Skip to content

Commit

Permalink
Merge pull request #1336 from JessterB/AG-1488-add-new-resource-section
Browse files Browse the repository at this point in the history 
AG-1488: Updates to resource cards and ordering
  • Loading branch information
@sagely1
sagely1 authored Nov 28, 2024
2 parents 377b5c4 + 91a8bb7 commit 9ef59c6
Show file tree
Hide file tree
Showing 3 changed files with 60 additions and 60 deletions.
4 changes: 2 additions & 2 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
56 changes: 28 additions & 28 deletions src/app/features/genes/components/gene-resources/gene-resources.component.html
View file
Original file line number Diff line number Diff line change
@@ -1,30 +1,3 @@
<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 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>
</div>

<ng-container *ngIf="gene">
<div *ngIf="gene.is_tep === true || gene.is_adi === true" class="section">
<div class="section-inner">
Expand Down Expand Up @@ -57,12 +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"
Expand Down
60 changes: 30 additions & 30 deletions src/app/features/genes/components/gene-resources/gene-resources.component.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ import { Gene, ResourceCard } from '../../../../models';
})
export class GeneResourcesComponent implements OnInit {
@Input() gene: Gene | undefined;

additionalResources: ResourceCard[] = [];
drugDevelopmentResources: ResourceCard[] = [];

Expand All @@ -34,43 +34,43 @@ export class GeneResourcesComponent implements OnInit {
{
title: 'Chemical Probes',
description:
'View expert reviews and evaluations of chemical probes.',
'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 PharmGKB for information on gene-drug and gene-phenotype relationships.',
'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=${this.gene?.ensembl_gene_id}`,
},
{
title: 'Probe Miner',
description:
'Search Probe Miner for information on chemical probes for this gene.',
'Search for information on chemical probes based on large-scale, publicly available, medicinal chemistry data.',
linkText: 'Visit Probe Miner',
link: 'https://probeminer.icr.ac.uk/#/',
},
{
title: 'Protein Data Bank',
description:
'Search PDB for experimental and computed protin structure information.',
linkText: 'Search PDB',
'Search for experimental and computed 3D protein structure information.',
linkText: 'Visit PDB',
link: 'https://www.rcsb.org',
},
];
Expand All @@ -79,16 +79,9 @@ export class GeneResourcesComponent implements OnInit {
{
title: 'AD Atlas',
description:
'View this gene on the AD Atlas site, a network-based resource for investigating AD in a multi-omic context.',
'Perform interactive network and enrichment analyses on this target using a heterogenous network of multiomic, association, and endophenotypic data.',
linkText: 'Visit AD Atlas',
link: `https://adatlas.org/?geneID=${this.gene?.ensembl_gene_id}`,
},
{
title: 'Allen Institute Transcriptomics',
description:
'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=${this.gene?.hgnc_symbol ?? this.gene?.ensembl_gene_id}`,
link: `https://adatlas.org/?type=geneEnsembl&ids=${this.gene?.ensembl_gene_id}`,
},
{
title: 'Alzforum',
Expand All @@ -100,62 +93,69 @@ export class GeneResourcesComponent implements OnInit {
{
title: 'AlzPED',
description:
'Search AlzPED for information on preclinical efficacy studies of candidate AD therapeutics.',
'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 this gene in the AMP-PD Target Explorer, a resource that hosts evidence about whether genes are associated with Parkinson\'s Disease.',
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:
'Visit GeneCards to view integrated information about this gene.',
'View integrated information about this target gathered from a comprehensive collection of public sources.',
linkText: 'Visit GeneCards',
link: `https://www.genecards.org/Search/Keyword?queryString=${this.gene?.ensembl_gene_id}`,
link: `https://www.genecards.org/cgi-bin/carddisp.pl?gene=${this.gene?.hgnc_symbol ?? 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.',
'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/${this.gene?.ensembl_gene_id}`,
},
{
title: 'Pub AD',
description:
'View dementia-related publication information for this gene on PubAD.',
'View dementia-related publication information for this target.',
linkText: 'Visit PubAD',
link: `${ 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=${this.gene?.ensembl_gene_id}`,
},
{
title: 'SEA-AD',
description:
'Explore the Seattle Alzheimer’s Disease Brain Cell Atlas resources.',
'Explore the Seattle Alzheimer’s Disease Brain Cell Atlas resources from the Allen Institute.',
linkText: 'Visit SEA-AD',
link: 'https://portal.brain-map.org/explore/seattle-alzheimers-disease',
},
{
title: 'UniProtKB',
description:
'View sequence and functional information about the protein(s) encoded by this gene.',
'View protein sequence and functional information about this target.',
linkText: 'Visit UniProtKB',
link: `https://www.uniprot.org/uniprotkb?query=${this.gene?.ensembl_gene_id}`,
},
Expand Down

0 comments on commit 9ef59c6

Please sign in to comment.