feat(associations): MEDIC/CTD drug-indication section + enriched details modal (#1348)

backend/src/monarch_py/utils/association_type_mappings.yaml

@@ -80,11 +80,11 @@
   category: "biolink:GenotypeToDiseaseAssociation"
   subject_category: "biolink:Genotype"
   object_category: "biolink:Disease"
-- subject_label: Medical Action
-  object_label: Medical Action
+- subject_label: Indications
+  object_label: Treatments
   category: "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"
-  # Note: subject_category/object_category omitted - this association uses disease_context_qualifier
-  # and requires special 1-hop handling that isn't yet implemented in the entity grid
+  subject_category: "biolink:ChemicalEntity"
+  object_category: "biolink:Disease"
 - subject_label: Variant to Phenotype
   object_label: Variant to Phenotype
   category: "biolink:VariantToPhenotypicFeatureAssociation"

backend/tests/fixtures/association_counts.py

@@ -3,4 +3,4 @@
 
 @pytest.fixture
 def association_counts():
-    return {'items': [{'label': 'Disease Model', 'count': 246, 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Medical Action', 'count': 6, 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]}
+    return {'items': [{'label': 'Disease Model', 'count': 246, 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Treatments', 'count': 6, 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]}

frontend/src/composables/use-association-categories.ts

@@ -3,9 +3,7 @@ import { startCase } from "lodash";
 import { TRAVERSE_ORTHOLOG_CATEGORIES } from "@/api/associations";
 import type { Node } from "@/api/model";
 
-const HIDDEN_CATEGORIES = new Set([
-  "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation",
-]);
+const HIDDEN_CATEGORIES = new Set<string>([]);
 
 export function useAssociationCategories(node: Node) {
   const options = computed(() => {

frontend/src/pages/node/SectionAssociationDetails.vue

@@ -48,6 +48,14 @@
         </span>
       </AppDetail>
 
+      <AppDetail
+        v-if="association.knowledge_level"
+        title="Knowledge Level"
+        icon="scale-balanced"
+      >
+        <span>{{ startCase(association.knowledge_level) }}</span>
+      </AppDetail>
+
       <AppDetail title="Primary Knowledge Source" icon="lightbulb">
         <span>{{ association.primary_knowledge_source }}</span>
       </AppDetail>
@@ -79,6 +87,42 @@
         </span>
       </AppDetail>
 
+      <AppDetail
+        v-if="retrievalSources.length"
+        title="Provenance"
+        icon="sitemap"
+        :full="true"
+      >
+        <AppFlex direction="col" gap="small" align-h="left">
+          <div
+            v-for="(source, index) in retrievalSources"
+            :key="index"
+            class="retrieval-source"
+          >
+            <span class="role">{{ formatRole(source.resource_role) }}:</span>
+            <code>{{ source.resource_id }}</code>
+            <span v-if="source.upstream_resource_ids?.length" class="upstream">
+              &larr; {{ source.upstream_resource_ids.join(", ") }}
+            </span>
+          </div>
+        </AppFlex>
+      </AppDetail>
+
+      <AppDetail
+        v-if="association.aggregator_knowledge_source?.length"
+        title="Aggregator Knowledge Source"
+        icon="database"
+        :full="true"
+      >
+        <AppFlex gap="small" align-h="left">
+          <code
+            v-for="(agg, index) in association.aggregator_knowledge_source"
+            :key="index"
+            >{{ agg }}</code
+          >
+        </AppFlex>
+      </AppDetail>
+
       <AppDetail title="Provided By" icon="notes-medical">
         <AppLink :to="association.provided_by_link?.url || ''" :replace="true">
           {{ association.provided_by_link?.id || association.provided_by }}
@@ -97,6 +141,61 @@
         </AppFlex>
       </AppDetail>
 
+      <AppDetail
+        v-if="association.original_predicate"
+        title="Original Predicate"
+        icon="code"
+      >
+        <code>{{ association.original_predicate }}</code>
+      </AppDetail>
+
+      <AppDetail
+        v-if="qualifierRows.length"
+        title="Qualifiers"
+        icon="clipboard-list"
+        :full="true"
+      >
+        <AppFlex direction="col" gap="small" align-h="left">
+          <div v-for="(qualifier, index) in qualifierRows" :key="index">
+            <strong>{{ qualifier.label }}:</strong> {{ qualifier.value }}
+          </div>
+        </AppFlex>
+      </AppDetail>
+
+      <AppDetail
+        v-if="hasFrequencyData"
+        title="Frequency Data"
+        icon="equals"
+        :full="true"
+      >
+        <AppFlex direction="col" gap="small" align-h="left">
+          <div v-if="association.has_count != null">
+            <strong>Count:</strong> {{ association.has_count }}
+          </div>
+          <div v-if="association.has_total != null">
+            <strong>Total:</strong> {{ association.has_total }}
+          </div>
+          <div v-if="association.has_percentage != null">
+            <strong>Percentage:</strong> {{ association.has_percentage }}
+          </div>
+          <div v-if="association.has_quotient != null">
+            <strong>Quotient:</strong> {{ association.has_quotient }}
+          </div>
+        </AppFlex>
+      </AppDetail>
+
+      <AppDetail
+        v-if="association.FDA_adverse_event_level"
+        title="FDA Adverse Event Level"
+        icon="circle-exclamation"
+      >
+        <span>{{ association.FDA_adverse_event_level }}</span>
+      </AppDetail>
+
+      <AppDetail v-if="association.negated" title="Negated" icon="circle-xmark">
+        <span>Yes</span>
+      </AppDetail>
+
       <AppDetail
         v-if="association.supporting_text?.length"
         icon="quote-left"
@@ -119,6 +218,7 @@
 
