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Connects to #378. PASS1B-06 phenotype data technical guide. #379

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Connects to #378. PASS1B-06 phenotype data technical guide. #379

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b3687d5
Chnage page title
jimmyzhen Nov 27, 2024
7fc6360
Re-order omes/assays per central dogma
jimmyzhen Nov 27, 2024
cf15233
Add external link to Discoourse community portal
jimmyzhen Nov 27, 2024
feac74c
Re-order omes per central dogma: GET, proteome, metabolome
jimmyzhen Nov 27, 2024
0e6a8c8
Rename data deposition dropdown menu link
jimmyzhen Nov 27, 2024
9ac98bd
Add link to phenotype data technical guide page
jimmyzhen Nov 27, 2024
9f8d93c
Initial commit of example figure for sample data linkage via vial lab…
jimmyzhen Nov 27, 2024
d0c0827
Re-order exercise benefit items
jimmyzhen Nov 27, 2024
acc1778
Initial commit of phenotype data technical guide component
jimmyzhen Nov 27, 2024
d6b30d4
Add new public route to phenotype data technical guide
jimmyzhen Nov 27, 2024
248573c
Re-order omes per central dogma
jimmyzhen Nov 27, 2024
d76e97e
Remove absolute height of treegraph and set its minHeight to 70vh via…
jimmyzhen Nov 29, 2024
117d338
Reformat treegraph data so that most omic nodes can be set to collaps…
jimmyzhen Nov 29, 2024
c15c40c
Fix typo
jimmyzhen Nov 30, 2024
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6 changes: 6 additions & 0 deletions src/App/App.jsx
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Expand Up @@ -32,6 +32,7 @@ import Tutorials from '../Tutorials/tutorials';
import License from '../License/licensePage';
import DataDeposition from '../DataDeposition/dataDepositionPage';
import Publications from '../Publications/publications';
import Phenotype from '../TechnicalGuides/phenotype';
import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups';
import FullTableEnduranceTraining from '../Publications/Data/Animal/Phenotype/fullTableEnduranceTraining';
import Pass1b06PhenotypeAnimalConnected from '../AnalysisPage/pass1b06PhenotypeAnimal';
Expand Down Expand Up @@ -159,6 +160,11 @@ function App({ history = History }) {
exact
component={withTracker(Publications)}
/>
<Route
path="/technical-guides/phenotype"
exact
component={withTracker(Phenotype)}
/>
<Route
path="/publications/data/animal/phenotype/full-table-endurance-training"
exact
Expand Down
2 changes: 1 addition & 1 deletion src/App/__test__/App.test.jsx
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Expand Up @@ -23,7 +23,7 @@ describe('<App />', () => {
});

test('It should contain fifteen <Route /> children', () => {
expect(component.find('Route').length).toBe(25);
expect(component.find('Route').length).toBe(26);
});

test('It should contain four <PrivateRoute /> children', () => {
Expand Down
10 changes: 8 additions & 2 deletions src/BrowseDataPage/components/dataDownloadsMain.jsx
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Expand Up @@ -100,8 +100,14 @@ function DataDownloadsMain({
<div className="col-12 mt-2">
<h2>Study Data</h2>
<p>
Browse and find the data of your interest by tissue, ome, or assay
types.
Browse and customze the data of your interest to download by tissue,
ome, or assay types. It is recommended to download the phenotypic data
along with the omics data for a comprehensive analysis. Learn more
about the
{' '}
<Link to="/technical-guides/phenotype">phenotypic data</Link>
{' '}
in MoTrPAC studies.
