Merge pull request #17 from ScilifelabDataCentre/NPC_add

update SCD format, add NPC collection
ScilifelabDataCentre · May 10, 2023 · e990cb3 · e990cb3
2 parents 4667ee6 + 0eb417c
commit e990cb3
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Showing 11 changed files with 260 additions and 52 deletions.
diff --git a/config.yaml b/config.yaml
@@ -3,7 +3,7 @@ languageCode: "en-us"
 title: "The Swedish COVID-19 Sample Collection Database"
 params:
   title: "The Swedish COVID-19 Sample Collection Database"
-  description: "The Swedish COVID-19 Sample Collection Database, part of the COVID-19 Data Portal Sweden"
+  description: "The Swedish COVID-19 Sample Collection Database, part of the Swedish COVID-19 and Pandemic Preparedness Portal"
 markup:
   goldmark:
     renderer:

diff --git a/content/collections/NAT/1.md b/content/collections/NAT/1.md
@@ -0,0 +1,38 @@
+---
+id: c19dp:collection:SE_NAT_1
+biobank: c19dp:biobank:SE_NAT
+name: National sample collection stored at National Pandemic Center (NPC)
+acronym:
+parent_collection:
+local_id: N/A
+bbmri_id:
+country: SE
+description: Personnel within Sweden's regions have worked intensively with both sample collection and handling of COVID-19-related samples. A large amount of samples are thereafter sequenced at the National Pandemic Center (NPC), Karolinska Institutet (KI; Stockholm), which also results in an extensive sample collection stored at the NPC. The regions are legally responsible for "their" subset of the sample collection. In theory, the sample collection at NPC is an enormous resource for research.
+website_url:
+bioresource_reference:
+ethics_id: N/A
+sampling_startdate: 2020-03-01T11:00:00+0000
+sampling_enddate:
+storage_duration:
+collection_type: [Hospital, Disease specific, Sample]
+collection_category: "National sample collection"
+data_categories: [Biological samples, Medical records]
+order_of_magnitude: 6
+timestamp: 2022-11-02T11:00:00+0000
+biobank_label:
+sub_collections:
+diagnosis_available: []
+order_of_magnitude_donors:
+autopsy:
+minors:
+inclusion_criteria:
+exclusion_criteria:
+materials: [Nasal swab,Throat swab]
+head_firstname:
+head_lastname:
+head_role:
+display_collection_contact: FALSE
+contact: c19dp:biobank:SE_NAT
+publications_list:
+contact_priority: 1
+---
diff --git a/content/collections/NAT/_index.md b/content/collections/NAT/_index.md
@@ -0,0 +1,17 @@
+---
+id: c19dp:biobank:SE_NAT
+name: National sample collections
+acronym: National sample collections
+juridical_person: NA
+country: SE
+biobank_sverige: TRUE
+ivo_regnum:
+bbmri_id:
+website_url: https://biobanksverige.se/kontakta-oss/biobankssamordnare-och-nej-talonger/
+description:
+address:
+contact: c19dp:contact:SE_NAT
+contact_priority: 1
+collections:
+email: [email protected]
+---
diff --git a/layouts/collections/single.html b/layouts/collections/single.html
@@ -110,19 +110,21 @@ <h4>General information</h4>
             <div class="col-auto pl-0 font-weight-bold">Ethical approval number:</div>
             <div class="col pl-0">{{ .Params.ethics_id }}</div>
           </div>
+          {{ if eq .Params.name "National sample collection stored at National Pandemic Center (NPC)" }}
+          {{ else }}
           <div class="row ml-0 mt-3">
             <h4>Donor information</h4>
-          </div>
+          </div> {{ end }}
           {{ if .Params.diagnosis_available }}<div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Diagnoses:</div>
             <div class="col pl-0">
               {{ range .Params.diagnosis_available}}
-                {{ if eq . "urn:miriam:icd:U07.1" }}
-                <span class="m-1 badge badge-primary">Laboratory-confirmed COVID-19 diagnosis; U07.1</span>
-                {{ end }}
-                {{ if eq . "urn:miriam:icd:U07.2" }}
-                <span class="m-1 badge badge-primary">Suspect or probable COVID-19 diagnosis; U07.2</span>
-                {{ end }}
+              {{ if eq . "urn:miriam:icd:U07.1" }}
+              <span class="m-1 badge badge-primary">Laboratory-confirmed COVID-19 diagnosis; U07.1</span>
+              {{ end }}
+              {{ if eq . "urn:miriam:icd:U07.2" }}
+              <span class="m-1 badge badge-primary">Suspect or probable COVID-19 diagnosis; U07.2</span>
+              {{ end }}
               {{ end }}
             </div>
           </div>{{ end }}
@@ -154,31 +156,33 @@ <h4>Donor information</h4>
           {{ $info_about_autopsy := string .Params.autopsy }}
           {{ if $info_about_autopsy }}<div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Samples from deceased (autopsy):</div>
-            <div class="col pl-0">{{ if eq $info_about_autopsy "true" }}yes{{ else if eq $info_about_autopsy "false" }}no{{ end }}</div>
+            <div class="col pl-0">
+              {{ if eq $info_about_autopsy "true" }}yes{{ else if eq $info_about_autopsy "false" }}no{{ end }}</div>
           </div> {{ end }}
           {{ $info_about_minors := string .Params.minors }}
           {{ if $info_about_minors }}<div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Samples from minors (&lt;18 years old):</div>
-            <div class="col pl-0">{{ if eq $info_about_minors "true" }}yes{{ else if eq $info_about_minors "false" }}no{{ end }}</div>
+            <div class="col pl-0">
