From 07d9acb2ff9dcd8b8f194d66b7305931002145f6 Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Mon, 13 Jan 2025 09:36:58 -0800
Subject: [PATCH] add original predicate to model

---
 backend/src/monarch_py/datamodels/model.py    | 10 ++++++++++
 backend/src/monarch_py/datamodels/model.yaml  |  6 ++++++
 frontend/src/api/model.ts                     |  2 ++
 frontend/src/pages/node/AssociationsTable.vue | 18 ++++++++++++++++++
 4 files changed, 36 insertions(+)

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index b093c635..4e54c8c9 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -477,6 +477,11 @@ class Association(ConfiguredBaseModel):
         ...,
         json_schema_extra={"linkml_meta": {"alias": "predicate", "domain_of": ["Association", "CompactAssociation"]}},
     )
+    original_predicate: Optional[str] = Field(
+        None,
+        description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""",
+        json_schema_extra={"linkml_meta": {"alias": "original_predicate", "domain_of": ["Association"]}},
+    )
     object: str = Field(
         ..., json_schema_extra={"linkml_meta": {"alias": "object", "domain_of": ["Association", "CompactAssociation"]}}
     )
@@ -1243,6 +1248,11 @@ class DirectionalAssociation(Association):
         ...,
         json_schema_extra={"linkml_meta": {"alias": "predicate", "domain_of": ["Association", "CompactAssociation"]}},
     )
+    original_predicate: Optional[str] = Field(
+        None,
+        description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""",
+        json_schema_extra={"linkml_meta": {"alias": "original_predicate", "domain_of": ["Association"]}},
+    )
     object: str = Field(
         ..., json_schema_extra={"linkml_meta": {"alias": "object", "domain_of": ["Association", "CompactAssociation"]}}
     )
diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
index 602399c7..9da15db8 100644
--- a/backend/src/monarch_py/datamodels/model.yaml
+++ b/backend/src/monarch_py/datamodels/model.yaml
@@ -37,6 +37,7 @@ classes:
       - subject_taxon
       - subject_taxon_label
       - predicate
+      - original_predicate
       - object
       - original_object
       - object_namespace
@@ -562,6 +563,11 @@ slots:
     range: string
   original_object:
     range: string
+  original_predicate:
+    range: string
+    description: >-
+      used to hold the original relation/predicate that an external knowledge
+      source uses before transformation to match the biolink-model specification.
   original_subject:
     range: string
   pathway:
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index d055530d..5a3827d1 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -126,6 +126,8 @@ export interface Association {
     subject_taxon?: string,
     subject_taxon_label?: string,
     predicate: string,
+    /** used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. */
+    original_predicate?: string,
     object: string,
     original_object?: string,
     /** The namespace/prefix of the object entity */
diff --git a/frontend/src/pages/node/AssociationsTable.vue b/frontend/src/pages/node/AssociationsTable.vue
index 99be842a..c1b449b2 100644
--- a/frontend/src/pages/node/AssociationsTable.vue
+++ b/frontend/src/pages/node/AssociationsTable.vue
@@ -80,6 +80,19 @@
       />
     </template>
 
+    <template #extension="{ row }">
+      <AppNodeBadge
+        v-if="row.subject_specialization_qualifier_label"
+        :node="{
+          id: row.subject_specialization_qualifier,
+          name: row.subject_specialization_qualifier_label,
+          category: row.subject_specialization_qualifier_category,
+        }"
+        :breadcrumbs="getBreadcrumbs(node, row, 'subject')"
+      />
+      <span v-else>{{ row.subject_specialization_qualifier }}</span>
+    </template>
+
     <template #disease="{ row }">
       <AppNodeBadge
         v-if="row.disease_context_qualifier"
@@ -269,6 +282,11 @@ const medicalActionColumns = computed<Cols<Datum>>(() => {
       key: "subject_label",
       heading: "Medical Action",
     },
+    {
+      slot: "extension",
+      key: "subject_specialization_qualifier",
+      heading: "Extension",
+    },
     {
       slot: "predicate",
       key: "predicate",