Add mondo ID to disease detail pages

griffithlab · May 9, 2024 · 5a7cec2 · 5a7cec2
1 parent 58708da
commit 5a7cec2
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Showing 8 changed files with 37 additions and 11 deletions.
diff --git a/client/src/app/components/diseases/my-disease-info/my-disease-info.component.html b/client/src/app/components/diseases/my-disease-info/my-disease-info.component.html
@@ -76,13 +76,18 @@
       <ng-container *ngSwitchCase="1">
         <div class="tab-padding">
           <nz-row [nzGutter]="8">
-            <nz-col [nzSpan]="12">
-              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="2">
+            <nz-col [nzSpan]="24">
+              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="1">
                 <nz-descriptions-item nzTitle="Definition">
                   <ng-container *ngIf="diseaseInfo.mondoDef; else noValue">
                     {{diseaseInfo.mondoDef}}
                   </ng-container>
                 </nz-descriptions-item>
+                <nz-descriptions-item nzTitle="ID">
+                  <ng-container *ngIf="diseaseInfo.mondoId; else noValue">
+                    {{diseaseInfo.mondoId}}
+                  </ng-container>
+                </nz-descriptions-item>
               </nz-descriptions>
             </nz-col>
           </nz-row>

diff --git a/client/src/app/generated/civic.apollo-helpers.ts b/client/src/app/generated/civic.apollo-helpers.ts
@@ -1417,7 +1417,7 @@ export type MyChemInfoFieldPolicy = {
 	pubchemCid?: FieldPolicy<any> | FieldReadFunction<any>,
 	rxnorm?: FieldPolicy<any> | FieldReadFunction<any>
 };
-export type MyDiseaseInfoKeySpecifier = ('diseaseOntologyExactSynonyms' | 'diseaseOntologyRelatedSynonyms' | 'doDef' | 'doDefCitations' | 'icd10' | 'icdo' | 'mesh' | 'mondoDef' | 'ncit' | 'omim' | MyDiseaseInfoKeySpecifier)[];
+export type MyDiseaseInfoKeySpecifier = ('diseaseOntologyExactSynonyms' | 'diseaseOntologyRelatedSynonyms' | 'doDef' | 'doDefCitations' | 'icd10' | 'icdo' | 'mesh' | 'mondoDef' | 'mondoId' | 'ncit' | 'omim' | MyDiseaseInfoKeySpecifier)[];
 export type MyDiseaseInfoFieldPolicy = {
 	diseaseOntologyExactSynonyms?: FieldPolicy<any> | FieldReadFunction<any>,
 	diseaseOntologyRelatedSynonyms?: FieldPolicy<any> | FieldReadFunction<any>,
@@ -1427,6 +1427,7 @@ export type MyDiseaseInfoFieldPolicy = {
 	icdo?: FieldPolicy<any> | FieldReadFunction<any>,
 	mesh?: FieldPolicy<any> | FieldReadFunction<any>,
 	mondoDef?: FieldPolicy<any> | FieldReadFunction<any>,
+	mondoId?: FieldPolicy<any> | FieldReadFunction<any>,
 	ncit?: FieldPolicy<any> | FieldReadFunction<any>,
 	omim?: FieldPolicy<any> | FieldReadFunction<any>
 };

diff --git a/client/src/app/generated/civic.apollo.ts b/client/src/app/generated/civic.apollo.ts
@@ -3702,6 +3702,7 @@ export type MyDiseaseInfo = {
   icdo?: Maybe<Scalars['String']>;
   mesh?: Maybe<Scalars['String']>;
   mondoDef?: Maybe<Scalars['String']>;
+  mondoId?: Maybe<Scalars['String']>;
   ncit: Array<Scalars['String']>;
   omim?: Maybe<Scalars['String']>;
 };
@@ -8450,11 +8451,11 @@ export type DiseasesSummaryQueryVariables = Exact<{
 }>;
 
 
-export type DiseasesSummaryQuery = { __typename: 'Query', disease?: { __typename: 'Disease', id: number, name: string, doid?: string | undefined, diseaseUrl?: string | undefined, displayName: string, diseaseAliases: Array<string>, link: string, deprecated: boolean, myDiseaseInfo?: { __typename: 'MyDiseaseInfo', diseaseOntologyExactSynonyms: Array<string>, diseaseOntologyRelatedSynonyms: Array<string>, mesh?: string | undefined, icdo?: string | undefined, icd10?: string | undefined, ncit: Array<string>, omim?: string | undefined, doDef?: string | undefined, doDefCitations: Array<string>, mondoDef?: string | undefined } | undefined } | undefined };
+export type DiseasesSummaryQuery = { __typename: 'Query', disease?: { __typename: 'Disease', id: number, name: string, doid?: string | undefined, diseaseUrl?: string | undefined, displayName: string, diseaseAliases: Array<string>, link: string, deprecated: boolean, myDiseaseInfo?: { __typename: 'MyDiseaseInfo', diseaseOntologyExactSynonyms: Array<string>, diseaseOntologyRelatedSynonyms: Array<string>, mesh?: string | undefined, icdo?: string | undefined, icd10?: string | undefined, ncit: Array<string>, omim?: string | undefined, doDef?: string | undefined, doDefCitations: Array<string>, mondoDef?: string | undefined, mondoId?: string | undefined } | undefined } | undefined };
 
