From ef225dc73cc573ccea06ab6a8459f56bbbe95c68 Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Tue, 2 Jan 2024 11:43:34 +0100 Subject: [PATCH 1/2] Remove Christmas message Leaving it in, but commented out, to benefit a later onboarding task --- layouts/index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/layouts/index.html b/layouts/index.html index 23129a54e..f7af08dd3 100644 --- a/layouts/index.html +++ b/layouts/index.html @@ -3,7 +3,7 @@
-
+ {{ range .Site.Menus.homepage_dashboards }} From d7ada8cad377816b23e16f5312f937caace13a4f Mon Sep 17 00:00:00 2001 From: Senthilkumar Panneerselvam Date: Thu, 11 Jan 2024 10:50:23 +0100 Subject: [PATCH 2/2] Rename repo --- .github/workflows/dockerhub.yml | 4 ++-- .github/workflows/trivy-scheduled.yaml | 2 +- CONTRIBUTING/adding_editing_information.md | 14 ++++++------ CONTRIBUTING/running_a_local_copy.md | 4 ++-- README.md | 8 +++---- content/english/about/_index.md | 6 ++--- content/english/contribute.md | 6 ++--- content/english/dashboards/RECOVAC.md | 6 ++--- .../english/dashboards/covid_publications.md | 10 ++++----- content/english/dashboards/post_covid.md | 22 +++++++++---------- content/english/dashboards/vaccines.md | 20 ++++++++--------- .../dashboards/variants_region_uppsala.md | 4 ++-- .../english/dashboards/wastewater/_index.md | 4 ++-- .../covid_quantification/covid_quant_GU.md | 2 +- .../covid_quantification/covid_quant_KTH.md | 4 ++-- .../covid_quantification/covid_quant_SLU.md | 2 +- .../enteric_quantification/_index.md | 2 +- .../influenza_quantification/_index.md | 6 ++--- content/english/partners.md | 2 +- content/english/publications/_index.md | 2 +- content/english/updates/first_year.md | 2 +- content/svenska/about/_index.md | 2 +- content/svenska/contribute.md | 6 ++--- content/svenska/dashboards/RECOVAC.md | 6 ++--- .../svenska/dashboards/covid_publications.md | 10 ++++----- content/svenska/dashboards/post_covid.md | 22 +++++++++---------- content/svenska/dashboards/vaccines.md | 20 ++++++++--------- .../dashboards/variants_region_uppsala.md | 4 ++-- .../svenska/dashboards/wastewater/_index.md | 4 ++-- .../covid_quantification/covid_quant_GU.md | 4 ++-- .../covid_quantification/covid_quant_KTH.md | 4 ++-- .../covid_quantification/covid_quant_SLU.md | 4 ++-- .../enteric_quantification/_index.md | 2 +- .../influenza_quantification/_index.md | 6 ++--- content/svenska/partners.md | 2 +- content/svenska/projects/dashboard.md | 8 +++---- content/svenska/publications/_index.md | 2 +- layouts/datasets/single.html | 2 +- layouts/partials/footer.html | 2 +- .../img/site_logo/CV19DP_logo_square_SWE.svg | 2 +- 40 files changed, 122 insertions(+), 122 deletions(-) diff --git a/.github/workflows/dockerhub.yml b/.github/workflows/dockerhub.yml index 8405b32ac..ffea517fe 100644 --- a/.github/workflows/dockerhub.yml +++ b/.github/workflows/dockerhub.yml @@ -20,7 +20,7 @@ jobs: push_to_registry: # only generate images when in the named repo # (to avoid running the action in forks) - if: github.repository == 'ScilifelabDataCentre/covid-portal' + if: github.repository == 'ScilifelabDataCentre/pathogens-portal' name: Publish Docker Image runs-on: ubuntu-latest # Cancel earlier job if there is a new one for the same branch/release @@ -32,7 +32,7 @@ jobs: matrix: include: - dockerfile: Dockerfiles/Dockerfile - images: ghcr.io/scilifelabdatacentre/covid-portal + images: ghcr.io/scilifelabdatacentre/pathogens-portal permissions: contents: read packages: write diff --git a/.github/workflows/trivy-scheduled.yaml b/.github/workflows/trivy-scheduled.yaml index 2079191c3..3dac358f7 100644 --- a/.github/workflows/trivy-scheduled.yaml +++ b/.github/workflows/trivy-scheduled.yaml @@ -32,7 +32,7 @@ jobs: - name: Run Trivy vulnerability scanner uses: aquasecurity/trivy-action@0.9.2 with: - image-ref: 'ghcr.io/${{ env.REPOSITORY_OWNER }}/covid-portal:develop' + image-ref: 'ghcr.io/${{ env.REPOSITORY_OWNER }}/pathogens-portal:develop' format: 'sarif' output: 'trivy-results.sarif' severity: 'CRITICAL,HIGH' diff --git a/CONTRIBUTING/adding_editing_information.md b/CONTRIBUTING/adding_editing_information.md index 1cd267dce..311654516 100644 --- a/CONTRIBUTING/adding_editing_information.md +++ b/CONTRIBUTING/adding_editing_information.md @@ -16,7 +16,7 @@ __Table of contents:__ ## How to propose changes or additions -All information displayed on the Portal is contained within [this GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal). Some of the sections use information that is stored in the `data` folder in .JSON format while other sections use information that is stored in the `content` folder in Markdown format. +All information displayed on the Portal is contained within [this GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal). Some of the sections use information that is stored in the `data` folder in .JSON format while other sections use information that is stored in the `content` folder in Markdown format. ### Using the web interface @@ -24,7 +24,7 @@ All information displayed on the Portal is contained within [this GitHub reposit - Click on the top right corner of the document ("Edit this file"). This should create a fork of the original repository in your own GitHub account. You should see a page where you can directly edit the content. - Make changes as described below; do not forget to change the last update date on top of the document if needed. - Scroll to the bottom of the page. Describe what you have changed and press 'Propose changes' -- You should now find yourself on a page where you can create a pull request. Check that the pull request will be sent to the base repository `SciLifeLabDataCentre/covid-portal` and base `develop`. You can also review the changes you made. Click on "Create pull request" if everything looks good. +- You should now find yourself on a page where you can create a pull request. Check that the pull request will be sent to the base repository `SciLifeLabDataCentre/pathogens-portal` and base `develop`. You can also review the changes you made. Click on "Create pull request" if everything looks good. - Once created, a member of the Portal team will review your changes. Once approved, they will be merged and published. @@ -33,14 +33,14 @@ Once approved, they will be merged and published. If you prefer, you can edit the website files on your computer in your favourite text editor. Fork this repository to your account. Then, clone the forked repository to your machine: ```bash -git clone git@github.com:[YOUR-USERNAME]/covid-portal.git -cd covid-portal +git clone git@github.com:[YOUR-USERNAME]/pathogens-portal.git +cd pathogens-portal ``` To make it easier to pull in changes made by others, you can add the main repository as a remote: ```bash -git remote add upstream https://github.com/ScilifelabDataCentre/covid-portal.git +git remote add upstream https://github.com/ScilifelabDataCentre/pathogens-portal.git ``` Then you can fetch changes at any time from this remote: @@ -59,7 +59,7 @@ git push Once you're finished with your edits and they are committed and pushed to your forked repository, it's time to open a pull request. In short: -- Visit the main repository: [https://github.com/ScilifelabDataCentre/covid-portal](https://github.com/ScilifelabDataCentre/covid-portal) +- Visit the main repository: [https://github.com/ScilifelabDataCentre/pathogens-portal](https://github.com/ScilifelabDataCentre/pathogens-portal) - Click