Additional Resources
- 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.
Date: Wed, 27 Nov 2024 11:39:35 -0800
Subject: [PATCH 6/8] Update resource strings and URLs
---
.../gene-resources.component.ts | 60 +++++++++----------
1 file changed, 30 insertions(+), 30 deletions(-)
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
index 0fa53683..b7b0905b 100644
--- a/src/app/features/genes/components/gene-resources/gene-resources.component.ts
+++ b/src/app/features/genes/components/gene-resources/gene-resources.component.ts
@@ -9,7 +9,7 @@ import { Gene, ResourceCard } from '../../../../models';
})
export class GeneResourcesComponent implements OnInit {
@Input() gene: Gene | undefined;
-
+
additionalResources: ResourceCard[] = [];
drugDevelopmentResources: ResourceCard[] = [];
@@ -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=${this.gene?.ensembl_gene_id}`,
},
{
title: 'Probe Miner',
description:
- 'Search Probe Miner for information on chemical probes for this gene.',
+ 'Search for information on chemical probes based on large-scale, publicly available, medicinal chemistry data.',
linkText: 'Visit Probe Miner',
link: 'https://probeminer.icr.ac.uk/#/',
},
{
title: 'Protein Data Bank',
description:
- 'Search PDB for experimental and computed protin structure information.',
- linkText: 'Search PDB',
+ 'Search for experimental and computed 3D protein structure information.',
+ linkText: 'Visit PDB',
link: 'https://www.rcsb.org',
},
];
@@ -79,16 +79,9 @@ export class GeneResourcesComponent implements OnInit {
{
title: 'AD Atlas',
description:
- 'View this gene on the AD Atlas site, a network-based resource for investigating AD in a multi-omic context.',
+ 'Perform interactive network and enrichment analyses on this target using a heterogenous network of multiomic, association, and endophenotypic data.',
linkText: 'Visit AD Atlas',
- link: `https://adatlas.org/?geneID=${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',
@@ -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}`,
},
From 91a8bb722d7493475af6b6e4b216a2dd7495dfe7 Mon Sep 17 00:00:00 2001
From: JessterB <89862046+JessterB@users.noreply.github.com>
Date: Wed, 27 Nov 2024 11:40:15 -0800
Subject: [PATCH 7/8] Update mongoDB install URLs in README
---
README.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 1ac18756..e4c67d16 100644
--- 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:
From dab1ac8f7225bcf4b933b1ea37e4a6e21e047a4e Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Wed, 27 Nov 2024 15:33:47 -0800
Subject: [PATCH 8/8] applied a margin under subheadings biodomains and pharos
class
---
.../components/gene-hero/gene-hero.component.html | 2 +-
.../components/gene-hero/gene-hero.component.scss | 12 +++++++++++-
2 files changed, 12 insertions(+), 2 deletions(-)
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
index cb2b483c..81728ab3 100644
--- a/src/app/features/genes/components/gene-hero/gene-hero.component.html
+++ b/src/app/features/genes/components/gene-hero/gene-hero.component.html
@@ -22,7 +22,7 @@
Biological Domains
{{ getBiodomains() }}
-
+
Pharos Class
{{ gene.druggability[0].pharos_class }}
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
index 46cedd97..332c004f 100644
--- 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 {