syncing changes from Q4 2024 and code cleanup

apps/agora/api/src/models/genes.ts

@@ -53,7 +53,7 @@ const DruggabilitySchema = new Schema<Druggability>({
   sm_druggability_bucket: { type: Number, required: true },
   safety_bucket: { type: Number, required: true },
   abability_bucket: { type: Number, required: true },
-  pharos_class: { type: String, required: true },
+  pharos_class: { type: [String], required: true },
   classification: { type: String, required: true },
   safety_bucket_definition: { type: String, required: true },
   abability_bucket_definition: { type: String, required: true },
@@ -67,6 +67,7 @@ const GeneSchema = new Schema<Gene>(
     summary: { type: String, required: true },
     hgnc_symbol: { type: String, required: true },
     alias: [{ type: String, required: true }],
+    uniprotkb_accessions: [{ type: String, required: true }],
     is_igap: { type: Boolean, required: true },
     is_eqtl: { type: Boolean, required: true },
     is_any_rna_changed_in_ad_brain: { type: Boolean, required: true },
@@ -75,7 +76,7 @@ const GeneSchema = new Schema<Gene>(
     protein_brain_change_studied: { type: Boolean, required: true },
     target_nominations: { type: [TargetNominationSchema], required: true },
     median_expression: { type: [MedianExpressionSchema], required: true },
-    druggability: { type: [DruggabilitySchema], required: true },
+    druggability: { type: DruggabilitySchema, required: true },
     total_nominations: { type: Number, required: true },
     ensembl_info: { type: EnsemblInfoSchema, required: true },
   },

apps/agora/app/src/app/app.routes.ts

@@ -60,6 +60,11 @@ export const routes: Route[] = [
       description: 'Nominate a gene as a new candidate for AD treatment or prevention.',
     },
   },
+  {
+    path: 'genes/:id/similar',
+    loadChildren: () =>
+      import('@sagebionetworks/agora/gene-similar').then((routes) => routes.routes),
+  },
   {
     path: 'genes/:id/:tab/:subtab',
     loadChildren: () =>

apps/agora/data/.env.example

@@ -7,6 +7,6 @@ DB_HOST="agora-mongo" # must match mongo service name
 
 # specifies data release manifest and team images folder
 DATA_FILE="syn13363290"
-DATA_VERSION="68"
+DATA_VERSION="71"
 TEAM_IMAGES_ID="syn12861877"
 SYNAPSE_AUTH_TOKEN="agora-service-user-pat-here"

libs/agora/api-client-angular/src/lib/model/druggability.ts

@@ -17,7 +17,7 @@ export interface Druggability {
   sm_druggability_bucket: number;
   safety_bucket: number;
   abability_bucket: number;
-  pharos_class: string;
+  pharos_class: Array<string>;
   classification: string;
   safety_bucket_definition: string;
   abability_bucket_definition: string;

libs/agora/api-client-angular/src/lib/model/gene.ts

@@ -31,6 +31,7 @@ export interface Gene {
   summary: string;
   hgnc_symbol: string;
   alias: Array<string>;
+  uniprotkb_accessions?: Array<string>;
   is_igap: boolean;
   is_eqtl: boolean;
   is_any_rna_changed_in_ad_brain: boolean;
@@ -39,7 +40,7 @@ export interface Gene {
   protein_brain_change_studied: boolean;
   target_nominations: Array<TargetNomination> | null;
   median_expression: Array<MedianExpression>;
-  druggability: Array<Druggability>;
+  druggability: Druggability;
   total_nominations: number | null;
   is_adi?: boolean;
   is_tep?: boolean;
@@ -57,7 +58,7 @@ export interface Gene {
   ab_modality_display_value?: string | null;
   safety_rating_display_value?: string | null;
   sm_druggability_display_value?: string | null;
-  pharos_class_display_value?: string | null;
+  pharos_class_display_value?: Array<string> | null;
   is_any_rna_changed_in_ad_brain_display_value?: string | null;
   is_any_protein_changed_in_ad_brain_display_value?: string | null;
   nominated_target_display_value?: boolean | null;

libs/agora/api-description/build/openapi.yaml

@@ -421,8 +421,9 @@ components:
           type: integer
           example: 3
         pharos_class:
-          type: string
-          example: Tclin
+          type: array
+          items:
+            type: string
         classification:
           type: string
           example: Enzyme
@@ -730,6 +731,10 @@ components:
           type: array
           items:
             type: string
+        uniprotkb_accessions:
+          type: array
+          items:
+            type: string
         is_igap:
           type: boolean
         is_eqtl:
@@ -752,9 +757,7 @@ components:
           items:
             $ref: '#/components/schemas/MedianExpression'
         druggability:
-          type: array
-          items:
-            $ref: '#/components/schemas/Druggability'
+          $ref: '#/components/schemas/Druggability'
         total_nominations:
           type: integer
           nullable: true
@@ -820,7 +823,9 @@ components:
           type: string
           nullable: true
         pharos_class_display_value:
-          type: string
+          type: array
+          items:
+            type: string
           nullable: true
         is_any_rna_changed_in_ad_brain_display_value:
           type: string