</p>
<div className="card-deck mb-3 text-center">
<SelectiveDataDownloadsCard
Expand Down
114 changes: 57 additions & 57 deletions src/DataDeposition/dataDepositionPage.jsx
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Expand Up @@ -8,9 +8,9 @@ function DataDeposition() {
<div className="dataDepositionPage px-3 px-md-4 mb-3 container">
<Helmet>
<html lang="en" />
<title>Data Deposition at Public Repositories - MoTrPAC Data Hub</title>
<title>MoTrPAC Data Accessible at Public Repositories - MoTrPAC Data Hub</title>
</Helmet>
<PageTitle title="Data Deposition at Public Repositories" />
<PageTitle title="MoTrPAC Data Accessible at Public Repositories" />
<div className="data-deposition-content-container row mb-4">
<div className="col-12">
<p className="lead">
Expand Down Expand Up @@ -55,61 +55,6 @@ function DataDeposition() {
</tbody>
</table>
</div>
{/* Immunoassay data deposition table */}
<h4 className="mt-4">Immunoassays</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
<tr>
<th>Repository</th>
<th>Data type</th>
<th>Accession</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<ExternalLink to="https://www.immport.org/home" label="IMMPORT" />
</td>
<td>Readouts, results</td>
<td>
<ExternalLink to="https://immport.org/shared/study/SDY2193" label="SDY2193" />
</td>
</tr>
</tbody>
</table>
</div>
{/* Metabolomics data deposition table */}
<h4 className="mt-4">Metabolomics (Targeted and Untargeted)</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
<tr>
<th>Repository</th>
<th>Data type</th>
<th>Project</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<ExternalLink to="https://www.metabolomicsworkbench.org/" label="Metabolomics Workbench" />
</td>
<td>Metabolomics raw + results files (identification and quantification)</td>
<td>
<ul className="list-unstyled">
<li>
<ExternalLink to="https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=PR001020" label="PR001020" />
</li>
<li>
<ExternalLink to="http://dx.doi.org/10.21228/M8V97D" label="DOI: 10.21228/M8V97D" />
</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
{/* Proteomics data deposition table */}
<h4 className="mt-4">Proteomics</h4>
<div className="table-responsive">
Expand Down Expand Up @@ -182,6 +127,61 @@ function DataDeposition() {
</tbody>
</table>
</div>
{/* Immunoassay data deposition table */}
<h4 className="mt-4">Immunoassays</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
<tr>
<th>Repository</th>
<th>Data type</th>
<th>Accession</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<ExternalLink to="https://www.immport.org/home" label="IMMPORT" />
</td>
<td>Readouts, results</td>
<td>
<ExternalLink to="https://immport.org/shared/study/SDY2193" label="SDY2193" />
</td>
</tr>
</tbody>
</table>
</div>
{/* Metabolomics data deposition table */}
<h4 className="mt-4">Metabolomics (Untargeted and Targeted)</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
<tr>
<th>Repository</th>
<th>Data type</th>
<th>Project</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<ExternalLink to="https://www.metabolomicsworkbench.org/" label="Metabolomics Workbench" />
</td>
<td>Metabolomics raw + results files (identification and quantification)</td>
<td>
<ul className="list-unstyled">
<li>
<ExternalLink to="https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=PR001020" label="PR001020" />
</li>
<li>
<ExternalLink to="http://dx.doi.org/10.21228/M8V97D" label="DOI: 10.21228/M8V97D" />
</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
Expand Down
20 changes: 10 additions & 10 deletions src/MainStudy/exerciseBenefitsData.js
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@@ -1,4 +1,14 @@
const exerciseBenefitsData = [
{
title: 'Reduced risk of all-cause mortality',
evidence: 'Regular physical activity is associated with a lower risk of all-cause mortality.',
citationNo: 4,
},
{
title: 'Reduced risk of cardiovascular diseases',
evidence: 'Exercise reduces the risk of cardiovascular diseases, including heart disease and stroke.',
citationNo: 4,
},
{
title: 'Younger-looking skin',
evidence: 'Exercise improves skin health by enhancing blood flow and delivering oxygen and nutrients to the skin, promoting collagen production and reducing signs of aging.',
Expand Down Expand Up @@ -69,16 +79,6 @@ const exerciseBenefitsData = [
evidence: 'Weight-bearing and resistance exercises improve bone density and joint health, reducing the risk of osteoporosis and fractures.',
