Merge pull request #220 from TheJacksonLaboratory/release/1.8.2

Release/1.8.2

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "hpo-web",
-  "version": "1.8.1",
+  "version": "1.8.2",
   "license": "MIT",
   "scripts": {
     "ng": "ng",

client/src/app/static/community/community.component.html

@@ -96,7 +96,6 @@ <h3 class="member-name">
       </mat-tab>
       <mat-tab label="Users">
         <p>	The following list provides an overview of the groups who are currently using HPO. If you notice an omission, please contact us.
-          The HPO is also a key component of the <a href="http://monarchinitiative.org/" target="__blank">Monarch Initiative</a>.
         </p>
         <ul>
           <li><a href="https://www.genome.gov/27544402/the-undiagnosed-diseases-program/" target="__blank">NIH Undiagnosed disease program (UDP)</a>. See also this paper that describes
@@ -142,7 +141,15 @@ <h3>Commerical entitites</h3>
             <li><a href="http://www.biodiscovery.com/nxclinical/" target="_blank">BioDiscovery’s NxClinical</a></li>
             <li>Diploid: Diagnosing rare diseases: <a href="http://www.diploid.com/moon" target="__blank"> Moon</a></li>
             <li><a href="https://www.centogene.com/" target="__blank">Centogene</a></li>
-            <li><a href="http://simulconsult.com/index.html" target="__blank">SimulConsult</a></li>
+            <li><a href="http://simulconsult.com/index.html" target="__blank">SimulConsult</a>
+              <ul>
+                <li>Michael M. Segal</li>
+                <li>Ayman W. El-Hattab</li>
+                <li>Nicole Nadeau</li>
+                <li>Kristina Brumme</li>
+                <li>Robert Sundel</li>
+              </ul>
+            </li>
             <li><a href="https://www.fabricgenomics.com/" target="_blank">Fabric Genomics</a></li>
             <li><a href="http://resources.qiagenbioinformatics.com/white-papers/IVA_white_paper_FINAL.pdf">Qiagen</a></li>
             <li><a href="https://track.health/">Track.Health</a></li>

client/src/app/static/home/home.component.html

@@ -27,7 +27,7 @@ <h2>The Human Phenotype Ontology</h2>
           projects</a> in the <a href=" https://www.ga4gh.org/" target="__blank">Global Alliance for Genomics and
           Health</a> (GA4GH) <a href="https://www.ga4gh.org/howwework/strategic-roadmap.html">strategic roadmap</a>.</p>
       <div class="button-wrapper">
-        <a mat-raised-button routerLink="help/introduction" class="mat-btn">Learn More About HPO</a>
+        <a mat-raised-button routerLink="about" class="mat-btn">Learn More About HPO</a>
       </div>
     </div>
   </div>
@@ -109,15 +109,12 @@ <h2 class="title">Profile Search</h2>
 </div>
 <br><br>
 <div fxLayout="row" fxLayoutAlign="space-between center">
-  <div class="phenopacket-banner mat-elevation-z1" fxFlex="80" fxFlexOffset="10">
-    <a href="https://www.ga4gh.org/news/phenopackets-v2-expands-utility-to-provide-a-more-complete-medical-picture/"
-       target="_blank">
+  <div class="phenopacket-banner mat-elevation-z1" fxFlex="80" fxFlexOffset="10" routerLink="resources/phenopacket">
     <img class="phenopacket-logo" src="assets/phenopackets.png"/>
     <div class="description" fxHide.lt-sm>
       <h4>Phenopackets</h4>
       <span class="text">A Global Alliance for Genomics and Health (GA4GH) international standard for phenotypic data exchange.</span>
     </div>
-    </a>
   </div>
 </div>
 <br><br>