-export type MyDiseaseInfoFieldsFragment = { __typename: 'MyDiseaseInfo', diseaseOntologyExactSynonyms: Array<string>, diseaseOntologyRelatedSynonyms: Array<string>, mesh?: string | undefined, icdo?: string | undefined, icd10?: string | undefined, ncit: Array<string>, omim?: string | undefined, doDef?: string | undefined, doDefCitations: Array<string>, mondoDef?: string | undefined };
+export type MyDiseaseInfoFieldsFragment = { __typename: 'MyDiseaseInfo', diseaseOntologyExactSynonyms: Array<string>, diseaseOntologyRelatedSynonyms: Array<string>, mesh?: string | undefined, icdo?: string | undefined, icd10?: string | undefined, ncit: Array<string>, omim?: string | undefined, doDef?: string | undefined, doDefCitations: Array<string>, mondoDef?: string | undefined, mondoId?: string | undefined };
 
-export type DiseasesSummaryFieldsFragment = { __typename: 'Disease', id: number, name: string, doid?: string | undefined, diseaseUrl?: string | undefined, displayName: string, diseaseAliases: Array<string>, link: string, deprecated: boolean, myDiseaseInfo?: { __typename: 'MyDiseaseInfo', diseaseOntologyExactSynonyms: Array<string>, diseaseOntologyRelatedSynonyms: Array<string>, mesh?: string | undefined, icdo?: string | undefined, icd10?: string | undefined, ncit: Array<string>, omim?: string | undefined, doDef?: string | undefined, doDefCitations: Array<string>, mondoDef?: string | undefined } | undefined };
+export type DiseasesSummaryFieldsFragment = { __typename: 'Disease', id: number, name: string, doid?: string | undefined, diseaseUrl?: string | undefined, displayName: string, diseaseAliases: Array<string>, link: string, deprecated: boolean, myDiseaseInfo?: { __typename: 'MyDiseaseInfo', diseaseOntologyExactSynonyms: Array<string>, diseaseOntologyRelatedSynonyms: Array<string>, mesh?: string | undefined, icdo?: string | undefined, icd10?: string | undefined, ncit: Array<string>, omim?: string | undefined, doDef?: string | undefined, doDefCitations: Array<string>, mondoDef?: string | undefined, mondoId?: string | undefined } | undefined };
 
 export type EvidenceDetailQueryVariables = Exact<{
   evidenceId: Scalars['Int'];
@@ -10920,6 +10921,7 @@ export const MyDiseaseInfoFieldsFragmentDoc = gql`
   doDef
   doDefCitations
   mondoDef
+  mondoId
 }
     `;
 export const DiseasesSummaryFieldsFragmentDoc = gql`

diff --git a/client/src/app/generated/server.model.graphql b/client/src/app/generated/server.model.graphql
@@ -6262,6 +6262,7 @@ type MyDiseaseInfo {
   icdo: String
   mesh: String
   mondoDef: String
+  mondoId: String
   ncit: [String!]!
   omim: String
 }

diff --git a/client/src/app/generated/server.schema.json b/client/src/app/generated/server.schema.json
@@ -29036,6 +29036,18 @@
               "isDeprecated": false,
               "deprecationReason": null
             },
+            {
+              "name": "mondoId",
+              "description": null,
+              "args": [],
+              "type": {
+                "kind": "SCALAR",
+                "name": "String",
+                "ofType": null
+              },
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
             {
               "name": "ncit",
               "description": null,

diff --git a/client/src/app/views/diseases/diseases-detail/diseases-summary/diseases-summary.query.gql b/client/src/app/views/diseases/diseases-detail/diseases-summary/diseases-summary.query.gql
@@ -15,6 +15,7 @@ fragment MyDiseaseInfoFields on MyDiseaseInfo {
     doDef
     doDefCitations
     mondoDef
+    mondoId
 }
 
 fragment DiseasesSummaryFields on Disease {

diff --git a/server/app/graphql/types/entities/my_disease_info_type.rb b/server/app/graphql/types/entities/my_disease_info_type.rb
@@ -10,5 +10,6 @@ class MyDiseaseInfoType < Types::BaseObject
     field :do_def, String, null: true
     field :do_def_citations, [String], null: false
     field :mondo_def, String, null: true
+    field :mondo_id, String, null: true
   end
 end
diff --git a/server/app/models/my_disease_info.rb b/server/app/models/my_disease_info.rb
@@ -30,7 +30,8 @@ def parse_response(resp)
 
       do_def, do_def_citations = process_do_def(data.dig('def'))
 
-      mondo_def = process_mondo_def(p)
+      mondo_data = p['hits'][0].dig('mondo')
+      mondo_def = process_mondo_def(mondo_data)
 
       return {
         'disease_ontology_exact_synonyms': Array(data.dig('synonyms', 'exact')),
@@ -42,7 +43,8 @@ def parse_response(resp)
         'omim': data.dig('xrefs', 'omim'),
         'do_def': do_def,
         'do_def_citations': do_def_citations,
-        'mondo_def': mondo_def
+        'mondo_def': mondo_def,
+        'mondo_id': mondo_data.dig('mondo')
       }
     end
 
@@ -60,7 +62,8 @@ def fields
       'disease_ontology.xrefs.omim',
       'disease_ontology.xrefs.icd10',
       'disease_ontology.xrefs.icdo',
-      'mondo.definition'
+      'mondo.definition',
+      'mondo.mondo',
     ]
   end
 
@@ -74,8 +77,8 @@ def cache_key(disease)
     "my_disease_info_#{disease.id}_#{disease.updated_at}"
   end
 
-  def process_mondo_def(p)
-    if md = p['hits'][0].dig('mondo', 'definition')
+  def process_mondo_def(mondo_data)
+    if md = mondo_data.dig('definition')
       md.gsub(/\[(.+)\]/, '').strip
     else
       nil