citationNo: 2,
},
{
title: 'Reduced risk of all-cause mortality',
evidence: 'Regular physical activity is associated with a lower risk of all-cause mortality.',
citationNo: 4,
},
{
title: 'Reduced risk of cardiovascular diseases',
evidence: 'Exercise reduces the risk of cardiovascular diseases, including heart disease and stroke.',
citationNo: 4,
},
{
title: 'Improved cognition',
evidence: 'Physical activity is linked to better cognitive function and a reduced risk of cognitive decline and dementia.',
Expand Down
32 changes: 16 additions & 16 deletions src/MainStudy/pass1b06AssayTissueTable.jsx
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Expand Up @@ -33,8 +33,8 @@ function Pass1b06AssayTissueTable() {
</tbody>
</table>
</div>
{/* Render metabolomics-targeted assay table */}
<h4 className="mt-4">Targeted Metabolomics</h4>
{/* Render transcriptomics assay table */}
<h4 className="mt-4">Transcriptomics</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
Expand All @@ -44,11 +44,11 @@ function Pass1b06AssayTissueTable() {
</tr>
</thead>
<tbody>
{pass1b06AssayByOmicJson['metabolomics-targeted'].map((item) => (
{pass1b06AssayByOmicJson['transcriptomics'].map((item) => (
<tr key={item.id}>
<td>{item.assay}</td>
<td>
{pass1b06AssayTissueJson['metabolomics-targeted'][item.id].map((tissue) => (
{pass1b06AssayTissueJson['transcriptomics'][item.id].map((tissue) => (
<span key={`${item.id}-${tissue}`} className="badge badge-pill badge-light mr-1">
{capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))}
</span>
Expand All @@ -59,8 +59,8 @@ function Pass1b06AssayTissueTable() {
</tbody>
</table>
</div>
{/* Render metabolomics-untargeted assay table */}
<h4 className="mt-4">Untargeted Metabolomics</h4>
{/* Render proteomics-untargeted assay table */}
<h4 className="mt-4">Untargeted Proteomics</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
Expand All @@ -70,11 +70,11 @@ function Pass1b06AssayTissueTable() {
</tr>
</thead>
<tbody>
{pass1b06AssayByOmicJson['metabolomics-untargeted'].map((item) => (
{pass1b06AssayByOmicJson['proteomics-untargeted'].map((item) => (
<tr key={item.id}>
<td>{item.assay}</td>
<td>
{pass1b06AssayTissueJson['metabolomics-untargeted'][item.id].map((tissue) => (
{pass1b06AssayTissueJson['proteomics-untargeted'][item.id].map((tissue) => (
<span key={`${item.id}-${tissue}`} className="badge badge-pill badge-light mr-1">
{capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))}
</span>
Expand All @@ -85,8 +85,8 @@ function Pass1b06AssayTissueTable() {
</tbody>
</table>
</div>
{/* Render proteomics-untargeted assay table */}
<h4 className="mt-4">Untargeted Proteomics</h4>
{/* Render metabolomics-untargeted assay table */}
<h4 className="mt-4">Untargeted Metabolomics</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
Expand All @@ -96,11 +96,11 @@ function Pass1b06AssayTissueTable() {
</tr>
</thead>
<tbody>
{pass1b06AssayByOmicJson['proteomics-untargeted'].map((item) => (
{pass1b06AssayByOmicJson['metabolomics-untargeted'].map((item) => (
<tr key={item.id}>
<td>{item.assay}</td>
<td>
{pass1b06AssayTissueJson['proteomics-untargeted'][item.id].map((tissue) => (
{pass1b06AssayTissueJson['metabolomics-untargeted'][item.id].map((tissue) => (
<span key={`${item.id}-${tissue}`} className="badge badge-pill badge-light mr-1">
{capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))}
</span>
Expand All @@ -111,8 +111,8 @@ function Pass1b06AssayTissueTable() {
</tbody>
</table>
</div>
{/* Render transcriptomics assay table */}
<h4 className="mt-4">Transcriptomics</h4>
{/* Render metabolomics-targeted assay table */}
<h4 className="mt-4">Targeted Metabolomics</h4>
<div className="table-responsive">
<table className="table table-bordered">
<thead>
Expand All @@ -122,11 +122,11 @@ function Pass1b06AssayTissueTable() {
</tr>
</thead>
<tbody>
{pass1b06AssayByOmicJson['transcriptomics'].map((item) => (
{pass1b06AssayByOmicJson['metabolomics-targeted'].map((item) => (
<tr key={item.id}>
<td>{item.assay}</td>
<td>
{pass1b06AssayTissueJson['transcriptomics'][item.id].map((tissue) => (
{pass1b06AssayTissueJson['metabolomics-targeted'][item.id].map((tissue) => (
<span key={`${item.id}-${tissue}`} className="badge badge-pill badge-light mr-1">
{capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))}
</span>
Expand Down
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