libs/agora/api-description/src/components/schemas/Druggability.yaml

@@ -11,8 +11,9 @@ properties:
     type: integer
     example: 3
   pharos_class:
-    type: string
-    example: 'Tclin'
+    type: array
+    items:
+      type: string
   classification:
     type: string
     example: 'Enzyme'

libs/agora/api-description/src/components/schemas/Gene.yaml

@@ -15,6 +15,10 @@ properties:
     type: array
     items:
       type: string
+  uniprotkb_accessions:
+    type: array
+    items:
+      type: string
   is_igap:
     type: boolean
   is_eqtl:
@@ -37,9 +41,7 @@ properties:
     items:
       $ref: MedianExpression.yaml
   druggability:
-    type: array
-    items:
-      $ref: Druggability.yaml
+    $ref: Druggability.yaml
   total_nominations:
     type: integer
     nullable: true
@@ -105,7 +107,9 @@ properties:
     type: string
     nullable: true
   pharos_class_display_value:
-    type: string
+    type: array
+    items:
+      type: string
     nullable: true
   is_any_rna_changed_in_ad_brain_display_value:
     type: string

libs/agora/charts/src/lib/score-barchart/score-barchart.component.ts

@@ -68,7 +68,6 @@ export class ScoreBarChartComponent implements OnChanges, AfterViewInit, OnDestr
 
   @HostListener('window:resize', ['$event.target'])
   onResize() {
-    console.log('sbc-onresize');
     if (this.shouldResize && this.initialized) {
       const divSize = this.scoreBarChartContainer.nativeElement.getBoundingClientRect().width;
       clearTimeout(this.resizeTimer);
@@ -79,8 +78,6 @@ export class ScoreBarChartComponent implements OnChanges, AfterViewInit, OnDestr
   }
 
   ngOnChanges(changes: SimpleChanges): void {
-    console.log('sbc-changes', changes);
-
     if (
       (changes['data'] && !changes['data'].firstChange) ||
       (changes['score'] && !changes['score'].firstChange) ||
@@ -98,8 +95,6 @@ export class ScoreBarChartComponent implements OnChanges, AfterViewInit, OnDestr
   }
 
   ngAfterViewInit(): void {
-    console.log('ngAfterViewInit');
-
     if (this.score === null) this.hideChart();
     else this.createChart();
   }

libs/agora/gene-comparison-tool/src/lib/gene-comparison-tool.component.ts

@@ -263,16 +263,13 @@ export class GeneComparisonToolComponent implements OnInit, AfterViewInit, OnDes
 
     combineLatest([genesApi$, distributionApi$]).subscribe(([genesResult, distributionResult]) => {
       if (genesResult.items) {
-        console.log('# of items', genesResult.items.length);
         this.initData(genesResult.items);
         this.sortTable(this.headerTable);
         this.refresh();
 
         this.scoresDistribution = distributionResult.overall_scores;
 
         this.isLoading = false;
-        // console.log('calling setLoading false');
-        // this.helperService.setLoading(false);
       }
     });
   }
@@ -1295,14 +1292,8 @@ export class GeneComparisonToolComponent implements OnInit, AfterViewInit, OnDes
 
   updateColumnWidth() {
     const count = this.columns.length < 5 ? 5 : this.columns.length;
-    console.log('count is: ', count);
-
     const width = this.headerTable?.containerViewChild?.nativeElement?.offsetWidth || 0;
-    console.log('ht', this.headerTable?.containerViewChild?.nativeElement?.offsetWidth);
-    console.log('width is: ', width);
-
     this.columnWidth = Math.ceil((width - 300) / count) + 'px';
-    console.log('column width is: ', this.columnWidth);
   }
 
   onResize() {

libs/agora/genes/src/index.ts

@@ -12,6 +12,7 @@ export * from './lib/components/gene-nominations/gene-nominations.component';
 export * from './lib/components/gene-protein-selector/gene-protein-selector.component';
 export * from './lib/components/gene-resources/gene-resources.component';
 export * from './lib/components/gene-search/gene-search.component';
+export * from './lib/components/gene-similar/gene-similar.component';
 export * from './lib/components/gene-soe/gene-soe.component';
 export * from './lib/components/gene-soe-charts/gene-soe-charts.component';
 export * from './lib/components/gene-soe-list/gene-soe-list.component';

libs/agora/genes/src/lib/components/gene-druggability/gene-druggability.component.ts

