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8 changes: 4 additions & 4 deletions assets/docs/README.md
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Expand Up @@ -20,18 +20,18 @@ technologies, computational tools, and generate foundational tissue maps in orde
construction of an atlas of the human body at single-cell resolution for understanding the relationship
between tissue organization and function.

# Common Coordinate Framework (CCF)
# Human Reference Atlas (HRA) and Common Coordinate Framework (CCF)

The HuBMAP common coordinate framework (CCF) is under active development. It aims to semantically annotate and
The Human Reference Atlas (HRA) is under active development. It aims to semantically annotate and
spatially index HuBMAP data for efficient spatial and semantic search, browsing, and filtering. The CCF v1.0.0
became available in June 2020. The CCF Ontology is available as an <a rel="noopener noreferrer"
href="http://purl.org/ccf/latest/ccf.owl" target="_blank">OWL file</a>,
on <a rel="noopener noreferrer" href="https://github.com/hubmapconsortium/hubmap-ontology"
target="_blank">GitHub</a>, and
on <a rel="noopener noreferrer" href="https://bioportal.bioontology.org/ontologies/CCF"
target="_blank">BioPortal</a>. For
documentation, see <a rel="noopener noreferrer" href="https://hubmapconsortium.github.io/ccf/"
target="_blank">CCF Portal</a> and preprint of CCF
documentation, see <a rel="noopener noreferrer" href="https://humanatlas.io"
target="_blank">HRA Portal</a> and preprint of CCF
Ontology publication on <a rel="noopener noreferrer" href="https://arxiv.org/abs/2007.14474 "
target="_blank">arxiv</a>.

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2 changes: 1 addition & 1 deletion docs/ccf-api/changelog.html
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<div class="content-data">

<h1 id="changelog">Changelog</h1>
<p>Changelog for the Common Coordinate Framework (CCF) User Interfaces</p>
<p>Changelog for the Human Reference Atlas (HRA) User Interfaces</p>
<h2 id="360---2022-10-15">3.6.0 - 2022-10-15</h2>
<h3 id="added-in-360">Added in 3.6.0.</h3>
<ul>
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4 changes: 2 additions & 2 deletions docs/ccf-api/index.html
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<div class="content getting-started">
<div class="content-data">

<h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User Interfaces</h1>
<h1 id="human-reference-atlas-hra-and-common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces</h1>
<p><a href="https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui"><img src="https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge" alt="Production CDN by JSDelivr" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml"><img src="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop" alt="Tests" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/commits/develop"><img src="https://img.shields.io/github/last-commit/hubmapconsortium/ccf-ui.svg" alt="GitHub last commit" class="img-responsive"></a>
Expand Down Expand Up @@ -76,7 +76,7 @@ <h2 id="website-links">Website Links</h2>
</li>
</ul>
<h2 id="background-and-more-information">Background and More Information</h2>
<p>For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <a href="https://hubmapconsortium.github.io/ccf/">https://hubmapconsortium.github.io/ccf/</a>.</p>
<p>For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <a href="https://humanatlas.io">https://humanatlas.io</a>.</p>
<h2 id="change-log">Change Log</h2>
<p>See the <a href="CHANGELOG.md">ChangeLog</a> for the latest developments.</p>
<h2 id="credits">Credits</h2>
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4 changes: 2 additions & 2 deletions docs/ccf-api/js/search/search_index.js
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2 changes: 1 addition & 1 deletion docs/ccf-body-ui-wc/changelog.html
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<div class="content-data">

<h1 id="changelog">Changelog</h1>
<p>Changelog for the Common Coordinate Framework (CCF) User Interfaces</p>
<p>Changelog for the Human Reference Atlas (HRA) User Interfaces</p>
<h2 id="360---2022-10-15">3.6.0 - 2022-10-15</h2>
<h3 id="added-in-360">Added in 3.6.0.</h3>
<ul>
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4 changes: 2 additions & 2 deletions docs/ccf-body-ui-wc/index.html
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<div class="content getting-started">
<div class="content-data">

<h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User Interfaces</h1>
<h1 id="human-reference-atlas-hra-and-common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces</h1>
<p><a href="https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui"><img src="https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge" alt="Production CDN by JSDelivr" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml"><img src="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop" alt="Tests" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/commits/develop"><img src="https://img.shields.io/github/last-commit/hubmapconsortium/ccf-ui.svg" alt="GitHub last commit" class="img-responsive"></a>
Expand Down Expand Up @@ -76,7 +76,7 @@ <h2 id="website-links">Website Links</h2>
</li>
</ul>
<h2 id="background-and-more-information">Background and More Information</h2>
<p>For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <a href="https://hubmapconsortium.github.io/ccf/">https://hubmapconsortium.github.io/ccf/</a>.</p>
<p>For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <a href="https://humanatlas.io">https://humanatlas.io</a>.</p>
<h2 id="change-log">Change Log</h2>
<p>See the <a href="CHANGELOG.md">ChangeLog</a> for the latest developments.</p>
<h2 id="credits">Credits</h2>
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2 changes: 1 addition & 1 deletion docs/ccf-body-ui/changelog.html
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<div class="content-data">

