23,6 +23,7 @@ import {
   custom,
   alias,
   optional,
+  SKIP,
 } from 'serializr';
 import {
   type PlainObject,
@@ -98,7 +99,14 @@ const V1_RawGenericTypeSchemaModelInner = createModelSchema(V1_RawGenericType, {
       INTERNAL__forceReturnEmptyInTest: true,
     },
   ),
-  // typeVariableValues: TODO
+  typeVariableValues: optionalCustomList(
+    // TODO
+    (value) => SKIP,
+    (value) => SKIP,
+    {
+      INTERNAL__forceReturnEmptyInTest: true,
+    },
+  ),
 });
 
 const V1_RawGenericTypeSchemaModel = createModelSchema(V1_RawGenericType, {
@@ -116,7 +124,14 @@ const V1_RawGenericTypeSchemaModel = createModelSchema(V1_RawGenericType, {
       INTERNAL__forceReturnEmptyInTest: true,
     },
   ),
-  // typeVariableValues: TODO
+  typeVariableValues: optionalCustomList(
+    // TODO
+    (value) => SKIP,
+    (value) => SKIP,
+    {
+      INTERNAL__forceReturnEmptyInTest: true,
+    },
+  ),
 });
 
 const V1_deserializeRawGenericType = (
diff --git a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_TypeSerializationHelper.ts b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_TypeSerializationHelper.ts
index 7d0de5ee46..c61dc5b465 100644
--- a/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_TypeSerializationHelper.ts
+++ b/packages/legend-graph/src/graph-manager/protocol/pure/v1/transformation/pureProtocol/serializationHelpers/V1_TypeSerializationHelper.ts
@@ -21,6 +21,7 @@ import {
   list,
   primitive,
   serialize,
+  SKIP,
 } from 'serializr';
 import { V1_GenericType } from '../../../model/packageableElements/type/V1_GenericType.js';
 import { V1_PackageableType } from '../../../model/packageableElements/type/V1_PackageableType.js';
@@ -109,7 +110,14 @@ export const V1_GenericTypeModelSchema = createModelSchema(V1_GenericType, {
       INTERNAL__forceReturnEmptyInTest: true,
     },
   ),
-  // typeVariableValues: TODO
+  typeVariableValues: optionalCustomList(
+    // TODO
+    (value) => SKIP,
+    (value) => SKIP,
+    {
+      INTERNAL__forceReturnEmptyInTest: true,
+    },
+  ),
 });
 
 const appendAnyGenericType = (current: V1_GenericType): void => {
diff --git a/packages/legend-graph/src/graph/MetaModelConst.ts b/packages/legend-graph/src/graph/MetaModelConst.ts
index 5474292ad7..f87b8194c3 100644
--- a/packages/legend-graph/src/graph/MetaModelConst.ts
+++ b/packages/legend-graph/src/graph/MetaModelConst.ts
@@ -161,6 +161,9 @@ export enum PackageableElementPointerType {
   FILE_GENERATION = 'FILE_GENERATION',
   SERVICE = 'SERVICE',
   DATA = 'DATA',
+  ENUMERATION = 'ENUMERATION',
+  ASSOCIATION = 'ASSOCIATION',
+  BINDING = 'BINDING',
 }
 
 export enum SUPPORTED_FUNCTIONS {
diff --git a/packages/legend-manual-tests/src/__tests__/roundtrip-grammar/RoundtripGrammar.engine-roundtrip-test.ts b/packages/legend-manual-tests/src/__tests__/roundtrip-grammar/RoundtripGrammar.engine-roundtrip-test.ts
index a2d57ca159..df72b1f1ac 100644
--- a/packages/legend-manual-tests/src/__tests__/roundtrip-grammar/RoundtripGrammar.engine-roundtrip-test.ts
+++ b/packages/legend-manual-tests/src/__tests__/roundtrip-grammar/RoundtripGrammar.engine-roundtrip-test.ts
@@ -305,6 +305,7 @@ const cases: [string, string, boolean][] = fs
   .readdirSync(TEST_CASE_DIR)
   .map((caseName) => resolve(TEST_CASE_DIR, caseName))
   .filter((filePath) => fs.statSync(filePath).isFile())
+  // .filter((filePath) => basename(filePath) === 'DSL_PersistenceV2-basic.pure')
   .map((filePath) => [
     testNameFrom(filePath),
     filePath,
@@ -315,7 +316,7 @@ describe('Grammar roundtrip test', () => {
   test.each(cases)('%s', async (testName, filePath, isSkipped) => {
     if (!isSkipped) {
       await checkGrammarRoundtrip(testName, filePath, {
-        debug: false,
+        debug: true,
       });
     }
   });