feat(associations): MEDIC + CTD drug-indications section + details modal (#1348)

backend/src/monarch_py/utils/association_type_mappings.yaml

@@ -80,11 +80,22 @@
   category: "biolink:GenotypeToDiseaseAssociation"
   subject_category: "biolink:Genotype"
   object_category: "biolink:Disease"
-- subject_label: Medical Action
-  object_label: Medical Action
-  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
+# Drug indications / treatments. Combines MEDIC (biolink:treats, FDA-approved,
+# text-mined) and CTD (biolink:treats_or_applied_or_studied_to_treat, curated),
+# which carry different association categories, into one section via the
+# multivalued category criterion. Shown as "Indications" on a drug/chemical page
+# and "Treatments" on a disease/phenotype page.
+- key: drug_indications
+  subject_label: Indications
+  object_label: Treatments
+  category:
+  - "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"
+  - "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation"
+  subject_category:
+  - "biolink:ChemicalEntity"
+  object_category:
+  - "biolink:Disease"
+  - "biolink:PhenotypicFeature"
 - 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, 'key': 'biolink:GenotypeToDiseaseAssociation', 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'key': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'key': 'biolink:CausalGeneToDiseaseAssociation', 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'key': 'biolink:CorrelatedGeneToDiseaseAssociation', 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'key': 'biolink:VariantToDiseaseAssociation', 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Medical Action', 'count': 6, 'key': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'key': 'biolink:CaseToDiseaseAssociation', 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]}
+    return {'items': [{'label': 'Disease Model', 'count': 246, 'key': 'biolink:GenotypeToDiseaseAssociation', 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'key': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'key': 'biolink:CausalGeneToDiseaseAssociation', 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'key': 'biolink:CorrelatedGeneToDiseaseAssociation', 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'key': 'biolink:VariantToDiseaseAssociation', 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Treatments', 'count': 6, 'key': 'drug_indications', 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'key': 'biolink:CaseToDiseaseAssociation', 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]}

docs/sources-manifest.yaml

@@ -45,6 +45,9 @@ sources:
   - repo: monarch-initiative/maxo-annotation-ingest
     branch: main
     filename: maxo.md
+  - repo: monarch-initiative/medic-ingest
+    branch: main
+    filename: medic.md
   - repo: monarch-initiative/mmrrc-ingest
     branch: main
     filename: mmrrc.md

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

@@ -3,9 +3,8 @@ import { startCase } from "lodash";
 import { TRAVERSE_ORTHOLOG_CATEGORIES } from "@/api/associations";
 import type { Node } from "@/api/model";
 
-const HIDDEN_CATEGORIES = new Set([
-  "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation",
-]);
+/** section keys (ac.key) to hide from node pages */
+const HIDDEN_CATEGORIES = new Set<string>([]);
 
 export function useAssociationCategories(node: Node) {
   const options = computed(() => {

frontend/src/pages/node/AssociationsTable.vue

@@ -232,6 +232,7 @@ import {
 import { getBreadcrumbs } from "@/pages/node/AssociationsSummary.vue";
 import SectionAssociationDetails from "@/pages/node/SectionAssociationDetails.vue";
 import { getAgentTypeMeta } from "@/util/agentType";
+import { isPredicateFilterable } from "@/util/predicateFilterConfig";
 import { taxonFieldFor } from "@/util/taxonFilterConfig";
 import { fieldFor } from "@/util/typeConfig";
 
@@ -246,6 +247,8 @@ type Props = {
   search: string;
   /** selected taxon labels to filter by */
   taxonFilters?: string[];
+  /** selected predicates to filter by */
+  predicateFilters?: string[];
 };
 
 const props = defineProps<Props>();
@@ -264,6 +267,10 @@ const emit = defineEmits<{
     e: "taxon-options",
     options: { id: string; label: string; count: number }[],
   ): void;
+  (
+    e: "predicate-options",
+    options: { id: string; label: string; count: number }[],
+  ): void;
 }>();
 
 const shouldTraverseOrthologs = computed(() =>
@@ -273,16 +280,33 @@ const shouldTraverseOrthologs = computed(() =>
 /** the single taxon field to facet/filter on for this category */
 const taxonField = computed(() => taxonFieldFor(props.category.id));
 
-/** facet fields to request when taxon filtering is enabled */
-const facetFields = computed(() =>
-  taxonField.value ? [taxonField.value] : undefined,
+/** whether this section offers a predicate filter */
+const predicateFilterable = computed(() =>
+  isPredicateFilterable(props.category.id),
 );
 