<h1 id="changelog">Changelog</h1>
<p>Changelog for the Common Coordinate Framework (CCF) User Interfaces</p>
<p>Changelog for the Human Reference Atlas (HRA) User Interfaces</p>
<h2 id="360---2022-10-15">3.6.0 - 2022-10-15</h2>
<h3 id="added-in-360">Added in 3.6.0.</h3>
<ul>
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4 changes: 2 additions & 2 deletions docs/ccf-body-ui/index.html
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<div class="content getting-started">
<div class="content-data">

<h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User Interfaces</h1>
<h1 id="human-reference-atlas-hra-and-common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces</h1>
<p><a href="https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui"><img src="https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge" alt="Production CDN by JSDelivr" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml"><img src="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop" alt="Tests" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/commits/develop"><img src="https://img.shields.io/github/last-commit/hubmapconsortium/ccf-ui.svg" alt="GitHub last commit" class="img-responsive"></a>
Expand Down Expand Up @@ -76,7 +76,7 @@ <h2 id="website-links">Website Links</h2>
</li>
</ul>
<h2 id="background-and-more-information">Background and More Information</h2>
<p>For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <a href="https://hubmapconsortium.github.io/ccf/">https://hubmapconsortium.github.io/ccf/</a>.</p>
<p>For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <a href="https://humanatlas.io">https://humanatlas.io</a>.</p>
<h2 id="change-log">Change Log</h2>
<p>See the <a href="CHANGELOG.md">ChangeLog</a> for the latest developments.</p>
<h2 id="credits">Credits</h2>
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2 changes: 1 addition & 1 deletion docs/ccf-database/changelog.html
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<div class="content-data">

<h1 id="changelog">Changelog</h1>
<p>Changelog for the Common Coordinate Framework (CCF) User Interfaces</p>
<p>Changelog for the Human Reference Atlas (HRA) User Interfaces</p>
<h2 id="360---2022-10-15">3.6.0 - 2022-10-15</h2>
<h3 id="added-in-360">Added in 3.6.0.</h3>
<ul>
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4 changes: 2 additions & 2 deletions docs/ccf-database/index.html
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<div class="content getting-started">
<div class="content-data">

<h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User Interfaces</h1>
<h1 id="human-reference-atlas-hra-and-common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces</h1>
<p><a href="https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui"><img src="https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge" alt="Production CDN by JSDelivr" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml"><img src="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop" alt="Tests" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/commits/develop"><img src="https://img.shields.io/github/last-commit/hubmapconsortium/ccf-ui.svg" alt="GitHub last commit" class="img-responsive"></a>
Expand Down Expand Up @@ -76,7 +76,7 @@ <h2 id="website-links">Website Links</h2>
</li>
</ul>
<h2 id="background-and-more-information">Background and More Information</h2>
<p>For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <a href="https://hubmapconsortium.github.io/ccf/">https://hubmapconsortium.github.io/ccf/</a>.</p>
<p>For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <a href="https://humanatlas.io">https://humanatlas.io</a>.</p>
<h2 id="change-log">Change Log</h2>
<p>See the <a href="CHANGELOG.md">ChangeLog</a> for the latest developments.</p>
<h2 id="credits">Credits</h2>
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2 changes: 1 addition & 1 deletion docs/ccf-eui/changelog.html
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<div class="content-data">

<h1 id="changelog">Changelog</h1>
<p>Changelog for the Common Coordinate Framework (CCF) User Interfaces</p>
<p>Changelog for the Human Reference Atlas (HRA) User Interfaces</p>
<h2 id="360---2022-10-15">3.6.0 - 2022-10-15</h2>
<h3 id="added-in-360">Added in 3.6.0.</h3>
<ul>
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4 changes: 2 additions & 2 deletions docs/ccf-eui/index.html
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<div class="content getting-started">
<div class="content-data">

