Merge pull request #1334 from sagely1/AG-1488-add-new-resource-section

AG-1488: Added new resource cards in Resources tab

src/app/features/genes/components/gene-resources/gene-resources.component.html

@@ -1,26 +1,25 @@
 <div *ngIf="gene" class="section">
-  <div class="section-inner pb-0">
+  <div class="section-inner">
     <div class="container-sm">
-      <div>
-        <h2>
-          Druggability of {{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-        </h2>
-        <p class="druggability-description">
-          AMP-AD pharmaceutical partners scored the tractability of targets
-          using publicly-available resources and have generated ratings of
-          small-molecule druggability, therapeutic antibody feasibility, and
-          safety.
-        </p>
-        <modal-link
-          text="Learn more about the analysis"
-          header="Druggability/Ligandability Information"
-          wikiId="612874"
-        >
-        </modal-link>
-
-        <hr class="separator separator-md" />
-
-        <gene-druggability *ngIf="gene" [gene]="gene"></gene-druggability>
+      <h2>
+        Drug Development Resources
+      </h2>
+      <p class="druggability-description">
+        These external sites provide drug development resources.
+      </p>
+      <div 
+        *ngFor="let r of drugDevelopmentResources; let i = index" 
+        class="row tab-row last-row"
+      >
+        <div class="col-md-3 col-sm-8 col-8 header-title">{{ r.title }}</div>
+        <div class="col-md-3 col-sm-4 col-4 text-center header-link">
+          <a class="additional-resource-links link no-bold" href="{{ r.link }}" target="_blank">{{
+            r.linkText
+          }}</a>
+        </div>
+        <div class="col-md-6 col-sm-12 col-12 header-description">
+          {{ r.description }}
+        </div>
       </div>
     </div>
   </div>

src/app/features/genes/components/gene-resources/gene-resources.component.ts

@@ -1,6 +1,6 @@
 import { Component, Input, OnInit } from '@angular/core';
 
-import { Gene, AdditionalResource } from '../../../../models';
+import { Gene, ResourceCard } from '../../../../models';
 
 @Component({
   selector: 'gene-resources',
@@ -10,7 +10,8 @@ import { Gene, AdditionalResource } from '../../../../models';
 export class GeneResourcesComponent implements OnInit {
   @Input() gene: Gene | undefined;
 
-  additionalResources: AdditionalResource[] = [];
+  additionalResources: ResourceCard[] = [];
+  drugDevelopmentResources: ResourceCard[] = [];
 
   ngOnInit(): void {
     this.init();
@@ -29,14 +30,28 @@ export class GeneResourcesComponent implements OnInit {
       return;
     }
 
