Merge pull request #1025 from ScilifelabDataCentre/develop

Pathogens portal and new VI

README.md

@@ -1,12 +1,12 @@
-# ![The Swedish COVID-19 & Pandemic Preparedness Data Portal](static/img/site_logo/CV19DP_logo_oneliner_SWE.png)
+# ![The Swedish Pathogens Portal](static/img/site_logo/eml_pathogens_logo.png)
 
-## The Swedish COVID-19 & Pandemic Preparedness Data Portal
+## The Swedish Pathogens Portal
 
-This is the source code for the Swedish COVID-19 & Pandemic Preparedness Data Portal:
-[https://www.covid19dataportal.se/](https://www.covid19dataportal.se/)
+This is the source code for the Swedish Pathogens Portal:
+[https://www.pathogens.se](https://www.pathogens.se/)
 
-The website is the Swedish node for the European Covid-19 Data Portal project.
-The main European site can be seen at [https://www.covid19dataportal.org/](https://www.covid19dataportal.org/)
+The website is the Swedish node for the European Pathogens Portal project.
+The main European site can be seen at [https://www.pathogensportal.org](https://www.pathogensportal.org/)
 
 ## Introduction
 

config.yaml

@@ -1,17 +1,17 @@
 baseURL: "https://www.covid19dataportal.se/"
-title: "The Swedish COVID-19 & Pandemic Preparedness Data Portal"
+title: "The Swedish Pathogens Portal"
 buildFuture: true
 params:
-  title: "The Swedish COVID-19 & Pandemic Preparedness Data Portal"
-  description: The Swedish COVID-19 & Pandemic Preparedness Data Portal
+  title: "The Swedish Pathogens Portal"
+  description: The Swedish Pathogens Portal
   images:
-    - /img/site_logo/CV19DP_logo_social_card_SWE.png
+    - /img/site_logo/eml_pathogens_logo.png
 
   # There is a hugo i18n package, but it seems like overkill for so few strings
   lang_strings:
     en:
-      home_title: Sharing resources to maximise pandemic preparedness 
-      enquire_email_footer_dc: "Contact the Swedish COVID-19 Data Portal"
+      home_title: Welcome to the new Swedish Pathogens Portal
+      enquire_email_footer_dc: "Contact the Swedish Pathogens Portal"
       support_feedback: Support & Feedback
       privacy: Privacy Notice
       github_link: Website code on GitHub
@@ -35,8 +35,8 @@ params:
       twitter_link: Twitter
       linkedin_link: LinkedIn
     sv:
-      home_title: Snabbare forskning genom datadelning
-      enquire_email_footer_dc: "Kontakta den svenska Covid-19 dataportalen"
+      home_title: Välkomna till den nya Svenska Patogens Portalen
+      enquire_email_footer_dc: "Kontakta den Svenska Patogens Portalen"
       support_feedback: Support och Feedback
       privacy: Integritetspolicy
       github_link: Webbplatskod på GitHub
@@ -68,7 +68,7 @@ languages:
     languageName: Svenska
     contentDir: content/svenska
     weight: 2
-    description: Svenska Dataportalen för Covid-19 & Pandemisk Beredskap
+    description: Svenska Pathogens Portalen
 
 markup:
   goldmark:

content/english/_index.md

@@ -1,5 +1,5 @@
 ---
-title: Swedish COVID-19 & Pandemic Preparedness Data Portal
+title: The Swedish Pathogens Portal
 teststats:
         name: Recent statistics on COVID-19 in Sweden
         desc: Pages with recent data and visualizations on SARS-CoV-2 and COVID-19 tests carried out at various research facilities.
@@ -12,9 +12,3 @@ teststats:
 
 plotly: true
 ---
-
-The *Swedish COVID-19 & Pandemic Preparedness Data Portal* is a hub for data, tools, services, and other resources centred around COVID-19 and pandemic preparedness in Sweden.
-
-The Portal is involved in multiple projects, platforms, and initiatives. It is the Swedish node of the [European COVID-19 Data Platform](https://www.covid19dataportal.org). It is a pillar of the [SciLifeLab Pandemic Laboratory Preparedness (PLP) Program](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/), and is involved in the [Horizon BY-COVID project](https://by-covid.org).
-
-The Portal is operated by the [SciLifeLab Data Centre](https://scilifelab.se/data/) and partners. To learn more about us, including meeting the team behind the Portal, see our [about page](/about/). We welcome contributions from the community, and have established an [editorial committee](/about/editorial_committee/) to increase engagement with the research community. There are multiple ways to [contribute](/contribute/), so please get in touch!

