Updates to emphasize the Human Reference Atlas

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-Changelog for the Common Coordinate Framework (CCF) User Interfaces
+Changelog for the Human Reference Atlas (HRA) User Interfaces
 
 ## 3.6.0 - 2022-10-15
 

README.md

@@ -1,4 +1,4 @@
-# Common Coordinate Framework (CCF) - User Interfaces
+# Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User Interfaces
 
 [![Production CDN by JSDelivr](https://data.jsdelivr.com/v1/package/gh/hubmapconsortium/ccf-ui/badge)](https://www.jsdelivr.com/package/gh/hubmapconsortium/ccf-ui)
 [![Tests](https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml/badge.svg?branch=develop)](https://github.com/hubmapconsortium/ccf-ui/actions/workflows/tests.yml)
@@ -37,7 +37,7 @@ This repository is a [monorepo](https://en.wikipedia.org/wiki/Monorepo) (multipl
 
 ## Background and More Information
 
-For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at <https://hubmapconsortium.github.io/ccf/>.
+For more information about the Human Reference Atlas (HRA) and the Common Coordinate Framework (CCF), see the HuBMAP HRA Portal at <https://humanatlas.io>.
 
 ## Change Log
 

docs/index.html

@@ -64,7 +64,7 @@
       <div class="content getting-started">
         <div class="content-data">
 
-          <h1 id="common-coordinate-framework-ccf---user-interfaces">Common Coordinate Framework (CCF) - User
+          <h1 id="common-coordinate-framework-ccf---user-interfaces">Human Reference Atlas (HRA) and Common Coordinate Framework (CCF) - User
             Interfaces - API Documentation</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"
@@ -131,8 +131,8 @@ <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>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="https://github.com/hubmapconsortium/ccf-ui/blob/main/CHANGELOG.md">ChangeLog</a> for the latest developments.</p>

projects/ccf-eui/src/assets/docs/README.md

@@ -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>.
 

projects/ccf-organ-info/src/app/modules/link-cards/link-cards.component.html

@@ -9,7 +9,7 @@
 </div>
 
 <div class="deep-dive-section" gaCategory="deep-dive">
-  <div class="title">Common Coordinate Framework (CCF) Deep Dive</div>
+  <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)">{{

projects/ccf-organ-info/src/app/modules/link-cards/link-cards.component.ts

@@ -15,12 +15,12 @@ interface LinkCard {
 export class LinkCardsComponent {
   linkCards: LinkCard[] = [
     {
-      body: 'Add tissue blocks using the CCF Registration User Interface (RUI).',
+      body: 'Add tissue blocks using the HRA Registration User Interface (RUI).',
       buttonTitle: 'Register Tissue',
       buttonUrl: 'https://hubmapconsortium.github.io/ccf-ui/rui/'
     },
     {
-      body: 'Explore tissue sections in tissue blocks with the CCF Exploration User Interface (EUI).',
+      body: 'Explore tissue sections in tissue blocks with the HRA Exploration User Interface (EUI).',
       buttonTitle: 'Explore Tissue',
       buttonUrl: 'https://portal.hubmapconsortium.org/ccf-eui'
     },
@@ -34,8 +34,8 @@ export class LinkCardsComponent {
   deepDives: LinkCard[] = [
     {
       body: '',
-      buttonTitle: 'CCF Portal',
-      buttonUrl: 'https://hubmapconsortium.github.io/ccf/'
+      buttonTitle: 'HRA Portal',
+      buttonUrl: 'https://humanatlas.io'
     },
     {
       body: '',
@@ -45,7 +45,7 @@ export class LinkCardsComponent {
     {
       body: '',
       buttonTitle: 'Paper',
-      buttonUrl: 'https://www.biorxiv.org/content/10.1101/2021.05.31.446440v2'
+      buttonUrl: 'https://www.nature.com/articles/s41556-021-00788-6'
     }
   ];
 

projects/ccf-rui/src/assets/docs/README.md

@@ -11,8 +11,8 @@
 
 # About
 
-This Registration User Interface (RUI) supports the registration of three-dimensional (3D) tissue blocks within 3D reference organs. A first beta of the CCF RUI became available in October 2020. The CCF RUI specification is available here, 3D reference organs are freely available on the CCF Portal, the ontology can be found on BioPortal, and the code is availble on GitHub.
-The registration data is used in current versions of the Common Coordinate Framework (CCF, see CCF Portal for details) and the CCF Exploration User Interface (EUI) developed within HuBMAP.
+This Registration User Interface (RUI) supports the registration of three-dimensional (3D) tissue blocks within 3D reference organs. A first beta of the CCF RUI became available in October 2020. The CCF RUI specification is available here, 3D reference organs are freely available on the HRA Portal, the ontology can be found on BioPortal, and the code is availble on GitHub.
+The registration data is used in current versions of the Human Reference Atlas (HRA, see HRA Portal for details) and the HRA Exploration User Interface (EUI) developed within HuBMAP.
 
 # Standard Operating Procedure (SOP)