 <script setup lang="ts">
 import { computed, onMounted, watch } from "vue";
+import { startCase } from "lodash";
 import type { DirectionalAssociation, Node } from "@/api/model";
 import AppDetail from "@/components/AppDetail.vue";
 import AppDetails from "@/components/AppDetails.vue";
@@ -127,6 +227,7 @@ import AppPredicateBadge from "@/components/AppPredicateBadge.vue";
 import { useSourceVersions } from "@/composables/use-source-versions";
 import { scrollTo } from "@/router";
 import { getAgentTypeMeta } from "@/util/agentType";
+import { parseRetrievalSources } from "@/util/retrievalSources";
 
 type Props = {
   /** current node */
@@ -148,6 +249,47 @@ const sourceVersion = computed(() =>
   props.association ? versionForEdge(props.association) : null,
 );
 
+/** parse the nested retrieval-source provenance chain (JSON-encoded) */
+const retrievalSources = computed(() =>
+  parseRetrievalSources(props.association?.sources),
+);
+
+/** humanize a retrieval-source role, e.g. "primary_knowledge_source" */
+const formatRole = (role?: string) => (role ? startCase(role) : "Source");
+
+/** present qualifier values, preferring labels over raw ids */
+const qualifierRows = computed(() => {
+  const a = props.association;
+  const rows: { label: string; value: string }[] = [];
+  if (!a) return rows;
+  const add = (label: string, value?: string | null) => {
+    if (value) rows.push({ label, value });
+  };
+  add("Frequency", a.frequency_qualifier_label || a.frequency_qualifier);
+  add("Onset", a.onset_qualifier_label || a.onset_qualifier);
+  add("Sex", a.sex_qualifier_label || a.sex_qualifier);
+  add("Stage", a.stage_qualifier_label || a.stage_qualifier);
+  add(
+    "Disease context",
+    a.disease_context_qualifier_label || a.disease_context_qualifier,
+  );
+  add("Object specialization", a.object_specialization_qualifier);
+  (a.qualifiers ?? []).forEach((qualifier) => add("Qualifier", qualifier));
+  return rows;
+});
+
+/** whether any frequency/count representation is present */
+const hasFrequencyData = computed(() => {
+  const a = props.association;
+  return (
+    a != null &&
+    (a.has_count != null ||
+      a.has_total != null ||
+      a.has_percentage != null ||
+      a.has_quotient != null)
+  );
+});
+
 /** scroll details section into view */
 async function scrollIntoView() {
   scrollTo("#association-details");
@@ -186,4 +328,19 @@ onMounted(scrollIntoView);
   color: $gray;
   font-size: 0.9em;
 }
+
+.retrieval-source {
+  display: flex;
+  flex-wrap: wrap;
+  align-items: baseline;
+  gap: 0 0.5em;
+}
+
+.retrieval-source .role {
+  color: $gray;
+}
+
+.retrieval-source .upstream {
+  color: $gray;
+}
 </style>

frontend/src/util/retrievalSources.ts

@@ -0,0 +1,26 @@
+export type RetrievalSource = {
+  resource_id?: string;
+  resource_role?: string;
+  upstream_resource_ids?: string[];
+};
+
+/**
+ * Parse the `sources` field of an association into a flat list of
+ * retrieval-source records. Each entry may be a JSON-encoded string holding an
+ * array of records (as the API serializes it); malformed entries are skipped.
+ */
+export const parseRetrievalSources = (
+  sources?: string[] | null,
+): RetrievalSource[] => {
+  const out: RetrievalSource[] = [];
+  for (const entry of sources ?? []) {
+    try {
+      const parsed = typeof entry === "string" ? JSON.parse(entry) : entry;
+      if (Array.isArray(parsed)) out.push(...parsed);
+      else if (parsed) out.push(parsed);
+    } catch {
+      /* skip unparseable source entries */
+    }
+  }
+  return out;
+};

frontend/unit/retrievalSources.test.ts

@@ -0,0 +1,41 @@
+import { expect, test } from "vitest";
+import { parseRetrievalSources } from "@/util/retrievalSources";
+
+test("parses a MEDIC-style nested retrieval-source chain", () => {
+  /** the API serializes `sources` as a list holding one JSON-encoded array */
+  const sources = [
+    JSON.stringify([
+      {
+        resource_id: "infores:medic",
+        resource_role: "primary_knowledge_source",
+        upstream_resource_ids: ["infores:dailymed"],
+      },
+      {
+        resource_id: "infores:dailymed",
+        resource_role: "supporting_data_source",
+        upstream_resource_ids: null,
+      },
+    ]),
+  ];
+  const parsed = parseRetrievalSources(sources);
+  expect(parsed).toHaveLength(2);
+  expect(parsed[0].resource_id).toBe("infores:medic");
+  expect(parsed[0].resource_role).toBe("primary_knowledge_source");
+  expect(parsed[0].upstream_resource_ids).toEqual(["infores:dailymed"]);
+  expect(parsed[1].resource_role).toBe("supporting_data_source");
+});
+
+test("returns empty for missing or empty sources", () => {
+  expect(parseRetrievalSources(undefined)).toEqual([]);
+  expect(parseRetrievalSources(null)).toEqual([]);
+  expect(parseRetrievalSources([])).toEqual([]);
+});
+
+test("skips unparseable entries without throwing", () => {
+  const parsed = parseRetrievalSources([
+    "not json",
+    JSON.stringify([{ resource_id: "infores:ctd" }]),
+  ]);
+  expect(parsed).toHaveLength(1);
+  expect(parsed[0].resource_id).toBe("infores:ctd");
+});