<h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User Interfaces</h1>
<h1 id="human-reference-atlas-hra-and-common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces</h1>
<p><a href="https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui"><img src="https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge" alt="Production CDN by JSDelivr" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml"><img src="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop" alt="Tests" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/commits/develop"><img src="https://img.shields.io/github/last-commit/hubmapconsortium/ccf-ui.svg" alt="GitHub last commit" class="img-responsive"></a>
Expand Down Expand Up @@ -76,7 +76,7 @@ <h2 id="website-links">Website Links</h2>
</li>
</ul>
<h2 id="background-and-more-information">Background and More Information</h2>
<p>For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <a href="https://hubmapconsortium.github.io/ccf/">https://hubmapconsortium.github.io/ccf/</a>.</p>
<p>For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <a href="https://humanatlas.io">https://humanatlas.io</a>.</p>
<h2 id="change-log">Change Log</h2>
<p>See the <a href="CHANGELOG.md">ChangeLog</a> for the latest developments.</p>
<h2 id="credits">Credits</h2>
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2 changes: 1 addition & 1 deletion docs/ccf-organ-info/changelog.html
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<div class="content-data">

<h1 id="changelog">Changelog</h1>
<p>Changelog for the Common Coordinate Framework (CCF) User Interfaces</p>
<p>Changelog for the Human Reference Atlas (HRA) User Interfaces</p>
<h2 id="360---2022-10-15">3.6.0 - 2022-10-15</h2>
<h3 id="added-in-360">Added in 3.6.0.</h3>
<ul>
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24 changes: 12 additions & 12 deletions docs/ccf-organ-info/components/LinkCardsComponent.html
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Expand Up @@ -270,8 +270,8 @@ <h3 id="inputs">
<i>Default value : </i><code>[
{
body: &#x27;&#x27;,
buttonTitle: &#x27;CCF Portal&#x27;,
buttonUrl: &#x27;https://hubmapconsortium.github.io/ccf/&#x27;
buttonTitle: &#x27;HRA Portal&#x27;,
buttonUrl: &#x27;https://humanatlas.io&#x27;
},
{
body: &#x27;&#x27;,
Expand All @@ -281,7 +281,7 @@ <h3 id="inputs">
{
body: &#x27;&#x27;,
buttonTitle: &#x27;Paper&#x27;,
buttonUrl: &#x27;https://www.biorxiv.org/content/10.1101/2021.05.31.446440v2&#x27;
buttonUrl: &#x27;https://www.nature.com/articles/s41556-021-00788-6&#x27;
}
]</code>
</td>
Expand Down Expand Up @@ -316,12 +316,12 @@ <h3 id="inputs">
<td class="col-md-4">
<i>Default value : </i><code>[
{
body: &#x27;Add tissue blocks using the CCF Registration User Interface (RUI).&#x27;,
body: &#x27;Add tissue blocks using the HRA Registration User Interface (RUI).&#x27;,
buttonTitle: &#x27;Register Tissue&#x27;,
buttonUrl: &#x27;https://hubmapconsortium.github.io/ccf-ui/rui/&#x27;
},
{
body: &#x27;Explore tissue sections in tissue blocks with the CCF Exploration User Interface (EUI).&#x27;,
body: &#x27;Explore tissue sections in tissue blocks with the HRA Exploration User Interface (EUI).&#x27;,
buttonTitle: &#x27;Explore Tissue&#x27;,
buttonUrl: &#x27;https://portal.hubmapconsortium.org/ccf-eui&#x27;
},
Expand Down Expand Up @@ -365,12 +365,12 @@ <h3 id="inputs">
export class LinkCardsComponent {
linkCards: LinkCard[] &#x3D; [
{
body: &#x27;Add tissue blocks using the CCF Registration User Interface (RUI).&#x27;,
body: &#x27;Add tissue blocks using the HRA Registration User Interface (RUI).&#x27;,
buttonTitle: &#x27;Register Tissue&#x27;,
buttonUrl: &#x27;https://hubmapconsortium.github.io/ccf-ui/rui/&#x27;
},
{
body: &#x27;Explore tissue sections in tissue blocks with the CCF Exploration User Interface (EUI).&#x27;,
body: &#x27;Explore tissue sections in tissue blocks with the HRA Exploration User Interface (EUI).&#x27;,
buttonTitle: &#x27;Explore Tissue&#x27;,
buttonUrl: &#x27;https://portal.hubmapconsortium.org/ccf-eui&#x27;
},
Expand All @@ -384,8 +384,8 @@ <h3 id="inputs">
deepDives: LinkCard[] &#x3D; [
{
body: &#x27;&#x27;,
buttonTitle: &#x27;CCF Portal&#x27;,
buttonUrl: &#x27;https://hubmapconsortium.github.io/ccf/&#x27;
buttonTitle: &#x27;HRA Portal&#x27;,
buttonUrl: &#x27;https://humanatlas.io&#x27;
},
{
body: &#x27;&#x27;,
Expand All @@ -395,7 +395,7 @@ <h3 id="inputs">
{
body: &#x27;&#x27;,
buttonTitle: &#x27;Paper&#x27;,
buttonUrl: &#x27;https://www.biorxiv.org/content/10.1101/2021.05.31.446440v2&#x27;
buttonUrl: &#x27;https://www.nature.com/articles/s41556-021-00788-6&#x27;
}
];

