Merge branch 'develop' into AG-1539-surface-uniprot-links-in-gene-hero

sagely1 · Nov 28, 2024 · 0737f41 · 0737f41
2 parents b0e0624 + 9ef59c6
commit 0737f41
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diff --git a/README.md b/README.md
@@ -43,8 +43,8 @@ The next sections focus on setting up a mongo database loaded with Agora's data.
 
 You will need to create a MongoDB database and name it `agora`. 
 
-- [Using the MongoDB Shell](https://www.mongodb.com/basics/create-database#option-2)
-- [Using MongoDB Compass](https://www.mongodb.com/basics/create-database#option-3)
+- [Using the MongoDB Shell](https://www.mongodb.com/resources/products/fundamentals/create-database#using-the-mongodb-shell)
+- [Using MongoDB Compass](https://www.mongodb.com/resources/products/fundamentals/create-database#using-the-mongodb-compass)
 - [Using Studio3T](https://studio3t.com/knowledge-base/articles/common-mongodb-commands/#1-mongodb-create-database)
 
 Note: You can use the following scripts to start the database:

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.html b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -22,6 +22,10 @@ <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
             {{ getBiodomains() }}
           </p>
         </div>
+        <div *ngIf="gene.druggability[0].pharos_class" class="gene-hero-pharos">
+          <h4 class="gene-hero-pharos-heading">Pharos Class</h4>
+          <p>{{ gene.druggability[0].pharos_class }}</p>
+        </div>
         <div class="gene-hero-aliases">
           <h4 class="gene-hero-aliases-heading">Also known as</h4>
           <ng-container *ngIf="getEnsemblUrl() !== ''">

diff --git a/src/app/features/genes/components/gene-hero/gene-hero.component.scss b/src/app/features/genes/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 {
@@ -49,7 +59,7 @@ hr {
   font-style: italic;
 }
 
-.gene-hero-aliases-heading, .gene-hero-biodomains-heading {
+.gene-hero-aliases-heading, .gene-hero-biodomains-heading, .gene-hero-pharos-heading {
   text-transform: uppercase;
   margin-bottom: 15px;
 }

diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.html b/src/app/features/genes/components/gene-resources/gene-resources.component.html
@@ -1,31 +1,3 @@
-<div *ngIf="gene" class="section">
-  <div class="section-inner pb-0">
-    <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>
-      </div>
-    </div>
-  </div>
-</div>
-
 <ng-container *ngIf="gene">
   <div *ngIf="gene.is_tep === true || gene.is_adi === true" class="section">
     <div class="section-inner">
@@ -58,12 +30,39 @@ <h2 id="target-enabling-resources-header">Target Enabling Resources</h2>
   </div>
 </ng-container>
 
+<div *ngIf="gene" class="section">
+  <div class="section-inner">
+    <div class="container-sm">
+      <h2>
+        Drug Development Resources
+      </h2>
+      <p class="druggability-description">
+        These external sites provide information and resources related to drug development.
+      </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>
+</div>
+
 <div *ngIf="additionalResources" class="section">
   <div class="section-inner">
     <div class="container-sm">
       <h2>Additional Resources</h2>
       <p>
-        These external sites provide additional useful information for exploring AD targets.
+        These external sites provide additional information about therapeutic targets for AD and related dementias.
       </p>
       <div
         *ngFor="let r of additionalResources; let i = index"

diff --git a/src/app/features/genes/components/gene-resources/gene-resources.component.ts b/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',
@@ -9,8 +9,9 @@ import { Gene, AdditionalResource } from '../../../../models';
 })
 export class GeneResourcesComponent implements OnInit {
   @Input() gene: Gene | undefined;
-
-  additionalResources: AdditionalResource[] = [];
+
+  additionalResources: ResourceCard[] = [];
+  drugDevelopmentResources: ResourceCard[] = [];
 
   ngOnInit(): void {
     this.init();
@@ -29,69 +30,135 @@ export class GeneResourcesComponent implements OnInit {
       return;
     }
 