content/english/about/_index.md

@@ -1,5 +1,5 @@
 ---
-title: About the data portal
+title: About the Swedish Pathogens Portal
 menu:
     navbar_top:
         name: About
@@ -29,15 +29,15 @@ menu:
 
 #### Introduction
 
-The *Swedish COVID-19 & Pandemic Preparedness Data Portal* provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university.
+The *Swedish Pathogens Portal* provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university.
 
 The Portal is operated by the [SciLifeLab Data Centre](https://scilifelab.se/data/) and [partners](partner_organisations). We welcome community contributions to the Portal and provide information on the different ways that the community can contribute, for more details see [contribute](/contribute/) page. In addition to running the Portal, the team can also either provide support on data-related questions surrounding pandemic preparedness research or help find suitable support services. For more general data support, please see our related research data management service([RDM Guidelines](https://data-guidelines.scilifelab.se/)).
 
 This website is built using [Hugo](https://gohugo.io/) in combination with [Bootstrap](https://getbootstrap.com/) for styling, [DataTables](https://datatables.net/) for tables, and [Vega/Vega-Lite](https://vega.github.io/vega-lite/) and [Plotly](https://plotly.com/) for interactive graphics. All code used for the Portal is open source (held under an [MIT licence](https://choosealicense.com/licenses/mit/)) and [is available on GitHub](https://github.com/ScilifelabDataCentre/covid-portal). We encourage the reuse of our code, either for generating another national portal, or recreating certain features.
 
 #### History of the Portal
 
-The Swedish COVID-19 & Pandemic Preparedness Portal was launched in June 2020 on assignment and with funding from the Swedish Research Council a.k.a. Vetenskapsrådet (more details [here](https://www.vr.se/english/just-now/news/news-archive/2020-06-03-new-national-portal-makes-research-data-on-covid-19-accessible.html)). The Portal was actually the first national node of the [European COVID-19 Data Platform](https://covid19dataportal.eu/), which was initiated and funded by the European Commission (more details [here](https://www.embl.org/news/science/embl-ebi-launches-covid-19-data-portal/)) and you can find an overview of other national nodes [here](/partners/). The Portal focused on SARS-CoV-2 and COVID-19 research data exclusively until the end of 2021. We released a [news item](/updates/first_year/) summarising our activities in 2021.
+The Swedish Pathogens Portal was originally launched as the 'Swedish COVID-19 Data Portal' in June 2020 on assignment and with funding from the Swedish Research Council a.k.a. Vetenskapsrådet (more details [here](https://www.vr.se/english/just-now/news/news-archive/2020-06-03-new-national-portal-makes-research-data-on-covid-19-accessible.html)). The Portal was actually the first national node of the [European COVID-19 Data Platform](https://covid19dataportal.eu/), which was initiated and funded by the European Commission (more details [here](https://www.embl.org/news/science/embl-ebi-launches-covid-19-data-portal/)) and you can find an overview of other national nodes [here](/partners/). The Portal focused on SARS-CoV-2 and COVID-19 research data exclusively until the end of 2021. We released a [news item](/updates/first_year/) summarising our activities in 2021.
 
 From 2022, the Portal expanded to cover other research relevant to pandemic preparedness and became a part of the [SciLifeLab Pandemic Laboratory Preparedness programme](https://www.scilifelab.se/pandemic-response/pandemic-laboratory-preparedness/). The SciLifeLab Pandemic Laboratory Preparedness Programme is funded by the earmarked governmental funding to SciLifeLab ([Research proposition Prop. 202/21:60](https://www.regeringen.se/rattsliga-dokument/proposition/2020/12/forskning-frihet-framtid--kunskap-och-innovation-for-sverige/)).
 