-    this.additionalResources = [
+    this.drugDevelopmentResources = [
+      {
+        title: 'Chemical Probes',
+        description:
+          'View expert reviews and evaluations of chemical probes.',
+        linkText: 'Visit Chemical Probes',
+        link: `https://www.chemicalprobes.org/?q=${this.gene?.hgnc_symbol}`,
+      },
       {
         title: 'Open Targets',
         description:
           'View this gene on Open Targets, a resource that provides evidence on the validity of therapeutic targets based on genome-scale experiments and analysis.',
         linkText: 'Visit Open Targets',
         link: `https://platform.opentargets.org/target/${this.gene?.ensembl_gene_id}`,
       },
+      {
+        title: 'PharmGKB',
+        description:
+          'Search PharmGKB for information on gene-drug and gene-phenotype relationships.',
+        linkText: 'Visit PharmGKB',
+        link: 'https://www.pharmgkb.org',
+      },
       {
         title: 'Pharos',
         description:
@@ -45,19 +60,22 @@ export class GeneResourcesComponent implements OnInit {
         link: `https://pharos.nih.gov/targets?q=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'Brain RNAseq',
+        title: 'Probe Miner',
         description:
-          'Search for this gene on the Brain RNAseq site, which hosts single-cell RNAseq data.',
-        linkText: 'Visit BrainRNAseq',
-        link: 'http://www.brainrnaseq.org/',
+          'Search Probe Miner for information on chemical probes for this gene.',
+        linkText: 'Visit Probe Miner',
+        link: 'https://probeminer.icr.ac.uk/#/',
       },
       {
-        title: 'Genomics DB',
+        title: 'Protein Data Bank',
         description:
-          'View this gene on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
-        linkText: 'Visit Genomics DB',
-        link: `https://www.niagads.org/genomics/app/record/gene/${this.gene?.ensembl_gene_id}`,
+          'Search PDB for experimental and computed protin structure information.',
+        linkText: 'Search PDB',
+        link: 'https://www.rcsb.org',
       },
+    ];
+
+    this.additionalResources = [
       {
         title: 'AD Atlas',
         description:
@@ -66,11 +84,31 @@ export class GeneResourcesComponent implements OnInit {
         link: `https://adatlas.org/?geneID=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'Pub AD',
+        title: 'Allen Institute Transcriptomics',
         description:
-          'View dementia-related publication information for this gene on PubAD.',
-        linkText: 'Visit PubAD',
-        link: `${ this.getPubADLink() }`,
+          'View single nucleus RNAseq data for this gene using the Allen Institute’s Transcriptomics Comparative Viewer.',
+        linkText: 'Visit AD Transcriptomics Viewer',
+        link: `https://knowledge.brain-map.org/data/5IU4U8BP711TR6KZ843/2CD0HDC5PS6A58T0P6E/compare?geneOption=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Alzforum',
+        description:
+          'Visit Alzforum for news and information resources about AD and related disorders.',
+        linkText: 'Visit Alzforum',
+        link: 'https://www.alzforum.org',
+      },
+      {
+        title: 'AlzPED',
+        description:
+          'Search AlzPED for information on preclinical efficacy studies of candidate AD therapeutics.',
+        linkText: 'Visit AlzPED',
+        link: 'https://alzped.nia.nih.gov',
+      },
+      {
+        title: 'AMP-PD Target Explorer', 
+        description: 'View this gene in the AMP-PD Target Explorer, a resource that hosts evidence about whether genes are associated with Parkinson\'s Disease.', 
+        linkText: 'Visit AMP-PD',
+        link: `https://target-explorer.amp-pd.org/genes/target-search?gene=${this.gene?.ensembl_gene_id}`
       },
       {
         title: 'Gene Ontology',
@@ -79,6 +117,27 @@ export class GeneResourcesComponent implements OnInit {
         linkText: 'Visit Ensembl',
         link: `https://www.ensembl.org/Homo_sapiens/Gene/Ontologies/molecular_function?g=${this.gene?.ensembl_gene_id}`,
       },
+      {
+        title: 'GeneCards',
+        description:
+          'Visit GeneCards to view integrated information about this gene.',
+        linkText: 'Visit GeneCards',
+        link: `https://www.genecards.org/Search/Keyword?queryString=${this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Genomics DB',
+        description:
+          'View this gene on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
+        linkText: 'Visit Genomics DB',
+        link: `https://www.niagads.org/genomics/app/record/gene/${this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Pub AD',
+        description:
+          'View dementia-related publication information for this gene on PubAD.',
+        linkText: 'Visit PubAD',
+        link: `${ this.getPubADLink() }`,
+      },
       {
         title: 'Reactome Pathways',
         description:
@@ -87,11 +146,19 @@ export class GeneResourcesComponent implements OnInit {
         link: `https://www.ensembl.org/Homo_sapiens/Gene/Pathway?g=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'AMP-PD Target Explorer', 
-        description: 'View this gene in the AMP-PD Target Explorer, a resource that hosts evidence about whether genes are associated with Parkinson\'s Disease.', 
-        linkText: 'Visit AMP-PD',
-        link: `https://target-explorer.amp-pd.org/genes/target-search?gene=${this.gene?.ensembl_gene_id}`
-      }
+        title: 'SEA-AD',
+        description:
+          'Explore the Seattle Alzheimer’s Disease Brain Cell Atlas resources.',
+        linkText: 'Visit SEA-AD',
+        link: 'https://portal.brain-map.org/explore/seattle-alzheimers-disease',
+      },
+      {
+        title: 'UniProtKB',
+        description:
+          'View sequence and functional information about the protein(s) encoded by this gene.',
+        linkText: 'Visit UniProtKB',
+        link: `https://www.uniprot.org/uniprotkb?query=${this.gene?.ensembl_gene_id}`,
+      },
     ];
   }
 }

src/app/models/AdditionalResource.ts → src/app/models/ResourceCard.ts

@@ -1,4 +1,4 @@
-export interface AdditionalResource {
+export interface ResourceCard {
     title: string;
     description: string;
     linkText: string;

src/app/models/index.ts

@@ -15,4 +15,4 @@ export * from './charts';
 export * from './scores';
 export * from './GCTColumn';
 export * from './biodomains';
-export * from './AdditionalResource';
+export * from './ResourceCard';