Expand All @@ -418,7 +418,7 @@ <h3 id="inputs">
&lt;/div&gt;

&lt;div class&#x3D;&quot;deep-dive-section&quot; gaCategory&#x3D;&quot;deep-dive&quot;&gt;
&lt;div class&#x3D;&quot;title&quot;&gt;Common Coordinate Framework (CCF) Deep Dive&lt;/div&gt;
&lt;div class&#x3D;&quot;title&quot;&gt;Human Reference Atlas (HRA) Deep Dive&lt;/div&gt;
&lt;div class&#x3D;&quot;button-container&quot;&gt;
&lt;div *ngFor&#x3D;&quot;let button of deepDives&quot; class&#x3D;&quot;btn-outline btn&quot; gaEvent&#x3D;&quot;visit-link&quot; [gaLabel]&#x3D;&quot;button.buttonUrl&quot;
(click)&#x3D;&quot;goToURL(button.buttonUrl)&quot;&gt;{{
Expand Down Expand Up @@ -535,7 +535,7 @@ <h3 id="inputs">
<script src="../js/libs/htmlparser.js"></script>
<script src="../js/libs/deep-iterator.js"></script>
<script>
var COMPONENT_TEMPLATE = '<div><div class="link-cards-container" gaCategory="link-cards"> <div class="link-card" *ngFor="let card of linkCards"> <div class="link-card-content"> <div class="body">{{ card.body }}</div> <div class="link-button btn" gaEvent="visit-link" [gaLabel]="card.buttonUrl" (click)="goToURL(card.buttonUrl)"> {{ card.buttonTitle }}</div> </div> </div></div><div class="deep-dive-section" gaCategory="deep-dive"> <div class="title">Common Coordinate Framework (CCF) Deep Dive</div> <div class="button-container"> <div *ngFor="let button of deepDives" class="btn-outline btn" gaEvent="visit-link" [gaLabel]="button.buttonUrl" (click)="goToURL(button.buttonUrl)">{{ button.buttonTitle }}</div> </div></div></div>'
var COMPONENT_TEMPLATE = '<div><div class="link-cards-container" gaCategory="link-cards"> <div class="link-card" *ngFor="let card of linkCards"> <div class="link-card-content"> <div class="body">{{ card.body }}</div> <div class="link-button btn" gaEvent="visit-link" [gaLabel]="card.buttonUrl" (click)="goToURL(card.buttonUrl)"> {{ card.buttonTitle }}</div> </div> </div></div><div class="deep-dive-section" gaCategory="deep-dive"> <div class="title">Human Reference Atlas (HRA) Deep Dive</div> <div class="button-container"> <div *ngFor="let button of deepDives" class="btn-outline btn" gaEvent="visit-link" [gaLabel]="button.buttonUrl" (click)="goToURL(button.buttonUrl)">{{ button.buttonTitle }}</div> </div></div></div>'
var COMPONENTS = [{'name': 'AppComponent', 'selector': 'ccf-root'},{'name': 'AppWebComponent', 'selector': 'ccf-root-wc'},{'name': 'LinkCardsComponent', 'selector': 'ccf-link-cards'},{'name': 'OrganComponent', 'selector': 'ccf-organ'},{'name': 'SlideToggleComponent', 'selector': 'ccf-slide-toggle'},{'name': 'StatsListComponent', 'selector': 'ccf-stats-list'}];
var DIRECTIVES = [];
var ACTUAL_COMPONENT = {'name': 'LinkCardsComponent'};
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<div class="content getting-started">
<div class="content-data">

<h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User Interfaces</h1>
<h1 id="human-reference-atlas-hra-and-common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces</h1>
<p><a href="https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui"><img src="https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge" alt="Production CDN by JSDelivr" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml"><img src="https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop" alt="Tests" class="img-responsive"></a>
<a href="https://github.com/hubmapconsortium/ccf-ui/commits/develop"><img src="https://img.shields.io/github/last-commit/hubmapconsortium/ccf-ui.svg" alt="GitHub last commit" class="img-responsive"></a>
Expand Down Expand Up @@ -76,7 +76,7 @@ <h2 id="website-links">Website Links</h2>
</li>
</ul>
<h2 id="background-and-more-information">Background and More Information</h2>
<p>For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <a href="https://hubmapconsortium.github.io/ccf/">https://hubmapconsortium.github.io/ccf/</a>.</p>
<p>For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <a href="https://humanatlas.io">https://humanatlas.io</a>.</p>
<h2 id="change-log">Change Log</h2>
<p>See the <a href="CHANGELOG.md">ChangeLog</a> for the latest developments.</p>
<h2 id="credits">Credits</h2>
Expand Down
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