content/english/about/partner_organisations.md

@@ -27,7 +27,7 @@ title: Partner organisations
   </div>
   <div class="col-sm-12 col-md-12 col-lg-9">
   <h6>European COVID-19 Data Platform</h6>
-    <p>The COVID-19 & Pandemic Preparedness Data Portal is a national node of the <a href="https://www.covid19dataportal.org/">European COVID-19 Data Platform</a>. The European COVID-19 Data Platform is operated by the <a href="https://ebi.ac.uk">European Bioinformatics Institute</a> (a part of the <a href="https://www.embl.org/">European Molecular Biology Laboratory</a> (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes <a href="/partners/">can be found here</a>.</p>
+    <p>The Swedish Pathogens Portal was originally launched as the ‘Swedish COVID-19 Data Portal’ and it was a national node of the <a href="https://www.covid19dataportal.org/">European COVID-19 Data Platform</a>. The European COVID-19 Data Platform is operated by the <a href="https://ebi.ac.uk">European Bioinformatics Institute</a> (a part of the <a href="https://www.embl.org/">European Molecular Biology Laboratory</a> (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes <a href="/partners/">can be found here</a>.</p>
     <p>The European COVID-19 Data Platform aims to facilitate data sharing and analysis in order to accelerate coronavirus research. It enables researchers to upload, access and analyse reference data and specialist datasets related to COVID-19. It is synchronised with COVID-19-related data and scientific literature held in EMBL-EBI's data resources, including ENA, UniProt, PDBe, EMDB, Expression Atlas and Europe PMC. The data continues to grow in diversity and volume, but include sequences, structures, expression data, compound screens, biochemistries and scientific publications.</p>
   </div>
 </div>
@@ -41,7 +41,7 @@ title: Partner organisations
   </div>
   <div class="col-sm-12 col-md-12 col-lg-9">
       <h6>BY-COVID consortium</h6>
-    <p>The Swedish COVID-19 & Pandemic Preparedness Data Portal is one of the partners in the <a href="https://by-covid.org/">BY-COVID consortium</a>. BY-COVID is a Horizon project <a href="https://by-covid.org/news-events/by-covid-launch/">funded by the European Comission</a> and brings together <a href="https://by-covid.org/about">53 partners from 19 countries</a>. Stakeholders include individuals and organisation from multiple areas, including the biomedical field, hospitals, public health, social sciences and humanities.</p>
+    <p>The Swedish Pathogens Portal is one of the partners in the <a href="https://by-covid.org/">BY-COVID consortium</a>. BY-COVID is a Horizon project <a href="https://by-covid.org/news-events/by-covid-launch/">funded by the European Comission</a> and brings together <a href="https://by-covid.org/about">53 partners from 19 countries</a>. Stakeholders include individuals and organisation from multiple areas, including the biomedical field, hospitals, public health, social sciences and humanities.</p>
     <p>The BeYond-COVID (BY-COVID) project aims to make COVID-19 data accessible to anyone that can use it, including medical staff in hospitals, researchers in labs, and government officials. The project will provide a framework for making data from other infectious diseases open and accessible to everyone. The project will integrate established national and European infrastructures with ELIXIR, BBMRI, ECRIN, PHIRI and CESSDA. It will build on existing efforts, such as the COVID-19 Data Platform and the Versatile Emerging infectious disease Observatory project (VEO), in order to maximise efficiency. It will also develop synergies with the European Health Data Space.</p>
     <p>Members of the Portal team are involved in the development of the <a href="https://www.infectious-diseases-toolkit.org">Infectious Disease Toolkit</a>, a major deliverable of the BY-COVID project.</p>
   </div>

content/english/contact/_index.md

@@ -13,4 +13,4 @@ aliases:
 recaptcha: true
 ---
 
-We welcome questions and suggestions regarding the *Swedish COVID-19 and Pandemic Preparedness Data Portal* and we can help with your data management or data sharing question (or at least point you to where your question can be answered). You can fill out the form below and the [the team behind the Portal](/about/) will be happy to help you find a good solution. Alternatively, you can send us an email: [[email protected]](mailto:[email protected]).
+We welcome questions and suggestions regarding the *Swedish Pathogens Portal* and we can help with your data management or data sharing question (or at least point you to where your question can be answered). You can fill out the form below and the [the team behind the Portal](/about/) will be happy to help you find a good solution. Alternatively, you can send us an email: [[email protected]](mailto:[email protected]).

content/english/contribute.md

@@ -7,7 +7,7 @@ menu:
         pre: <i class="bi bi-plus-circle-fill me-2"></i>
 ---
 
-The *Swedish COVID-19 & Pandemic Preparedness Data Portal* was built to serve the community of researchers working on relevant topics and we welcome any contributions from the community or suggestions on how the Portal can help the community. Whenever there is anything that you would like to share with your colleagues, do not hesistate to share it through the Portal. We welcome suggestions for new information or edits in all sections as well as ideas for new sections that could be launched.
+The *Swedish Pathogens Portal* was built to serve the community of researchers working on relevant topics and we welcome any contributions from the community or suggestions on how the Portal can help the community. Whenever there is anything that you would like to share with your colleagues, do not hesistate to share it through the Portal. We welcome suggestions for new information or edits in all sections as well as ideas for new sections that could be launched.
 