the button that reads _"New Pull Request"_ - Click the text link near the top that says _"compare across forks"_ - In the right-hand _"head repository"_ drop down, select your username / fork. @@ -70,7 +70,7 @@ Once approved, they will be merged and published. #### Testing with a local copy of the Portal -Because the Portal is built on Hugo, it is quite easy to run a full version of the Portal on your computer and see how your changes look while doing that. See [this page for information on how to do that](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md). +Because the Portal is built on Hugo, it is quite easy to run a full version of the Portal on your computer and see how your changes look while doing that. See [this page for information on how to do that](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md). ## Available datasets diff --git a/CONTRIBUTING/running_a_local_copy.md b/CONTRIBUTING/running_a_local_copy.md index e2aa37e74..2cb9ceb25 100644 --- a/CONTRIBUTING/running_a_local_copy.md +++ b/CONTRIBUTING/running_a_local_copy.md @@ -29,8 +29,8 @@ $ hugo serve Cleaned | 0 | 0 Built in 123 ms -Watching for changes in /Users/philewels/GitHub/covid-portal/{archetypes,content,layouts,static} -Watching for config changes in /Users/philewels/GitHub/covid-portal/config.yaml +Watching for changes in /Users/philewels/GitHub/pathogens-portal/{archetypes,content,layouts,static} +Watching for config changes in /Users/philewels/GitHub/pathogens-portal/config.yaml Environment: "development" Serving pages from memory Running in Fast Render Mode. For full rebuilds on change: hugo server --disableFastRender diff --git a/README.md b/README.md index dc14c196b..d7fc8e13c 100644 --- a/README.md +++ b/README.md @@ -26,15 +26,15 @@ It uses the [Bootstrap](https://getbootstrap.com/) framework. In addition, it us ### Adding and editing information in different sections -We prepared detailed instructions on how to add or edit information in each specific section of the portal, see [the page on adding and editing information in the CONTRIBUTING folder](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/adding_editing_information.md). +We prepared detailed instructions on how to add or edit information in each specific section of the portal, see [the page on adding and editing information in the CONTRIBUTING folder](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/adding_editing_information.md). ### Testing changes with a local copy of the portal -Users who are technically more advanced are welcome to make contributions by running a local copy of the portal on their own computers, we prepared [instructions on how to do that here](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md). +Users who are technically more advanced are welcome to make contributions by running a local copy of the portal on their own computers, we prepared [instructions on how to do that here](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md). ### Using ImJoy Plugins -This website supports [ImJoy](https://imjoy.io) plugins which can be used to visualize, annotate, run analysis directly from the website. See [an example here](https://covid19dataportal.se/highlights/immunofluorescence/). Please see the file [CONTRIBUTING/ImJoy.md](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/ImJoy.md) for examples of usage. +This website supports [ImJoy](https://imjoy.io) plugins which can be used to visualize, annotate, run analysis directly from the website. See [an example here](https://covid19dataportal.se/highlights/immunofluorescence/). Please see the file [CONTRIBUTING/ImJoy.md](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/ImJoy.md) for examples of usage. ### The Swedish COVID-19 Sample Collection Database @@ -42,7 +42,7 @@ The portal team works closely with [Biobank Sverige](https://biobanksverige.se) ### Data visualisations -Unless otherwise specified, the data visualisations on the portal have been developed in-house by the portal team. A link to the code underlying each visualisation is provided on the portal page on which it is displayed. All visualisations on the portal can be found on our dedicated [GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). +Unless otherwise specified, the data visualisations on the portal have been developed in-house by the portal team. A link to the code underlying each visualisation is provided on the portal page on which it is displayed. All visualisations on the portal can be found on our dedicated [GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations). ## How to get help diff --git a/content/english/about/_index.md b/content/english/about/_index.md index fe668deb8..ece52ec18 100644 --- a/content/english/about/_index.md +++ b/content/english/about/_index.md @@ -20,7 +20,7 @@ The _Swedish Pathogens Portal_ provides information about available datasets, re 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. +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/pathogens-portal). We encourage the reuse of our code, either for generating another national portal, or recreating certain features. #### History of the Portal @@ -28,11 +28,11 @@ The Swedish Pathogens Portal was originally launched as the 'Swedish COVID-19 Da 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/)). -From the start, the Portal has been operated by the SciLifeLab Data Centre and partners. However, it has received considerable input from the community. Indeed, many people contributed to building the initial site, and to content throughout. An overview of some of the contributors that have been instrumental to establishing and advancing the Portal can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal/graphs/contributors). +From the start, the Portal has been operated by the SciLifeLab Data Centre and partners. However, it has received considerable input from the community. Indeed, many people contributed to building the initial site, and to content throughout. An overview of some of the contributors that have been instrumental to establishing and advancing the Portal can be found on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal/graphs/contributors). #### Portal team -Many people from SciLifeLab, NBIS, other organisations, and the community have been involved in the Portal since its conception in early 2020. A complete list of contributors can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal/graphs/contributors). Below, we show the current team of people actively working on the Portal. +Many people from SciLifeLab, NBIS, other organisations, and the community have been involved in the Portal since its conception in early 2020. A complete list of contributors can be found on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal/graphs/contributors). Below, we show the current team of people actively working on the Portal. The team are happy to help with using the Portal, to take suggestions regarding new and existing sections, and to answer any questions that you may have. Please just get in touch using for [contact](/contact/) form. diff --git a/content/english/contribute.md b/content/english/contribute.md index 0488919fa..7099f2b2d 100644 --- a/content/english/contribute.md +++ b/content/english/contribute.md @@ -22,9 +22,9 @@ There are multiple ways to add/edit information on the Portal. Choose any method