@@ -45,20 +45,18 @@ export class GeneDruggabilityComponent {
     // Update the initial buckets
     if (this.gene) {
       if (!this.gene.druggability) {
-        this.gene.druggability = [
-          {
-            sm_druggability_bucket: this.getDefaultBucketNumber(),
-            safety_bucket: this.getDefaultBucketNumber(),
-            abability_bucket: this.getDefaultBucketNumber(),
-            pharos_class: '',
-            classification: this.getDefaultText(),
-            safety_bucket_definition: this.getDefaultText(),
-            abability_bucket_definition: this.getDefaultText(),
-          },
-        ];
+        this.gene.druggability = {
+          sm_druggability_bucket: this.getDefaultBucketNumber(),
+          safety_bucket: this.getDefaultBucketNumber(),
+          abability_bucket: this.getDefaultBucketNumber(),
+          pharos_class: [],
+          classification: this.getDefaultText(),
+          safety_bucket_definition: this.getDefaultText(),
+          abability_bucket_definition: this.getDefaultText(),
+        };
       }
 
-      this.druggability = this.gene.druggability[0];
+      this.druggability = this.gene.druggability;
       this.currentBucketSM = this.druggability.sm_druggability_bucket;
       this.currentBucketAB = this.druggability.abability_bucket;
       this.currentBucketSF = this.druggability.safety_bucket;

libs/agora/genes/src/lib/components/gene-hero/gene-hero.component.html

@@ -19,7 +19,7 @@ <h2 class="gene-hero-name">
         <p class="gene-hero-provider">
           {{ getSummary() }}
         </p>
-        @if (gene.bio_domains || getAlias() || getEnsemblUrl() !== '') {
+        @if (gene.bio_domains || getAliases() || getEnsemblUrl() !== '') {
           <hr />
           @if (gene.bio_domains) {
             <div class="gene-hero-biodomains">
@@ -29,22 +29,29 @@ <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
               </p>
             </div>
           }
+          @if (gene.druggability && gene.druggability.pharos_class) {
+            <div class="gene-hero-pharos">
+              <h4 class="gene-hero-pharos-heading">Pharos Class</h4>
+              <p>{{ gene.druggability.pharos_class.join(', ') }}</p>
+            </div>
+          }
           <div class="gene-hero-aliases">
             <h4 class="gene-hero-aliases-heading">Also known as</h4>
-            @if (getEnsemblUrl() !== '') {
-              <p>
+            @if (getEnsemblUrl()) {
+              <p class="aliases">
                 <a [href]="getEnsemblUrl()" target="_blank">{{ gene.ensembl_gene_id }}</a>
                 @if (gene.ensembl_info.ensembl_release) {
                   <span> (Ensembl Release {{ gene.ensembl_info.ensembl_release }}) </span>
                 }
               </p>
             }
             @if (getEnsemblUrl() === '') {
-              <span>{{ gene.ensembl_gene_id }}</span>
+              <p class="aliases">
+                <span>{{ gene.ensembl_gene_id }}</span>
+              </p>
             }
-
             @if (gene.ensembl_info.ensembl_possible_replacements.length > 0) {
-              <p>
+              <p class="aliases">
                 <a [href]="getPossibleReplacementsURL()"
                   >Possible replacement value<span
                     *ngIf="gene.ensembl_info.ensembl_possible_replacements.length > 1"
@@ -54,8 +61,20 @@ <h4 class="gene-hero-aliases-heading">Also known as</h4>
                 {{ gene.ensembl_info.ensembl_possible_replacements.join(', ') }}
               </p>
             }
-            @if (alias !== '') {
-              <p>{{ alias }}</p>
+            @if (gene.uniprotkb_accessions) {
+              <p class="aliases">
+                UNIPROTKB
+                <ng-container
+                  *ngFor="let accession of gene.uniprotkb_accessions; let isLast = last"
+                  class="aliases"
+                >
+                  <a [href]="getUniProtKBLink(accession)" target="_blank">{{ accession }}</a
+                  ><span *ngIf="!isLast">, </span>
+                </ng-container>
+              </p>
+              <p *ngIf="gene.alias.length > 0" class="aliases">
+                {{ getAliases() }}
+              </p>
             }
           </div>
         }

libs/agora/genes/src/lib/components/gene-hero/gene-hero.component.scss

@@ -38,7 +38,17 @@ hr {
 }
 
 .gene-hero-biodomains {
-  margin-bottom: 30px;
+  margin-bottom: 15px;
+
+  p {
+    margin-left: 10px;
+  }
+}
+
+.gene-hero-pharos {
+  p {
+    margin-left: 10px;
+  }
 }
 
 .gene-hero-summary {
@@ -50,11 +60,16 @@ hr {
 }
 
 .gene-hero-aliases-heading,
-.gene-hero-biodomains-heading {
+.gene-hero-biodomains-heading,
+.gene-hero-pharos-heading {
   text-transform: uppercase;
   margin-bottom: 15px;
 }
 
+.aliases {
+  margin: 0 0 0 10px;
+}
+
 .possible-replacements {
   margin-bottom: 15px;
 }