-    this.additionalResources = [
+    this.drugDevelopmentResources = [
+      {
+        title: 'Chemical Probes',
+        description:
+          'View expert reviews and evaluations of any chemical probes that are available for this target.',
+        linkText: 'Visit Chemical Probes',
+        link: `https://www.chemicalprobes.org/?q=${this.gene?.hgnc_symbol}`,
+      },
       {
         title: 'Open Targets',
         description:
-          'View this gene on Open Targets, a resource that provides evidence on the validity of therapeutic targets based on genome-scale experiments and analysis.',
+          'View evidence on the validity of this therapeutic target based on genome-scale experiments and analysis.',
         linkText: 'Visit Open Targets',
         link: `https://platform.opentargets.org/target/${this.gene?.ensembl_gene_id}`,
       },
+      {
+        title: 'PharmGKB',
+        description:
+          'Search for information on gene-drug and gene-phenotype relationships.',
+        linkText: 'Visit PharmGKB',
+        link: 'https://www.pharmgkb.org',
+      },
       {
         title: 'Pharos',
         description:
-          'View this gene on Pharos, a resource that provides access to the integrated knowledge-base from the Illuminating the Druggable Genome program.',
+          'View information about this target in the Knowledge Management Center for the Illuminating the Druggable Genome program.',
         linkText: 'Visit Pharos',
         link: `https://pharos.nih.gov/targets?q=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'Brain RNAseq',
+        title: 'Probe Miner',
         description:
-          'Search for this gene on the Brain RNAseq site, which hosts single-cell RNAseq data.',
-        linkText: 'Visit BrainRNAseq',
-        link: 'http://www.brainrnaseq.org/',
+          'Search for information on chemical probes based on large-scale, publicly available, medicinal chemistry data.',
+        linkText: 'Visit Probe Miner',
+        link: 'https://probeminer.icr.ac.uk/#/',
       },
       {
-        title: 'Genomics DB',
+        title: 'Protein Data Bank',
         description:
-          'View this gene on the National Institute on Aging Genetics of Alzheimer\'s Disease Data Storage Site (NIAGADS) Genomics Database.',
-        linkText: 'Visit Genomics DB',
-        link: `https://www.niagads.org/genomics/app/record/gene/${this.gene?.ensembl_gene_id}`,
+          'Search for experimental and computed 3D protein structure information.',
+        linkText: 'Visit PDB',
+        link: 'https://www.rcsb.org',
       },
+    ];
+
+    this.additionalResources = [
       {
         title: 'AD Atlas',
         description:
-          'View this gene on the AD Atlas site, a network-based resource for investigating AD in a multi-omic context.',
+          'Perform interactive network and enrichment analyses on this target using a heterogenous network of multiomic, association, and endophenotypic data.',
         linkText: 'Visit AD Atlas',
-        link: `https://adatlas.org/?geneID=${this.gene?.ensembl_gene_id}`,
+        link: `https://adatlas.org/?type=geneEnsembl&ids=${this.gene?.ensembl_gene_id}`,
       },
       {
-        title: 'Pub AD',
+        title: 'Alzforum',
         description:
-          'View dementia-related publication information for this gene on PubAD.',
-        linkText: 'Visit PubAD',
-        link: `${ this.getPubADLink() }`,
+          'Visit Alzforum for news and information resources about AD and related disorders.',
+        linkText: 'Visit Alzforum',
+        link: 'https://www.alzforum.org',
+      },
+      {
+        title: 'AlzPED',
+        description:
+          'Search for information on preclinical efficacy studies of candidate AD therapeutics.',
+        linkText: 'Visit AlzPED',
+        link: 'https://alzped.nia.nih.gov',
+      },
+      {
+        title: 'AMP-PD Target Explorer',
+        description: 'View evidence about whether this target is associated with Parkinson\'s Disease.',
+        linkText: 'Visit AMP-PD',
+        link: `https://target-explorer.amp-pd.org/genes/target-search?gene=${this.gene?.ensembl_gene_id}`
+      },
+      {
+        title: 'Brain Knowledge Platform',
+        description:
+          'View single nucleus RNAseq results for this target using the Allen Institute SEA-AD Comparative Viewer.',
+        linkText: 'Visit Brain Knowledge Platform',
+        link: `https://knowledge.brain-map.org/data/5IU4U8BP711TR6KZ843/2CD0HDC5PS6A58T0P6E/compare?geneOption=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
       },
       {
         title: 'Gene Ontology',
         description:
-          'View the gene ontology information for this gene on Ensembl.',
-        linkText: 'Visit Ensembl',
-        link: `https://www.ensembl.org/Homo_sapiens/Gene/Ontologies/molecular_function?g=${this.gene?.ensembl_gene_id}`,
+          'View the GO terms associated with this target and explore ontology-related tools.',
+        linkText: 'Visit AmiGO 2',
+        link: `https://amigo.geneontology.org/amigo/search/annotation?q=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'GeneCards',
+        description:
+          'View integrated information about this target gathered from a comprehensive collection of public sources.',
+        linkText: 'Visit GeneCards',
+        link: `https://www.genecards.org/cgi-bin/carddisp.pl?gene=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Genomics DB',
+        description:
+          'View information about this target 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/${this.gene?.ensembl_gene_id}`,
+      },
+      {
+        title: 'Pub AD',
+        description:
+          'View dementia-related publication information for this target.',
+        linkText: 'Visit PubAD',
+        link: `${ this.getPubADLink() }`,
       },
       {
         title: 'Reactome Pathways',
         description:
-          'View the reactome pathway information for this gene on Ensembl.',
+          'View the reactome pathway information for this target on Ensembl.',
         linkText: 'Visit Ensembl',
         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 from the Allen Institute.',
+        linkText: 'Visit SEA-AD',
+        link: 'https://portal.brain-map.org/explore/seattle-alzheimers-disease',
+      },
+      {
+        title: 'UniProtKB',
+        description:
+          'View protein sequence and functional information about this target.',
+        linkText: 'Visit UniProtKB',
+        link: `https://www.uniprot.org/uniprotkb?query=${this.gene?.ensembl_gene_id}`,
+      },
     ];
   }
 }
diff --git a/src/app/models/AdditionalResource.ts → src/app/models/ResourceCard.ts b/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;

diff --git a/src/app/models/index.ts b/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';