Send a GitHub pull request

-

All information which is displayed on the Portal is stored on GitHub. 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.

-

The information for each section of the Portal is stored in a particular folder and needs to be formatted in a certain way. To make it easier for you to contribute, we have written detailed instructions for each of the sections. Moreover, you can even easily run a local copy of the Portal on your computer and see all changes live before sending them to us. If you run into an issue, send us an email so that we can help you.

-

Contribute through GitHub

+

All information which is displayed on the Portal is stored on GitHub. 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.

+

The information for each section of the Portal is stored in a particular folder and needs to be formatted in a certain way. To make it easier for you to contribute, we have written detailed instructions for each of the sections. Moreover, you can even easily run a local copy of the Portal on your computer and see all changes live before sending them to us. If you run into an issue, send us an email so that we can help you.

+

Contribute through GitHub

diff --git a/content/english/dashboards/RECOVAC.md b/content/english/dashboards/RECOVAC.md index 089740933..b8d255f0a 100644 --- a/content/english/dashboards/RECOVAC.md +++ b/content/english/dashboards/RECOVAC.md @@ -27,7 +27,7 @@ EPN Nr 2020-01800, 2020-05829, 2021-00267, 2021-00829, 2021-02106, 2021-04098, 2
All data last updated: {{% RECOVAC_date_modified %}}
-_All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/RECOVAC). The particular scripts used in each case are linked below the plots._ +_All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/RECOVAC). The particular scripts used in each case are linked below the plots._ The visualisations on this page broadly relate to two types of data; (a) data regarding the Swedish population at large, and (b) data on individuals in the Swedish population with certain comorbidities (at the start of the pandemic, assessed as of 1st Jan 2020, based on information from 2015-2019). More detail about the data used to produce the visualisations is available in the two subsections below. Instructions on how to manipulate the interactive plots are provided above the plots in each subsection. @@ -97,7 +97,7 @@ When hovering over the plot with the cursor, additional grey icons appear in the
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}
-**Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py). +**Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py). ### Data related to patients with comorbidities @@ -151,7 +151,7 @@ When hovering over the plot with the cursor, additional grey icons appear in the
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}
-**Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py). +**Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py). ## Determinants of vaccination diff --git a/content/english/dashboards/covid_publications.md b/content/english/dashboards/covid_publications.md index bb7222718..050e8a721 100644 --- a/content/english/dashboards/covid_publications.md +++ b/content/english/dashboards/covid_publications.md @@ -13,9 +13,9 @@ aliases: dashboards_topics: [COVID-19, Infectious diseases] --- -The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/), and is available for download, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details. The database is manually curated, so may not be exhaustive. From May 2023, we began to use the Europe PMC REST API to idenfy publications. The scripts that we use to do this are [openly available on GitHub](https://github.com/ScilifelabDataCentre/covid-portal-scripts/tree/main/All_publications) and can be reused for work with other pathogens. The database is updated monthly at the start of the month. +The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/), and is available for download, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details. The database is manually curated, so may not be exhaustive. From May 2023, we began to use the Europe PMC REST API to idenfy publications. The scripts that we use to do this are [openly available on GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-scripts/tree/main/All_publications) and can be reused for work with other pathogens. The database is updated monthly at the start of the month. -The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). ## Number of new publications @@ -33,7 +33,7 @@ This graph displays the number of publications (including both journal publicati {{< publications_per_month >}} --> -**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Count_publications/count_publications.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Count_publications/count_publications.py). ## Ten most recent publications @@ -47,7 +47,7 @@ This table displays the ten most recent publications in our database (including These wordclouds display the words and two word phrases that appear most frequently in the titles of preprints or journal publications within the database. Note that we have filtered out commonly used words that are uninformative (e.g. 'the', 'a', 'this') as well as the words 'COVID-19' and 'SARS-CoV-2', since these appeared in almost all titles. The wordclouds are updated weekly. -**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). #### All publications @@ -63,7 +63,7 @@ Wordclouds are displayed for each funder that we identified as having been assoc These wordclouds display the words and two word phrases that appear most frequently in the abstracts of preprints or journal publications within the database. Note that we have filtered out commonly used words that are uninformative (e.g. 'the', 'a', 'this') as well as the words 'COVID-19' and 'SARS-CoV-2', since these appeared in almost all abstracts. The wordclouds are updated weekly. -**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). #### All publications diff --git a/content/english/dashboards/post_covid.md b/content/english/dashboards/post_covid.md index 01ed06080..76e0d40a2 100644 --- a/content/english/dashboards/post_covid.md +++ b/content/english/dashboards/post_covid.md @@ -33,7 +33,7 @@ The data underlying the visualisations on this page are from [The Swedish Board ### Code -All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/postCOVID). The particular scripts used in each case are linked below the individual visualisations. +All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/postCOVID). The particular scripts used in each case are linked below the individual visualisations. ## Statistics on Post COVID-19 condition in Sweden @@ -53,7 +53,7 @@ These plots display the number of times that patients were assigned the diagnose
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_agesex_casedist.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). #### Diagnosis Z86.1A/U08.9 @@ -61,7 +61,7 @@ These plots display the number of times that patients were assigned the diagnose
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_agesex_casedist.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). ### Geographic distribution of diagnosed cases relative to population size @@ -73,7 +73,7 @@ The maps below show the number of people that received the diagnoses of interest
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U099.json" height="500px" >}}
-**Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U099.py). +**Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U099.py). #### Diagnosis Z86.1A/U08.9 @@ -81,7 +81,7 @@ The maps below show the number of people that received the diagnoses of interest
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U089.json" height="500px" >}}
-**Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U089.py). +**Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U089.py). @@ -121,7 +121,7 @@ The below table displays the most common types of diagnosis (diagnosis groups) t _Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once_ -**Code used to produce table:** [Script to produce table (English)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Script to produce table (Swedish)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py). +**Code used to produce table:** [Script to produce table (English)](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Script to produce table (Swedish)](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py). ### Contacts with healthcare @@ -135,7 +135,7 @@ The below plot shows the number of times that patients given the diagnoses of in
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py). ### Contacts with healthcare, divided by patient sex @@ -151,7 +151,7 @@ The below plots show the number of times that patients given one of the diagnose
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). #### Diagnosis Z86.1A/U08.9 @@ -163,7 +163,7 @@ The below plots show the number of times that patients given one of the diagnose
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). ## Ongoing research projects diff --git a/content/english/dashboards/vaccines.md b/content/english/dashboards/vaccines.md index 9a7125dfc..c996d3ce0 100644 --- a/content/english/dashboards/vaccines.md +++ b/content/english/dashboards/vaccines.md @@ -51,7 +51,7 @@ For more information on vaccination in Sweden, please also see the [RECOVAC dash The [Swedish Health Agency (Folkhälsomyndigheten, FoHM)](https://folkhalsomyndigheten.se) provide information, summary statistics, and data related to COVID-19 vaccination in Sweden [(only available in Swedish)](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistikdatabaser-och-visualisering/vaccinationsstatistik/statistik-for-vaccination-mot-covid-19/). The visualisations below are based on the publicly available COVID-19 vaccination data from FoHM, which can be [downloaded directly](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). For each visualisation, we describe which data in the dataset were used, how calculations were completed, and provide a link to the script(s) used to produce it. -The source data is updated weekly (on Thursdays), and the visualisations on this page will be updated shortly thereafter (usually on Fridays). All of our code related to this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Vaccine_page). All of the vaccine data is processed using a single [data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_dataprep_Swedentots.py). The code required to generate each visualisation/number set is linked close to the corresponding plot/text. +The source data is updated weekly (on Thursdays), and the visualisations on this page will be updated shortly thereafter (usually on Fridays). All of our code related to this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Vaccine_page). All of the vaccine data is processed using a single [data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_dataprep_Swedentots.py). The code required to generate each visualisation/number set is linked close to the corresponding plot/text. ### General summary statistics @@ -73,9 +73,9 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/Total_vaccinated_barchart.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_indicator_barchart.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_indicator_barchart.py). -**Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py). +**Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py). To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week. @@ -93,7 +93,7 @@ The below graph shows vaccine coverage across the whole of Sweden. We use the 'w
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/vaccine_timeseries_pop_barchart.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_timeseries_barchart.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_timeseries_barchart.py). ### Administration of vaccinations in each Swedish county (län) @@ -109,7 +109,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/onedose_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least two vaccine doses @@ -117,7 +117,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/twodoses_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least three vaccine doses @@ -125,7 +125,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/threedoses_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least four vaccine doses @@ -133,7 +133,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/fourdoses_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least five vaccine doses @@ -148,7 +148,7 @@ Please note the differences between the two below maps. Coverage appears to be v -**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). ### Administration of vaccinations according to age group @@ -166,7 +166,7 @@ Data is available on the number of individuals aged 65-69 that have received the
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/vaccine_heatmap.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce heatmap](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_heatmaps.py). +**Code used to produce plot:** [Script to produce heatmap](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_heatmaps.py). ## Ongoing research projects diff --git a/content/english/dashboards/variants_region_uppsala.md b/content/english/dashboards/variants_region_uppsala.md index 21a9df36e..816832aa4 100644 --- a/content/english/dashboards/variants_region_uppsala.md +++ b/content/english/dashboards/variants_region_uppsala.md @@ -39,7 +39,7 @@ Use the **‘Last 16 weeks’ button** to see data only from the last 16 weeks,
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}
-**Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py). +**Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py). ### All sequences with WHO label/Pango lineage) @@ -55,7 +55,7 @@ Use the **’Deselect all lineages’ button** to clear data from all lineages f
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_one_wholetime.json" height="600px" >}}
-**Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_one_plot.py). +**Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/ClinMicro/lineage_one_plot.py). ## Commentary from the research group diff --git a/content/english/dashboards/wastewater/_index.md b/content/english/dashboards/wastewater/_index.md index e76d8c379..e8c42d0f5 100644 --- a/content/english/dashboards/wastewater/_index.md +++ b/content/english/dashboards/wastewater/_index.md @@ -43,7 +43,7 @@ The work on this dashboard is divided according to different topics explored. Se ## Availability of code -All code used to produce the visualisations on the tabs on this dashboard is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/wastewater). The particular scripts used in each case are linked below the individual visualisations. +All code used to produce the visualisations on the tabs on this dashboard is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/wastewater). The particular scripts used in each case are linked below the individual visualisations. ## Sample collection sites @@ -53,7 +53,7 @@ Below is a map showing the wastewater treatment plants (WWTPs) from which wastew
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_map_test.json" height="600px" >}}
-**Code used to produce map:** [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/interactive_wastewater_map.py). +**Code used to produce map:** [Script to produce map](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/interactive_wastewater_map.py). The table below lists; the towns/cities monitored by groups sharing data on this dashboard, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), whether monitoring is actively ongoing (Active?), the viruses monitored at the site (Viruses monitored), and the group(s) that have monitored/are monitored the site. An asterisk (\*) next to the number of people indicates that the value is a BOD-7 value (an estimate of the people connected), rather than the number of people physically connected to each WWTP. The information in the below table is [available for download as an excel file](https://blobserver.dc.scilifelab.se/blob/overall_ww_collection_sites.xlsx). diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md index 3a5a1b8b2..9f97b6570 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md @@ -63,7 +63,7 @@ _The blue block on the graph indicates the period where sample collection was no
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/gothenburg_covid.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/gothenburg_covid.py). ## Commentary from the research group diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md index dd9f04558..dceb01b4a 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md @@ -73,7 +73,7 @@ Please also note that although the same methods are used for all cities shown on
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_stockholm.json" height="550px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_stockholm_regular.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_stockholm_regular.py). ### Malmö @@ -87,7 +87,7 @@ Please also note that although the same methods are used for all cities shown on
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_kthmalmo.json" height="550px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/quant_malmo_kthplot.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/quant_malmo_kthplot.py). ## Commentary from the research group diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index 17c713b2a..fb84bb35b 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md @@ -73,7 +73,7 @@ Please note that although the same methods are used for all cities shown on this
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="800px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_regular.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_regular.py). ## Commentary from the research group diff --git a/content/english/dashboards/wastewater/enteric_quantification/_index.md b/content/english/dashboards/wastewater/enteric_quantification/_index.md index 3228ddb62..8b2c284cc 100644 --- a/content/english/dashboards/wastewater/enteric_quantification/_index.md +++ b/content/english/dashboards/wastewater/enteric_quantification/_index.md @@ -42,7 +42,7 @@ Please see [the section with summary information about the viruses](#basic-virus
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/enteric_graph_gu.json" height="550px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/enteric_viruses_gu.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/enteric_viruses_gu.py). ## Commentary from the research group diff --git a/content/english/dashboards/wastewater/influenza_quantification/_index.md b/content/english/dashboards/wastewater/influenza_quantification/_index.md index 240df14d5..bf32d186f 100644 --- a/content/english/dashboards/wastewater/influenza_quantification/_index.md +++ b/content/english/dashboards/wastewater/influenza_quantification/_index.md @@ -40,7 +40,7 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infA.json" height="600px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_influenza_a.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_influenza_a.py). ### Influenza B @@ -52,7 +52,7 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infB.json" height="600px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_influenza_b.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_influenza_b.py). ## Commentary from the research group @@ -68,7 +68,7 @@ The group provide reports to summarise their latest findings. The latest report **Contact:** and -**Download the data:** [Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file](https://raw.githubusercontent.com/ScilifelabDataCentre/covid-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data are available for Influenza A from week 42 of 2022 and for Influenza B from week 12 of 2023; updated weekly. +**Download the data:** [Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file](https://raw.githubusercontent.com/ScilifelabDataCentre/pathogens-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data are available for Influenza A from week 42 of 2022 and for Influenza B from week 12 of 2023; updated weekly. **How to cite the dataset:** diff --git a/content/english/partners.md b/content/english/partners.md index 2135f69f9..c5f33cd48 100644 --- a/content/english/partners.md +++ b/content/english/partners.md @@ -9,7 +9,7 @@ menu: The Swedish Pathogens Portal originated as the 'Swedish COVID-19 Data Portal'. It was the first national node of the [European COVID-19 Data Platform](https://covid19dataportal.org/); a Europe-wide platform allowing researchers to upload, access, and analyse COVID-19 related datasets. The [European COVID-19 Data Platform](https://covid19dataportal.org/) was launched in the spring of 2020 when the European Commission [took the initiative to develop a European data sharing platform for COVID-19 research efforts](https://www.embl.org/news/science/embl-ebi-launches-covid-19-data-portal/). It is operated by the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) and [partners](https://www.covid19dataportal.org/partners). -Besides [Sweden](https://www.pathogens.se), a number of other countries also launched national portals, many of which used [our source code](https://github.com/ScilifelabDataCentre/covid-portal) to get started! Below is a list of the other national COVID-19 data portals: +Besides [Sweden](https://www.pathogens.se), a number of other countries also launched national portals, many of which used [our source code](https://github.com/ScilifelabDataCentre/pathogens-portal) to get started! Below is a list of the other national COVID-19 data portals: - [COVID-19 Data Portal Estonia](https://covid19dataportal.ee) - [COVID-19 Data Portal Greece](https://www.covid19dataportal.gr) diff --git a/content/english/publications/_index.md b/content/english/publications/_index.md index 2ad014659..50d28b02a 100644 --- a/content/english/publications/_index.md +++ b/content/english/publications/_index.md @@ -7,7 +7,7 @@ menu: weight: 40 --- -This section presents a list of published scientific journal articles and preprints on COVID-19 and SARS-CoV-2 where at least one author has an affiliation with a Swedish research institute. Note that this database is primarily a manually curated database and thus it may not be exhaustive. Note that from May 2023, we began to use the Europe PMC REST API to idenfy publications. The scripts that we use to do this are [openly available on GitHub](https://github.com/ScilifelabDataCentre/covid-portal-scripts/tree/main/All_publications) and can be reused with other pathogens. +This section presents a list of published scientific journal articles and preprints on COVID-19 and SARS-CoV-2 where at least one author has an affiliation with a Swedish research institute. Note that this database is primarily a manually curated database and thus it may not be exhaustive. Note that from May 2023, we began to use the Europe PMC REST API to idenfy publications. The scripts that we use to do this are [openly available on GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-scripts/tree/main/All_publications) and can be reused with other pathogens. If you would like your publication to be added here or information about your publication to be corrected, [please get in touch with us](/suggestions/). We also have a [page with visualisations of the publications in this database](/dashboards/covid_publications/). diff --git a/content/english/updates/first_year.md b/content/english/updates/first_year.md index c247e1ae4..2b3e97ee9 100644 --- a/content/english/updates/first_year.md +++ b/content/english/updates/first_year.md @@ -36,7 +36,7 @@ The Swedish COVID-19 Data Portal also works to increase the visibility of public The Portal also provides a place for various community-driven projects to publish their results or reach researchers in Sweden. Among the general public and policy-makers, the section of the Portal displaying recent SARS-CoV-2 testing results has been especially popular. This section contains regularly updated results from [antibody testing carried out at the SciLifeLab Autoimmunity and Serology profiling facility](/data_types/health_data/serology-statistics/) as well as from the [analyses of wastewater across Sweden](/data_types/environment/wastewater/). The Portal also has sections dedicated to partner projects, currently including [CRUSH Covid](/data_types/health_data/crush_covid/) and [COVID Symptom Study Sweden](/data_types/health_data/symptom_study_sweden/) (but we are always on the lookout for new partners). -> "All code developed for the Portal has been [shared on GitHub](https://github.com/ScilifelabDataCentre/covid-portal/tree/master) under an open source licence. As the underlying code for the Portal is freely available on GitHub, parts of it have been reused by a number of teams in other countries in order to rapidly develop their own national portals. This means that the Portal itself functions as a demonstration of the value of openly sharing code," says Arnold Kochari, one of the web developers in the Portal team. +> "All code developed for the Portal has been [shared on GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal/tree/master) under an open source licence. As the underlying code for the Portal is freely available on GitHub, parts of it have been reused by a number of teams in other countries in order to rapidly develop their own national portals. This means that the Portal itself functions as a demonstration of the value of openly sharing code," says Arnold Kochari, one of the web developers in the Portal team. Finally, the Portal team has multiple plans for the future. For example, work is ongoing to develop new sections and visualisations that should be made available later in 2021. The COVID-19 pandemic is now in a new phase in Sweden, where the vaccination coverage is increasing and vaccine research is coming into focus. The Portal is planning to launch corresponding sections devoted to vaccine research in the near future. Recently, the [COVID-19 Data & Code Reuse Competition](/data_code_reuse) was launched by the Portal. In this competition, both researchers and the general public are invited to prepare small projects that make use of publicly available data and/or code to combat the COVID-19 and future pandemics. diff --git a/content/svenska/about/_index.md b/content/svenska/about/_index.md index c39fef0a0..3ea5d1b14 100644 --- a/content/svenska/about/_index.md +++ b/content/svenska/about/_index.md @@ -19,7 +19,7 @@ Den Patogens Portal Sverige tillhandahåller information, riktlinjer, verktyg oc Portalen drivs av [SciLifeLab Data Centre](https://scilifelab.se/data/) och samarbetspartners och har som syfte att stödja forskare vid svenska lärosäten verksamma inom forskningsfältet pandemisk beredskap. Vi välkomnar forskarsamhället att bidra med innehåll och förslag på förändringar och nytt innehåll. Som forskare kan du interagera med Portalen på ett flertal sätt, genom att fylla i formuläret, kontakta oss via epost eller via sociala media. Portalenteamet kan även ge stöd i datarelaterade frågor och hjälpa forskare att hitta lämpliga [supporttjänster](/sv/support/). -Den här webbplatsen är byggd med hjälp av [Hugo](https://gohugo.io/) och använder [Bootstrap](https://getbootstrap.com/) ramverket, [DataTables](https://datatables.net/) används för att skapa tabeller, [Vega/Vega-Lite](https://vega.github.io/vega-lite/) och [Plotly](https://plotly.com/) för interaktiv grafik. Koden är öppen källkod ([MIT-licens](https://choosealicense.com/licenses/mit/)) och [finns tillgänglig på GitHub](https://github.com/ScilifelabDataCentre/covid-portal). Vi välkomnar att Portalens källkod återanvänds och att forskare bidrar till webbsidans källkod. +Den här webbplatsen är byggd med hjälp av [Hugo](https://gohugo.io/) och använder [Bootstrap](https://getbootstrap.com/) ramverket, [DataTables](https://datatables.net/) används för att skapa tabeller, [Vega/Vega-Lite](https://vega.github.io/vega-lite/) och [Plotly](https://plotly.com/) för interaktiv grafik. Koden är öppen källkod ([MIT-licens](https://choosealicense.com/licenses/mit/)) och [finns tillgänglig på GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal). Vi välkomnar att Portalens källkod återanvänds och att forskare bidrar till webbsidans källkod. Om du vill bidra med innehåll eller har förslag på förbättringar av webbplatsen, vänligen kontakt oss på diff --git a/content/svenska/contribute.md b/content/svenska/contribute.md index 365743534..6f8923a02 100644 --- a/content/svenska/contribute.md +++ b/content/svenska/contribute.md @@ -27,9 +27,9 @@ Det finns flera sätt att ge förslag på eller redigera informationen som ligge -->

Skicka en GitHub pull-request

-

All information som visas på Portalen ligger på GitHub. Informationen lagras som .JSON-filer eller som Markdown-filer, vilket gör att de är enkelt läsbara och lätta att redigera. Om du är van med webbgränssnittet för GitHub eller GitHub CLI kan du enkelt redigera eller lägga till information själv och skicka oss en pull request.

-

Informationen för varje sektion av Portalen lagras i en viss mapp och måste formateras på ett visst sätt. För att göra det enklare för dig att bidra till Portalens har vi skrivit detaljerade instruktioner för varje avsnitt. Dessutom kan du enkelt köra en lokal kopia av portalen på din egen dator och se alla ändringar live innan du skickar dem till oss. Om du stöter på ett problem, kontakta oss på epost så hjälper vi dig.

-

Bidra med GitHub

+

All information som visas på Portalen ligger på GitHub. Informationen lagras som .JSON-filer eller som Markdown-filer, vilket gör att de är enkelt läsbara och lätta att redigera. Om du är van med webbgränssnittet för GitHub eller GitHub CLI kan du enkelt redigera eller lägga till information själv och skicka oss en pull request.

+

Informationen för varje sektion av Portalen lagras i en viss mapp och måste formateras på ett visst sätt. För att göra det enklare för dig att bidra till Portalens har vi skrivit detaljerade instruktioner för varje avsnitt. Dessutom kan du enkelt köra en lokal kopia av portalen på din egen dator och se alla ändringar live innan du skickar dem till oss. Om du stöter på ett problem, kontakta oss på epost så hjälper vi dig.