 For example, you can suggest a dataset that should be covered in the data highlights section or even write one, you can suggest an available dataset that would be useful to others in the community, add information about your own or your colleague's ongoing research project, share data from your project in a new [dashboard](/dashboards/), and so on.
 
@@ -20,10 +20,6 @@ There are multiple ways to add/edit information on the Portal. Choose any method
       <p>The easiest way to send a quick suggestion or start a conversation with the Portal team is to simply send us an email. Email us at <a href="mailto:[email protected]">[email protected]</a> where your ticket will be assigned to one of the members of the Portal team.</p>
       <p><b><a href="mailto:[email protected]">Contribute through e-mail <i class="bi bi-arrow-right-circle-fill"></i></a></b></p>
     </div>
-    <!--<div class="col-md-6">
-      <h3><i class="bi bi-hand-index-thumb-fill"></i> Send a suggestion through a form</h3>
-      <p>Each section of the Portal contains a special form through which you can make a suggestion for that specific section.</p>
-    </div>-->
     <div class="col-md-6">
       <h3><i class="bi bi-github"></i> Send a GitHub pull request</h3>
       <p>All information which is displayed on the Portal is <a href="https://github.com/ScilifelabDataCentre/covid-portal/tree/develop">stored on GitHub</a>. The information is stored as .JSON files or as Markdown files, making it human-readable and easy to edit. If you know your way around the web interface of GitHub or GitHub CLI, you can easily edit or add information yourself and send us a pull request.</p>

content/english/dashboards/_index.md

@@ -14,3 +14,6 @@ aliases:
 ---
 
 The *Dashboards* section describes research done on a given subject relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about COVID-19 and SARS-CoV-2, infectious diseases in general, antibiotic resistance, enteric viruses and Mpox. The goal is to highlight and visualise openly shared data that can potentially be used by many other researchers to make further discoveries.
+
+To easily find dashboards relevant to a specific topic, simply click on the colored tag and the page will filter and display only the dashboards related to that topic.
+

content/english/dashboards/crush_covid.md

@@ -2,6 +2,7 @@
 title: CRUSH Covid data and dashboard, Region Uppsala
 description: CRUSH Covid maps outbreaks in Uppsala County by visualising the number of cases, test positivity, and geographic distribution, among other things. Data for each postal code is available for download and reuse.
 banner: /dashboard_thumbs/CRUSH.png
+banner_border: true
 toc: false
 menu:
   dashboard_menu:

content/english/dashboards/npc-statistics.md

@@ -2,6 +2,7 @@
 title: National Pandemic Centre SARS-CoV-2 (COVID-19) test statistics
 description: The national Pandemic Centre (NPC) conducted testing related to SARS-CoV-2 from the start of the pandemic. They show positive, negative, and inconclusive tests. This dashboard is historic, so no longer updated.
 banner: /dashboard_thumbs/NPC_logo.png
+banner_border: true
 menu:
      dashboard_menu:
         identifier: npc-statistics

content/english/dashboards/post_covid.md

@@ -7,7 +7,7 @@ plotly: true
 menu:
     dashboard_menu:
         identifier: post_covid
-        name: Post COVID-19 condition in Sweden
+        name: Post COVID-19 condition
 aliases:
     - /data_types/health_data/post_covid/
 dashboards_topics: [COVID-19, Infectious diseases]

content/english/dashboards/symptom_study_sweden.md

@@ -2,6 +2,7 @@
 title: COVID Symptom Study Sweden
 description: The COVID Symptom Study Sweden (CSSS) collects data on COVID-19 prevalence, symptoms, and vaccinations through a smart phone app with over 200.000 users in Sweden. Raw data can be requested for use in research projects.
 banner: /dashboard_thumbs/symptoms_study.png
+banner_border: true
 toc: false
 plotly: true
 menu: