Merge pull request #1107 from ScilifelabDataCentre/develop

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CITATION.cff

@@ -0,0 +1,41 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Hughes"
+  given-names: "Liane"
+- family-names: "Stark"
+  given-names: "Katarina Öjefors"
+- family-names: "Kochari"
+  given-names: "Arnold"
+- family-names: "Panneerselvam"
+  given-names: "Senthilkumar"
+- family-names: "Ewels"
+  given-names: "Phil"
+- family-names: "Ostberg"
+  given-names: "Linus"
+- family-names: "Kraulis"
+  given-names: "Per"
+- family-names: "Rung"
+  given-names: "Johan"
+- family-names: "Lorenz"
+  given-names: "Jan"
+- family-names: "Asklof"
+  given-names: "Anna"
+- family-names: "Kallberg"
+  given-names: "Yvonne"
+- family-names: "Islam"
+  given-names: "Kazi Jahurul"
+- family-names: "Ouyang"
+  given-names: "Wei"
+- family-names: "Kronander"
+  given-names: "Elin"
+- family-names: "Tewatia"
+  given-names: "Parul"
+- family-names: "Englund"
+  given-names: "Markus"
+- family-names: "Hammaren"
+  given-names: "Rickard"
+- family-names: "Xu"
+  given-names: "Hao"
+title: "Swedish Pathogens Portal"
+url: "https://github.com/ScilifelabDataCentre/pathogens-portal"

CONTRIBUTING/running_a_local_copy.md

@@ -1,18 +1,28 @@
-# Running a local copy of the Portal
+# Running a local copy of the portal
 
-Because the Portal is built using [Hugo](https://gohugo.io/), a static site generator, it is quite easy to run a full version of the Portal on your computer and see how your changes look while doing that.
+The portal is built using [Hugo](https://gohugo.io/), a static site generator. This makes it relatively easy to run a full version of the portal on your computer (i.e. locally). This means that you can see how the changes that you're making would look on the site.
+
+#### Clone a copy of the portal code
+
+All of the code behind the portal is stored in [this GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal). There are multiple ways to clone a GitHub repository so that you have your own copy on your computer. Please view the information in [the GitHub documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) in order to do this.
 
 #### Using Hugo
 
-To view your changes as they will appear in the final website, you need to install Hugo. You can find instructions on the Hugo website: [https://gohugo.io/](https://gohugo.io/)
+In order to run a local copy, you first need to install Hugo on your computer. Instructions for how to do this are available on the Hugo website: [https://gohugo.io/](https://gohugo.io/).
 
-If you're using Mac OSX, it's recommended to use [Homebrew](https://brew.sh/) - if homebrew is already set up, installing Hugo is just a case of:
+On Mac OSX, it is recommended to use [Homebrew](https://brew.sh/) to install Hugo. Once Hugo is set up, you can run the following command in a terminal window to install Hugo:
 
 ```bash
 brew install hugo
 ```
 
-Once Hugo is installed, navigate to the folder where you cloned this repository and simply run the following command in the repository root directory:
+Once Hugo has finished installing, you can use it to view the site locally right away. To do this, first navigate to the folder that holds your copy of the portal code (i.e. the cloned copy of the GitHub repository). You can do this with the cd command in the terminal window e.g.
+
+```bash
+cd FILE_PATH/TO/CLONED/REPOSITORY
+```
+
+Once you've navigated to the folder that holds your code, you can type 'hugo serve' in your terminal window. You will then see something like this:
 
 ```console
 $ hugo serve
@@ -39,8 +49,8 @@ Press Ctrl+C to stop
 ```
 
 Use the URL printed at the bottom of this message (here, it's `http://localhost:1313/`) to view the site.
-Every time you save a file, the page will automatically refresh in the browser.
+Every time you save a file, the page will automatically refresh in the browser, so you can see the effect of the changes in real time.
 
 #### Using Docker
 
-If you would prefer not to use Hugo, you can use the provided Dockerfile to build and run a container.
+If you would prefer not to use Hugo, you can use the provided Dockerfile to build and run a container instead.

config.yaml

@@ -10,7 +10,7 @@ params:
   # There is a hugo i18n package, but it seems like overkill for so few strings
   lang_strings:
     en:
-      home_title: Welcome to the new Swedish Pathogens Portal
+      home_title: "Swedish Pathogens Portal: supporting pandemic preparedness"
       enquire_email_footer_dc: "Contact the Swedish Pathogens Portal"
       support_feedback: Support & Feedback
       privacy: Privacy Notice
@@ -35,7 +35,7 @@ params:
       twitter_link: Twitter
       linkedin_link: LinkedIn
     sv:
-      home_title: Välkomna till den nya Svenska Patogens Portalen
+      home_title: "Patogens Portal Sverige: stöd för pandemiberedskap"
       enquire_email_footer_dc: "Kontakta den Svenska Patogens Portalen"
       support_feedback: Support och Feedback
       privacy: Integritetspolicy
@@ -97,7 +97,7 @@ permalinks:
 related:
   includeNewer: false
   indices:
-  - name: tags
-    weight: 100
-    threshold: 80
-    toLower: false
+    - name: tags
+      weight: 100
+      threshold: 80
+      toLower: false

content/english/citation.md

@@ -11,43 +11,43 @@ menu:
 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 when reusing/referencing 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.
+In line with the principles of _FAIR_ and _Open Science_, we encourage the reuse and recognition of material made available on the Swedish Pathogens Portal. On this page, you will find information about how to cite the portal when reusing and referencing 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.
+In this section, you'll find instructions on how to cite the portal website, or underlying code, in research 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**.
+The RRID for the Swedish Pathogens Portal is [**SCR_024866**](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_024866/resolver?q=SCR_024866&l=SCR_024866&i=rrid:scr_024866).
 
 By citing the portal using the RRID, you will facilitate further reuse of the portal, enable us to track that activity, and allow others to easily find the _Summary Report_ for usage of the Swedish Pathogens Portal.
 
 ##### APA format
 
-**In-text citation**: The data was made available on the Swedish Pathogens Portal (RRID: SCR_024866) (year)
+For official guidance see the [SciCrunch page on RRID citations](https://scicrunch.org/resources/about/guidelines).
 
-**Reference list** SciLifeLab Data Centre (2024). Swedish Pathogens Portal, version (version number) from <https://pathogens.se>, RRID:SCR_024866.
+**In-text citation**: Swedish Pathogens Portal, SciLifeLab Data Centre, _version number_, RRID: SCR_024866. (Access date: date of access).
 
-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> under 'releases'.
+**Reference list**: Swedish Pathogens Portal (_access date_), SciLifeLab Data Centre, version (version number) from https://pathogens.se, RRID:SCR_024866.
 
-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.
+You will find the version number 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> under 'releases'.
+
+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. There are also some pages were information for how to cite the data itself is provided (e.g. where a DOI is given on a dashboard page). In those cases, you should use that citation.
 
 ### 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.
+The portal is 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. version: (version number), DOI: (insert version DOI shown on the badge in the README.md file of our <a target="_blank" href="https://github.com/ScilifelabDataCentre/pathogens-portal">pathogens-portal repository</a>). An example of the bedge is below:
-
-[![DOI](https://zenodo.org/badge/256458920.svg)](https://zenodo.org/doi/10.5281/zenodo.10629602)
+SciLifeLab Data Centre (year) pathogens-portal. version: (version number)[Software]. Zenodo. <https://zenodo.org/doi/10.5281/zenodo.10629602>.
 
-SciLifeLab Data Centre (year) pathogens-portal-visualisations. version: (version number), <https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations>
+SciLifeLab Data Centre (year) pathogens-portal-visualisations. version: (version number)[Software]. Zenodo. _DOI to be confirmed_.
 
 ## Journalists