+              {{ if eq $info_about_minors "true" }}yes{{ else if eq $info_about_minors "false" }}no{{ end }}</div>
           </div> {{ end }}
           {{ if .Params.inclusion_criteria }}<div class="row ml-0">
             <div class="mb-3">
               <b>Inclusion criteria:</b> {{ .Params.inclusion_criteria }}
             </div>
-            </div>{{ end }}
+          </div>{{ end }}
           {{ if .Params.exclusion_criteria }}<div class="row ml-0">
             <div class="mb-3">
               <b>Exclusion criteria:</b> {{ .Params.exclusion_criteria }}
             </div>
-            </div>{{ end }}
+          </div>{{ end }}
           <div class="row ml-0 mt-3">
             <h4>Sample information</h4>
           </div>
           <div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Materials:</div>
             <div class="col pl-0">{{ range (.GetTerms "materials") }}
               <span class="m-1 badge badge-danger taxonomy-term"><a href="{{ .Permalink }}">{{ .LinkTitle }}</a></span>
-            {{ end }}
+              {{ end }}
             </div>
           </div>
         </div>
@@ -188,17 +192,40 @@ <h4>Sample information</h4>
               <div class="card-text">
                 {{ if .Params.display_collection_contact }}
                 <h5>Collection contact information</h5>
-                {{ if .Params.head_firstname }}<div class="row"><div class="col">Collection head: {{ .Params.head_firstname }} {{ .Params.head_lastname }} {{ if .Params.head_role }}({{ .Params.head_role }}){{ end }}</div></div>{{ end }}
-                <div class="row"><div class="col">Contact person: {{ .Params.collection_contact.first_name }} {{ .Params.collection_contact.last_name }}</div></div>
-                <div class="row"><div class="col"><i class="bi bi-envelope-fill mr-2"></i><span>{{ .Params.collection_contact.email }} </span></div></div>
-                {{ if .Params.website_url }}<div class="row"><div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Params.website_url }}" target="_blank"><span>Collection homepage</span></a></div></div>{{ end }}
+                {{ if .Params.head_firstname }}<div class="row">
+                  <div class="col">Collection head: {{ .Params.head_firstname }} {{ .Params.head_lastname }}
+                    {{ if .Params.head_role }}({{ .Params.head_role }}){{ end }}</div>
+                </div>{{ end }}
+                <div class="row">
+                  <div class="col">Contact person: {{ .Params.collection_contact.first_name }}
+                    {{ .Params.collection_contact.last_name }}</div>
+                </div>
+                <div class="row">
+                  <div class="col"><i class="bi bi-envelope-fill mr-2"></i><span>{{ .Params.collection_contact.email }}
+                    </span></div>
+                </div>
+                {{ if .Params.website_url }}<div class="row">
+                  <div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Params.website_url }}"
+                      target="_blank"><span>Collection homepage</span></a></div>
+                </div>{{ end }}
                 {{ end }}
                 <h5>Biobank contact information</h5>
-                <div class="row"><div class="col">{{ .Parent.Params.name }}</div></div>
-                {{ if .Parent.Params.ivo_regnum }}<div class="row"><div class="col">Registration number at IVO: {{ .Parent.Params.ivo_regnum }}</div></div>{{ end }}
-                {{ if .Parent.Params.email }}<div class="row"><div class="col"><i class="bi bi-envelope-fill mr-2"></i>{{ .Parent.Params.email }}</div></div>{{ end }}
-                {{ if .Parent.Params.website_url }}<div class="row"><div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Parent.Params.website_url }}" target="_blank"><span>Biobank homepage</span></a></div></div>{{ end }}
-                <div class="row mt-2"><div class="col"><a href="{{ .Parent.RelPermalink }}" class=""><span>All collections of {{ .Parent.Params.name }}</span> <i class="bi bi-arrow-right-circle-fill"></i></a></div></div>
+                <div class="row">
+                  <div class="col">{{ .Parent.Params.name }}</div>
+                </div>
+                {{ if .Parent.Params.ivo_regnum }}<div class="row">
+                  <div class="col">Registration number at IVO: {{ .Parent.Params.ivo_regnum }}</div>
+                </div>{{ end }}
+                {{ if .Parent.Params.email }}<div class="row">
+                  <div class="col"><i class="bi bi-envelope-fill mr-2"></i>{{ .Parent.Params.email }}</div>
+                </div>{{ end }}
+                {{ if .Parent.Params.website_url }}<div class="row">
+                  <div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Parent.Params.website_url }}"
+                      target="_blank"><span>Biobank homepage</span></a></div>
+                </div>{{ end }}
+                <div class="row mt-2">
+                  <div class="col"><a href="{{ .Parent.RelPermalink }}" class=""><span>All collections of
+                        {{ .Parent.Params.name }}</span> <i class="bi bi-arrow-right-circle-fill"></i></a></div>
                 </div>
               </div>
             </div>
@@ -207,5 +234,6 @@ <h5>Biobank contact information</h5>
       </div>
     </div>
   </div>
+</div>
 
-{{ end }}
+{{ end }}
diff --git a/layouts/index.html b/layouts/index.html
@@ -61,6 +61,7 @@
           <div id="collapseCollectionTypes" class="collapse" aria-labelledby="headingCollectionTypes">
           <div class="card-body">
               <div class="custom-control"><input type="checkbox" name="collectiontypes" class="form-check-input" value="Healthcare sample collection">Healthcare sample collection</div>
+              <div class="custom-control"><input type="checkbox" name="collectiontypes" class="form-check-input" value="National sample collection">National sample collection</div>
               <div class="custom-control"><input type="checkbox" name="collectiontypes" class="form-check-input" value="Research sample collection">Research sample collection</div>
           </div>
         </div>

diff --git a/layouts/partials/footer.html b/layouts/partials/footer.html
@@ -2,31 +2,45 @@
   <div class="container border-top">
     <div class="row">
       <div class="col mx-1 mt-2">
-              <p>The Swedish COVID-19 Sample Collection Database is a section of the <a href="https://covid19dataportal.se" target="_blank">COVID-19 Data Portal Sweden</a> maintained in collaboration with <a href="https://biobanksverige.se/" target="_blank">Biobank Sverige</a>.
-                The project is funded by the <a href="https://vr.se/" target="_blank">Swedish Research Council</a> as part of the effort to coordinate the collection of and access to samples linked to COVID-19. Please <a href="https://covid19dataportal.se/biobanks/" target="_blank">see this page</a> for more information about the database. Questions, comments, and suggestions regarding the database can be sent to <a href="mailto:[email protected]">[email protected]</a>.</p>
+        <p>The Swedish COVID-19 Sample Collection Database is a section of the <a href="https://covid19dataportal.se"
+            target="_blank">Swedish COVID-19 and Pandemic Preparedness Portal</a> (formerly the Swedish COVID-19 Data
+          Portal) maintained in collaboration with <a href="https://biobanksverige.se/" target="_blank">Biobank
+            Sverige</a>.
+          The project was initially funded by the <a href="https://vr.se/" target="_blank">Swedish Research Council</a>
+          as part of
+          the effort to coordinate the collection of and access to samples linked to COVID-19. The Portal is now funded
+          by the <a href="https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/"
+            target="_blank">SciLifeLab Pandemic Laboratory Preparedness (PLP) Program</a> to continue this work. Please
+          <a href="https://covid19dataportal.se/biobanks/" target="_blank">see this page</a> for more information about
+          the database. Questions, comments, and suggestions regarding the database can be sent to <a
+            href="mailto:[email protected]">[email protected]</a>.</p>
+      </div>
     </div>
-  </div>
 
-  <div class="row">
-    <div class="col">
-      <img class="mr-3" src="https://covid19dataportal.se/img/logos/scilifelab-logo.svg" alt="SciLifeLab" height="40">
-      <img class="mr-3" src="https://covid19dataportal.se/img/logos/biobanksverige_logo.jpg" alt="Biobank Sverige" height="40">
+    <div class="row">
+      <div class="col">
+        <img class="mr-3" src="/img/scilifelab-logo.svg" alt="SciLifeLab" height="40">
+        <img class="mr-3" src="/img/biobanksverige_logo.jpg" alt="Biobank Sverige" height="40">
+        <img class="mr-3" src="/img/KAW_logo.png" alt="Knut and Alice Wallenberg Foundation logo" height="100">
+      </div>
     </div>
-  </div>
 
-  <div class="row">
-    <div class="col mx-1 mt-4">
-            <p class="small"><a href="https://github.com/ScilifelabDataCentre/covid-sample-collection-database">Website code on GitHub</a></p>
-            <p class="small"><a href="https://covid19dataportal.se/privacy/">Privacy notice</a></p>
-  </div>
-</div>
+    <div class="row">
+      <div class="col mx-1 mt-4">
+        <p class="small"><a href="https://github.com/ScilifelabDataCentre/covid-sample-collection-database">Website code
+            on GitHub</a></p>
+        <p class="small"><a href="https://covid19dataportal.se/privacy/">Privacy notice</a></p>
+      </div>
+    </div>
 
-</div>
+  </div>
 </footer>
 
 <!-- Bootstrap-->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js"
+  integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"
+  integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
 
 <!-- Bootstrap icons -->
 <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
@@ -40,11 +54,11 @@
   _paq.push(["disableCookies"]);
   _paq.push(['trackPageView']);
   _paq.push(['enableLinkTracking']);
-  (function() {
-    var u="//matomo.dckube.scilifelab.se/";
-    _paq.push(['setTrackerUrl', u+'matomo.php']);
+  (function () {
+    var u = "//matomo.dckube.scilifelab.se/";
+    _paq.push(['setTrackerUrl', u + 'matomo.php']);
     _paq.push(['setSiteId', '2']);
-    var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
-    g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
+    var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
+    g.async = true; g.src = u + 'matomo.js'; s.parentNode.insertBefore(g, s);
   })();
-</script>
+</script>
diff --git a/layouts/partials/header.html b/layouts/partials/header.html
@@ -1,20 +1,24 @@
-  <header>
-    <nav class="navbar navbar-expand-md navbar-light bg-white">
+<header>
+  <nav class="navbar navbar-expand-md navbar-light bg-white">
     <div class="container pb-2 border-bottom">
       <a class="navbar-brand" href="https://covid19dataportal.se/">
-        <img src="https://covid19dataportal.se/img/site_logo/CV19DP_logo_oneliner_SWE.svg" alt="COVID-19 Biobank Registry, part of the COVID-19 Data Portal Sweden">
+        <img src="https://covid19dataportal.se/img/site_logo/CV19DP_logo_oneliner_SWE.svg"
+          alt="COVID-19 Biobank Registry, part of the Swedish COVID-19 and Pandemic Preparedness Portal">
       </a>
-      <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarCollapseBottom" aria-controls="navbarCollapseBottom" aria-expanded="false" aria-label="Toggle navigation">
+      <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarCollapseBottom"
+        aria-controls="navbarCollapseBottom" aria-expanded="false" aria-label="Toggle navigation">
         <span class="navbar-toggler-icon"></span>
       </button>
       <div class="collapse navbar-collapse" id="navbarCollapseBottom">
         <div class="navbar-primary-links">
           <a class="nav-link" href="/">Sample Collection Database</a>
         </div>
         <ul class="navbar-nav">
-          <li class="nav-item"><a class="nav-link" href="https://covid19dataportal.se/"><i class="bi bi-arrow-left-circle-fill"></i> back to the COVID-19 Data Portal Sweden</a></li>
+          <li class="nav-item"><a class="nav-link" href="https://covid19dataportal.se/"><i
+                class="bi bi-arrow-left-circle-fill"></i> back to the COVID-19 and Pandemic Preparedness
+              Portal</a></li>
         </ul>
       </div>
     </div>
   </nav>
-  </header>
+</header>
diff --git a/static/img/KAW_logo.png b/static/img/KAW_logo.png
diff --git a/static/img/biobanksverige_logo.jpg b/static/img/biobanksverige_logo.jpg
diff --git a/static/img/knut-and-alice-wallenberg.jpg b/static/img/knut-and-alice-wallenberg.jpg