Merge pull request #1094 from ScilifelabDataCentre/develop

Make latest changes live

content/english/citation.md

@@ -0,0 +1,52 @@
+---
+title: How to cite the Portal
+menu:
+  top_actions:
+    name: Cite us
+    weight: 80
+    pre: <i class="bi bi-patch-exclamation-fill me-2"></i>
+  footer_about:
+    name: Cite us
+    weight: 30
+toc: true
+---
+
+In line with the principles of _FAIR_ and _Open Science_, we encourage the reuse of material made available on the Swedish Pathogens Portal. On this page, you will find information about how to cite the portal in the event that you reuse the content. Please note that the information on the portal is updated continuously, therefore it is important to refer to specific versions (or to provide access dates) within citations.
+
+## Research community
+
+In this section, you'll find instructions on how to cite the portal website, or underlying code, in reearch publications.
+
+### Citing website content
+
+##### Research Resource Identifier of Swedish Pathogens Portal
+
+The Resource Identification Portal was created in support of the <a target="_blank" href="https://www.rrids.org/">Resource Identification Initiative</a>. It aims to promote the identification, discovery, and reuse of research resources. Research Resource Identifiers (**RRIDs**) are persistent and unique identifiers for referencing a research resource.
+
+The RRID for the Swedish Pathogens Portal is **SCR_024866**.
+
+By citing the portal using the RRID, you will facilitate further reuse of the portal, enable us to track reuse of the portal, and allow others to easily find the _Summary Report_ for usage the Swedish Pathogens Portal.
+
+##### APA format
+
+**In-text citation**: The data was made available on the Swedish Pathogens Portal (RRID:SCR\*024866)(_insert year_)
+
+**Reference list** SciLifeLab Data Centre (2024). Swedish Pathogens Portal, version (_insert version_) from <https://pathogens.se>, RRID:SCR_024866.
+
+You will find the version of the Portal at the bottom of the footer on any page, or on our <a target="_blank" href="https://github.com/ScilifelabDataCentre/pathogens-portal">Github repository</a>.
+
+If you are aiming to cite particular pages of the portal in particular (e.g. the Data Highlights), you may find that an author is mentioned and a date is given. In this case, you should include the appropriate date and author instead, but must still include the RRID.
+
+### Citing underlying code
+
+From the start, the portal has been operated by the <a target="_blank" href="https://scilifelab.se/data">SciLifeLab Data Centre</a> and partners. Many individuals from the wider community have also contributed to the code over time. All of the source code used on the website is available on GitHub. The code used to produce the website is available in our <a target="_blank" href="https://github.com/ScilifelabDataCentre/pathogens-portal">pathogens-portal repository</a>, and all code used for visualisations are in our <a target="_blank" href="https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations">visualisations repository</a>. All of the code that we have produced is available for reuse under an MIT licence.
+
+##### APA format
+
+SciLifeLab Data Centre (year) pathogens-portal. Retrieved: (date) from <https://github.com/ScilifelabDataCentre/pathogens-portal>
+
+SciLifeLab Data Centre (year) pathogens-portal-visualisations. Retrieved: (date) from <https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations>
+
+## Journalists
+
+Journalists are welcome to reuse images, content, or other material from the **Swedish Pathogens Portal** for articles, blogs, social media etc., provided that the portal is acknowledged. Please refer to the portal as the **Swedish Pathogens Portal** and link to our webpage <https://pathogens.se> when you use content from the Portal. You may also include our RRID: **SCR_024866** (see above for information on RRIDs).

content/english/dashboards/variants_region_uppsala.md

@@ -36,7 +36,7 @@ Use the **‘Last 16 weeks’ button** to see data only from the last 16 weeks,
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="850px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py).

content/english/highlights/covimapp.md

@@ -39,6 +39,8 @@ In order to provide estimates of the alterations that occurred due to COVID-19,
 
 In summary, this study is a comprehensive analysis of the soluble blood proteome alterations that occur in COVID-19. The results validate multiple previous findings and pinpoint new alterations. Furthermore, this study provides the current MS-based state-of-the-art concluding estimates for soluble blood proteome alterations in COVID-19. The researchers aim for CoViMAPP to be used as a dynamic tool for future meta-analyses. Additional curated studies can and will be included to update the summary estimates.
 
+**CoViMAPP is now listed as a service in the [Services section](https://data.scilifelab.se/services/) of the SciLifeLab Data Platform, where we list tools, databases, and other services that could be beneficial in data-driven life science.**
+
 #### Data and code availability
 
 - All results described in the manuscript are presented in main or supplementary figures or datasets. All results from the meta-analysis are available as an R Shiny app, [CoViMAPP](https://covimapp.serve.scilifelab.se), which is available on [SciLifeLab Serve](https://serve.scilifelab.se/apps/). To understand more about CoViMAPP, please see the associated entry in the [SciLifeLab Data Repository](https://doi.org/10.17044/scilifelab.22293148).

content/svenska/dashboards/variants_region_uppsala.md

@@ -38,7 +38,7 @@ Använd knappen **'Last 16 weeks'** för att endast se data från de senaste 16
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="850px" >}}</div>
 </div>
 
 **Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py).

layouts/partials/navbar.html

@@ -22,8 +22,7 @@
       <div class="collapse navbar-collapse">
         <ul class="navbar-nav ml-auto navbar-top">
           {{ range .Site.Menus.navbar_top }}
-          <li class="nav-item"><a class="nav-link {{ .Post }}" href="{{ .Page.RelPermalink }}">{{ .Pre }}{{ .Name }}</a>
-          </li>
+          <li class="nav-item"><a class="nav-link" href="{{ .Page.RelPermalink }}">{{ .Name }}</a></li>
           {{ end }}
           {{ if .IsTranslated }}
           {{ range .AllTranslations }}