client/src/app/static/resources/phenopacket/phenopacket.component.html

@@ -0,0 +1,24 @@
+<div class="container phenopacket">
+  <h1 class="center pageTitle">Global Alliance for Genomic Health Phenopacket</h1>
+
+  <p>The Monarch Initiative, the consortium that includes the HPO team, has led the development of the
+    the <a target="__blank" href="https://phenopacket-schema.readthedocs.io/en/latest/">Phenopacket Schema</a>
+    for the <a target="__blank" href="https://www.ga4gh.org/">Global Alliance for Genomics and Health (GA4GH)</a>.
+    The Phenopacket Schema was approved by the GA4GH in 2022 and additional certified by the International Standards
+    Organization (ISO) as <a href="https://www.iso.org/standard/79991.html"  target="__blank">ISO 4454:2022
+      Genomics informatics — Phenopackets: A format for phenotypic data exchange</a>.</p>
+
+  <p>More information is available in <a href="https://pubmed.ncbi.nlm.nih.gov/35705716/"  target="__blank">Jacobsen JOB, et al. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. 2022 Jun;40(6):817-820.</a>.
+
+  <p>A Phenopacket characterizes an individual person or biosample, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. The Phenopacket schema supports the FAIR principles (findable, accessible, interoperable, and reusable), and computability. Specifically, Phenopackets are designed to be both human and machine-interpretable, enabling computing operations and validation on the basis of defined relationships between diagnoses, lab measurements, and genotypic information.</p>
+
+  <p>The Phenopacket schema enables comparison of sets of phenotypic attributes from individual patients. Such comparisons can aid in diagnosis and facilitate patient classification and stratification for identifying new diseases and treatments. The Phenopacket schema is designed to support interoperability between people, organizations, and systems that comprise the worldwide effort to understand human disease. The structure of the information in a phenopacket was designed for integration within clinical laboratories, journals, data repositories, patient registries, electronic health records (EHRs), and knowledge bases. Increasing the volume of computable data across a diversity of systems will support global disease analysis by integrating genotype, phenotype, and other multi-modal data for precision health applications.</p>
+    <figure class="phenopacket-figure">
+      <img alt="GA4GH Phenopacket" src="https://onlinelibrary.wiley.com/cms/asset/1cc0a141-da65-45a3-b7b0-6316b7b02069/ggn2202200016-fig-0002-m.jpg"/>
+      <figcaption class="phenopacket-figure-caption">Phenopacket Schema overview. The GA4GH Phenopacket Schema is a hierarchical structure that consists of two required fields, ID and MetaData, as well as eight optional fields, Individual, Disease, Interpretation, Biosample, PhenotypicFeature, Measurement, MedicalAction, and files.</figcaption>
+    </figure>
+  <p>
+    The Phenopacket provides a standardized way of reporting HPO terms and providing additional context. A detailed introduction in how to represent clinical data as a phenopacket is provided in <a target="__blank" href="https://onlinelibrary.wiley.com/doi/full/10.1002/ggn2.202200016">Ladewig et al., GA4GH Phenopackets: A Practical Introduction, Advanced Genetics 2022</a>.
+  </p>
+</div>
+

client/src/app/static/resources/phenopacket/phenopacket.component.scss

@@ -0,0 +1,22 @@
+.phenopacket {
+  & .phenopacket-figure {
+    margin: 0 auto;
+    text-align: center;
+
+    & .phenopacket-figure-caption {
+      margin: inherit;
+      text-align: left;
+      width: 600px
+    }
+
+    & img {
+      width: 600px;
+    }
+  }
+
+  @media screen and (max-width: 640px) {
+    .phenopacket-figure {
+      display: none;
+    }
+  }
+}

client/src/app/static/resources/phenopacket/phenopacket.component.spec.ts

@@ -0,0 +1,25 @@
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { PhenopacketComponent } from './phenopacket.component';
+
+describe('PhenopacketComponent', () => {
+  let component: PhenopacketComponent;
+  let fixture: ComponentFixture<PhenopacketComponent>;
+
+  beforeEach(async(() => {
+    TestBed.configureTestingModule({
+      declarations: [ PhenopacketComponent ],
+    })
+    .compileComponents();
+  }));
+
+  beforeEach(() => {
+    fixture = TestBed.createComponent(PhenopacketComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should create', () => {
+    expect(component).toBeTruthy();
+  });
+});

client/src/app/static/resources/phenopacket/phenopacket.component.ts

@@ -0,0 +1,12 @@
+import { Component, OnInit } from '@angular/core';
+
+
+@Component({
+  selector: 'app-phenopacket',
+  templateUrl: './phenopacket.component.html',
+  styleUrls: ['./phenopacket.component.scss']
+})
+export class PhenopacketComponent implements OnInit {
+  constructor() { }
+  ngOnInit() { }
+}

client/src/app/static/resources/resources-routing.module.ts

@@ -4,6 +4,7 @@ import {ClinicianGuideComponent} from './clinician-guide/clinician-guide.compone
 import {ContributingComponent} from './collaboration/contributing.component';
 import {FaqComponent} from './faq/faq.component';
 import {PublicationsComponent} from './publications/publications.component';
+import { PhenopacketComponent } from './phenopacket/phenopacket.component';
 
 
 const resourcesRoutes: Routes = [
@@ -13,7 +14,8 @@ const resourcesRoutes: Routes = [
       {path: 'clinician-guide', component: ClinicianGuideComponent},
       {path: 'contributing', component: ContributingComponent},
       {path: 'faq', component: FaqComponent},
-      {path: 'publications', component: PublicationsComponent}
+      {path: 'publications', component: PublicationsComponent},
+      {path: 'phenopacket', component: PhenopacketComponent}
     ]
   },
 ];

client/src/app/static/resources/resources.module.ts

@@ -8,6 +8,7 @@ import {ContributingComponent} from './collaboration/contributing.component';
 import {FaqComponent} from './faq/faq.component';
 import {PublicationsService} from './publications/publications.service';
 import {PublicationsComponent} from './publications/publications.component';
+import { PhenopacketComponent } from './phenopacket/phenopacket.component';
 
 
 @NgModule({
@@ -19,7 +20,7 @@ import {PublicationsComponent} from './publications/publications.component';
     ReactiveFormsModule
   ],
   declarations: [
-    ClinicianGuideComponent, ContributingComponent, FaqComponent, PublicationsComponent
+    ClinicianGuideComponent, ContributingComponent, FaqComponent, PublicationsComponent, PhenopacketComponent
   ],
   providers: [PublicationsService]
 })

server/build.gradle

@@ -16,7 +16,7 @@ buildscript {
   }
 }
 
-version "1.17.18"
+version "1.17.19"
 group "hpo.api"
 
 apply plugin: "idea"