+

Bidra med GitHub

diff --git a/content/svenska/dashboards/RECOVAC.md b/content/svenska/dashboards/RECOVAC.md index 6e91f9214..2dc7cc06f 100644 --- a/content/svenska/dashboards/RECOVAC.md +++ b/content/svenska/dashboards/RECOVAC.md @@ -31,7 +31,7 @@ EPN Nr 2020-01800, 2020-05829, 2021-00267, 2021-00829, 2021-02106, 2021-04098, 2
All data last updated: {{% RECOVAC_date_modified %}}
-_All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/RECOVAC). The particular scripts used in each case are linked below the plots._ +_All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/RECOVAC). The particular scripts used in each case are linked below the plots._ The visualisations on this page broadly relate to two types of data; (a) data regarding the Swedish population at large, and (b) data on individuals in the Swedish population with certain comorbidities (at the start of the pandemic, assessed as of 1st Jan 2020, based on information from 2015-2019). More detail about the data used to produce the visualisations is available in the two subsections below. Instructions on how to manipulate the interactive plots are provided above the plots in each subsection. @@ -101,7 +101,7 @@ When hovering over the plot with the cursor, additional grey icons appear in the
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}
-**Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py). +**Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py). ### Data related to patients with comorbidities @@ -155,7 +155,7 @@ When hovering over the plot with the cursor, additional grey icons appear in the
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}
-**Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py). +**Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py). ## Determinants of vaccination diff --git a/content/svenska/dashboards/covid_publications.md b/content/svenska/dashboards/covid_publications.md index eac64836f..26f0b10ef 100644 --- a/content/svenska/dashboards/covid_publications.md +++ b/content/svenska/dashboards/covid_publications.md @@ -17,9 +17,9 @@ aliases: En svensk översättning av denna sida kommer inom kort. -The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/), and is available for download, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details. The database is manually curated, so may not be exhaustive. From May 2023, we began to use the Europe PMC REST API to idenfy publications. The scripts that we use to do this are [openly available on GitHub](https://github.com/ScilifelabDataCentre/covid-portal-scripts/tree/main/All_publications) and can be reused for work with other pathogens. The database is updated monthly at the start of the month. +The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/), and is available for download, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details. The database is manually curated, so may not be exhaustive. From May 2023, we began to use the Europe PMC REST API to idenfy publications. The scripts that we use to do this are [openly available on GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-scripts/tree/main/All_publications) and can be reused for work with other pathogens. The database is updated monthly at the start of the month. -The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). ## Number of new publications @@ -37,7 +37,7 @@ This graph displays the number of publications (including both journal publicati {{< publications_per_month >}} --> -**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Count_publications/count_publications.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Count_publications/count_publications.py). ## Ten most recent publications @@ -51,7 +51,7 @@ This table displays the ten most recent publications in our database (including These wordclouds display the words and two word phrases that appear most frequently in the titles of preprints or journal publications within the database. Note that we have filtered out commonly used words that are uninformative (e.g. 'the', 'a', 'this') as well as the words 'COVID-19' and 'SARS-CoV-2', since these appeared in almost all titles. The wordclouds are updated weekly. -**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). #### All publications @@ -67,7 +67,7 @@ Wordclouds are displayed for each funder that we identified as having been assoc These wordclouds display the words and two word phrases that appear most frequently in the abstracts of preprints or journal publications within the database. Note that we have filtered out commonly used words that are uninformative (e.g. 'the', 'a', 'this') as well as the words 'COVID-19' and 'SARS-CoV-2', since these appeared in almost all abstracts. The wordclouds are updated weekly. -**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +**Code used to produce plot:** [Script to produce wordclouds](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Wordcloud/livewordcloud.py). Note that the script relies on multiple external files that can be found in the [same folder in the GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). #### All publications diff --git a/content/svenska/dashboards/post_covid.md b/content/svenska/dashboards/post_covid.md index de665e0d9..9795d4248 100644 --- a/content/svenska/dashboards/post_covid.md +++ b/content/svenska/dashboards/post_covid.md @@ -34,7 +34,7 @@ Alla data som presenteras här finns tillgängliga för nedladdning från [Socia ### Källkod -All källkod som används för att göra visualiseringarna på denna sidan finns tillgängliga på [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/postCOVID). Källkod som används är länkad under respektive visualisering. +All källkod som används för att göra visualiseringarna på denna sidan finns tillgängliga på [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/postCOVID). Källkod som används är länkad under respektive visualisering. ## Statistik om postcovid i Sverige @@ -56,7 +56,7 @@ Detta diagram visar antalet gånger patienter som diagnostiserats med diagnoser
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_agesex_casedist.json" height="500px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa visualisering](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). +**Källkod som används för att skapa grafen:** [Källkod som används för att skapa visualisering](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). #### Diagnoskod Z86.1A/U08.9 @@ -64,7 +64,7 @@ Detta diagram visar antalet gånger patienter som diagnostiserats med diagnoser
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_agesex_casedist.json" height="500px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa visualisering](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). +**Källkod som används för att skapa grafen:** [Källkod som används för att skapa visualisering](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py). ### Geografisk fördelning av diagnostiserade fall relativt populationens storlek @@ -76,7 +76,7 @@ Geografisk fördelning av diagnostiserade fall i förhållande till befolkningss
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U099_Swedish.json" height="500px" >}}
-**Källkod som används för att skapa visualisering:** [Källkod som används för databeredning](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Källkod som används för att skapa kartan](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U099.py). +**Källkod som används för att skapa visualisering:** [Källkod som används för databeredning](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Källkod som används för att skapa kartan](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U099.py). #### Diagnoskod Z86.1A/U08.9 @@ -84,7 +84,7 @@ Geografisk fördelning av diagnostiserade fall i förhållande till befolkningss
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U089_Swedish.json" height="500px" >}}
-**Källkod som används för att skapa visualisering:** [Källkod som används för databeredning](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Källkod som används för att skapa kartan](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U089.py). +**Källkod som används för att skapa visualisering:** [Källkod som används för databeredning](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Källkod som används för att skapa kartan](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U089.py). @@ -124,7 +124,7 @@ Denna tabell visar de vanligaste diagnosgrupper som har rapporterats tillsammans _Observera att en individ kan ha mer än en diagnosgrupp som rapporteras tillsammans med U09.9 Postinfektiöst tillstånd efter covid-19 (Postcovid). Om en individ har samma besvär vid flera vårdtillfällen/läkarbesök räknas diagnosen bara en gång._ -**Källkod som används för att skapa tabellen:** [Källkod som används för att skapa tabellen (engelska)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Källkod som används för att skapa tabellen (svenska)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py). +**Källkod som används för att skapa tabellen:** [Källkod som används för att skapa tabellen (engelska)](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Källkod som används för att skapa tabellen (svenska)](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py). ### Vårdkontakter @@ -138,7 +138,7 @@ Denna graf visar antal vårdkontakter för patienter med de av de tre diagnoskod
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py). +**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py). ### Antal vårdkontakter uppdelat på kön @@ -154,7 +154,7 @@ Dessa grafer visar antal vårdkontakter för patienter som diagnostiserats med e
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). +**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). #### Diagnoskod Z86.1A/U08.9 @@ -166,7 +166,7 @@ Dessa grafer visar antal vårdkontakter för patienter som diagnostiserats med e