-/** build filter queries from selected taxon labels */
+/** facet fields to request for the enabled filters */
+const facetFields = computed(() => {
+  const fields: string[] = [];
+  if (taxonField.value) fields.push(taxonField.value);
+  if (predicateFilterable.value) fields.push("predicate");
+  return fields.length ? fields : undefined;
+});
+
+/** build filter queries from the selected taxon and predicate filters */
 const filterQueries = computed(() => {
-  if (!props.taxonFilters?.length || !taxonField.value) return undefined;
-  const clauses = props.taxonFilters.map((t) => `${taxonField.value}:"${t}"`);
-  return [clauses.join(" OR ")];
+  const queries: string[] = [];
+  if (props.taxonFilters?.length && taxonField.value) {
+    queries.push(
+      props.taxonFilters.map((t) => `${taxonField.value}:"${t}"`).join(" OR "),
+    );
+  }
+  if (props.predicateFilters?.length) {
+    queries.push(
+      props.predicateFilters.map((p) => `predicate:"${p}"`).join(" OR "),
+    );
+  }
+  return queries.length ? queries : undefined;
 });
 
 /** track last emitted taxon options to avoid redundant emits */
@@ -313,6 +337,44 @@ function emitTaxonOptions(facetFieldsData?: FacetField[]) {
   emit("taxon-options", options);
 }
 
+/** track last emitted predicate options to avoid redundant emits */
+let lastPredicateOptionsKey = "";
+
+/**
+ * Emit predicate options from the union of the direct and inferred datasets'
+ * predicate facets, so the filter toggle reflects the whole section regardless
+ * of the active tab. (A predicate can appear in one set but not the other —
+ * e.g. biolink:treats in the direct set while the weaker CTD predicate only
+ * shows up in the inferred/all set — and the checkbox must not depend on which
+ * tab loads first.)
+ */
+function emitPredicateOptions() {
+  if (!predicateFilterable.value) return;
+
+  /** see emitTaxonOptions: only build options from unfiltered queries */
+  if (props.predicateFilters?.length) return;
+
+  const counts = new Map<string, number>();
+  for (const data of [directData.value, allData.value]) {
+    const field = data?.facet_fields?.find((f) => f.label === "predicate");
+    for (const fv of field?.facet_values ?? []) {
+      if (!fv.label) continue;
+      counts.set(fv.label, Math.max(counts.get(fv.label) ?? 0, fv.count ?? 0));
+    }
+  }
+  if (!counts.size) return;
+
+  const options = [...counts.entries()]
+    .map(([label, count]) => ({ id: label, label, count }))
+    .sort((a, b) => b.count - a.count);
+
+  const key = JSON.stringify(options);
+  if (key === lastPredicateOptionsKey) return;
+  lastPredicateOptionsKey = key;
+
+  emit("predicate-options", options);
+}
+
 function openModal(association: DirectionalAssociation) {
   selectedAssociation.value = association;
   showModal.value = true;
@@ -582,16 +644,26 @@ watch([perPage, sort, start], async () => {
   }
 });
 
-/** refetch when taxon filters change (compare by value, not reference) */
+/**
+ * refetch when a filter changes (compare by value, not reference). Both the
+ * direct and inferred/all datasets are refetched so either tab reflects the
+ * current filter — otherwise switching tabs would show the other dataset's
+ * mount-time, unfiltered result (e.g. the inferred treatments tab not matching
+ * the indications checkbox).
+ */
 watch(
   () => JSON.stringify(props.taxonFilters ?? []),
   async () => {
     start.value = 0;
-    if (props.direct.id === "true") {
-      await fetchDirect();
-    } else {
-      await fetchAll();
-    }
+    await Promise.all([fetchDirect(), fetchAll()]);
+  },
+);
+
+watch(
+  () => JSON.stringify(props.predicateFilters ?? []),
+  async () => {
+    start.value = 0;
+    await Promise.all([fetchDirect(), fetchAll()]);
   },
 );
 
@@ -600,13 +672,25 @@ onMounted(async () => {
   await Promise.all([fetchDirect(), fetchAll()]);
 });
 
-/** emit taxon options whenever data changes */
+/** emit taxon options from the active dataset whenever it changes */
 watch(
   () =>
     props.direct.id === "true"
       ? directData.value?.facet_fields
       : allData.value?.facet_fields,
-  (facetFieldsData) => emitTaxonOptions(facetFieldsData),
+  (facetFieldsData) => {
+    emitTaxonOptions(facetFieldsData);
+  },
+  { immediate: true },
+);
+
+/**
+ * emit predicate options from BOTH datasets (union) so the filter toggle is
+ * independent of which tab is active or loads first
+ */
+watch(
+  () => [directData.value?.facet_fields, allData.value?.facet_fields],
+  () => emitPredicateOptions(),
   { immediate: true },
 );