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). +**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py). ## Pågående forskningsprojekt diff --git a/content/svenska/dashboards/vaccines.md b/content/svenska/dashboards/vaccines.md index 2d73ed204..34dc6edd6 100644 --- a/content/svenska/dashboards/vaccines.md +++ b/content/svenska/dashboards/vaccines.md @@ -50,7 +50,7 @@ For more information on vaccination in Sweden, please also see the [RECOVAC dash The [Swedish Health Agency (Folkhälsomyndigheten, FoHM)](https://folkhalsomyndigheten.se) provide information, summary statistics, and data related to COVID-19 vaccination in Sweden [(only available in Swedish)](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistikdatabaser-och-visualisering/vaccinationsstatistik/statistik-for-vaccination-mot-covid-19/). The visualisations below are based on the publicly available COVID-19 vaccination data from FoHM, which can be [downloaded directly](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). For each visualisation, we describe which data in the dataset were used, how calculations were completed, and provide a link to the script(s) used to produce it. -The source data is updated weekly (on Thursdays), and the visualisations on this page will be updated shortly thereafter (usually on Fridays). All of our code related to this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Vaccine_page). All of the vaccine data is processed using a single [data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_dataprep_Swedentots.py). The code required to generate each visualisation/number set is linked close to the corresponding plot/text. +The source data is updated weekly (on Thursdays), and the visualisations on this page will be updated shortly thereafter (usually on Fridays). All of our code related to this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Vaccine_page). All of the vaccine data is processed using a single [data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_dataprep_Swedentots.py). The code required to generate each visualisation/number set is linked close to the corresponding plot/text. ### General summary statistics @@ -72,9 +72,9 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/Total_vaccinated_barchart.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_indicator_barchart.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_indicator_barchart.py). -**Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py). +**Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py). To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week. @@ -92,7 +92,7 @@ The below graph shows vaccine coverage across the whole of Sweden. We use the 'w
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/vaccine_timeseries_pop_barchart.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_timeseries_barchart.py). +**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_timeseries_barchart.py). ### Administration of vaccinations in each Swedish county (län) @@ -108,7 +108,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/onedose_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least two vaccine doses @@ -116,7 +116,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/twodoses_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least three vaccine doses @@ -124,7 +124,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/threedoses_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least four vaccine doses @@ -132,7 +132,7 @@ Again, please note that percentage values calculated using the 'whole population
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/fourdoses_pop_map.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). #### Received at least five vaccine doses @@ -147,7 +147,7 @@ Please note the differences between the two below maps. Coverage appears to be v -**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). +**Code used to produce plot:** [Script to produce maps](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_maps_population.py). ### Administration of vaccinations according to age group @@ -165,7 +165,7 @@ Data is available on the number of individuals aged 65-69 that have received the
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/vaccine_heatmap.json" height="500px" >}}
-**Code used to produce plot:** [Script to produce heatmap](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_heatmaps.py). +**Code used to produce plot:** [Script to produce heatmap](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_heatmaps.py). ## Ongoing research projects diff --git a/content/svenska/dashboards/variants_region_uppsala.md b/content/svenska/dashboards/variants_region_uppsala.md index 80919b540..1b8f7247a 100644 --- a/content/svenska/dashboards/variants_region_uppsala.md +++ b/content/svenska/dashboards/variants_region_uppsala.md @@ -41,7 +41,7 @@ Använd knappen **'Last 16 weeks'** för att endast se data från de senaste 16
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py). +**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). ### Alla sekvenser med WHO-märkning/Pangolinje) @@ -57,7 +57,7 @@ Använd knappen **'Deselect all lineages'** för att rensa bort data från alla
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_one_wholetime.json" height="600px" >}}
-**Källkod som används för att skapa grafen:** [Källkod som används för att skapa grafen](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_one_plot.py). +**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_one_plot.py). ## Kommentarer från forskargruppen diff --git a/content/svenska/dashboards/wastewater/_index.md b/content/svenska/dashboards/wastewater/_index.md index f917ab1df..e27f8e39a 100644 --- a/content/svenska/dashboards/wastewater/_index.md +++ b/content/svenska/dashboards/wastewater/_index.md @@ -44,7 +44,7 @@ Data som visas på den här dashboarden är uppdelad efter de olika patogener so ## Tillgänglighet av källkod -All källkod som skapats för visualiseringarna under de olika flikarna på denna dashboard finns öppet tillgänglig på [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/wastewater). Skripten finns tillgängliga under respektive visualisering. +All källkod som skapats för visualiseringarna under de olika flikarna på denna dashboard finns öppet tillgänglig på [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/wastewater). Skripten finns tillgängliga under respektive visualisering. ## Insamlingsplatser för avloppsvatten @@ -54,7 +54,7 @@ Nedan finns en karta som visar de avloppsreningsverk (på engelska wastewater tr
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_map_test.json" height="600px" >}}
-**Källkod som använts för att skapa kartan:** [Källkod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/interactive_wastewater_map.py). +**Källkod som använts för att skapa kartan:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/interactive_wastewater_map.py). Tabellen nedan listar; städerna/orterna som monitoreras av de forskargrupper som delar data, vilka avloppsreningsverk (WWTP) som avloppsprover samlats in ifrån, antal personer i upptagningsområdet (Number of people), om övervakningen är pågående eller inte (Active?), vilket virus som övervakas på platsen (Viruses monitored) och forskargrupp(er) som har övervakat/övervakar platsen. En asterisk (\*) bredvid antal personer indikerar att värdet är ett BO-7-värde (en uppskattning av de personer som är anslutna till ett avloppsreningsverk), snarare än antalet personer som är fysiskt anslutna. Informationen i tabellen nedan är [tillgänglig för nedladdning som en excel-fil](https://blobserver.dc.scilifelab.se/blob/overall_ww_collection_sites.xlsx). diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md index a7a79a0c7..2a209bb6a 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md @@ -32,7 +32,7 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng.
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}
-**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/gothenburg_covid.py). +**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/gothenburg_covid.py). ## Kommentarer från forskargruppen @@ -44,7 +44,7 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng. **Kontakt:** -**Nedladdning av data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://github.com/ScilifelabDataCentre/covid-portal/raw/develop/static/ww_data_temp/wastewater_data_gu_allviruses.xlsx). Resultat finns tillgängliga för mängd SARS-CoV-2 från vecka 7 2020 (ett mindre uppehåll under vintern 2022-2023) , och för enterovirus från vecka 2 2023. Data uppdateras veckovis.\ +**Nedladdning av data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://github.com/ScilifelabDataCentre/pathogens-portal/raw/develop/static/ww_data_temp/wastewater_data_gu_allviruses.xlsx). Resultat finns tillgängliga för mängd SARS-CoV-2 från vecka 7 2020 (ett mindre uppehåll under vintern 2022-2023) , och för enterovirus från vecka 2 2023. Data uppdateras veckovis.\ **För att citera datasetet:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501). diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md index c20872a57..b7ddc71ee 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md @@ -72,7 +72,7 @@ Notera också att även om samma metoder används för alla städer som visas p
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_stockholm.json" height="550px" >}}
-**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_stockholm_regular.py). +**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_stockholm_regular.py). ### Malmö @@ -86,7 +86,7 @@ Notera också att även om samma metoder används för alla städer som visas p
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_kthmalmo.json" height="550px" >}}
-**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/quant_malmo_kthplot.py). +**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/quant_malmo_kthplot.py). ## Kommentarer från forskargruppen diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index c11b9717f..924e9c0a4 100644 --- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md @@ -72,7 +72,7 @@ Notera också att även om samma metoder används för alla städer som visas p
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="800px" >}}
-**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_regular.py). +**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_regular.py). ## Kommentarer från forskargruppen @@ -88,7 +88,7 @@ Forskargruppen tillhandahåller även en rapport som sammanfattar informationen **Kontakt:** och -**Ladda ner data:** [Genkopieantal av luftvägsvirus normaliserat mot PMMoV-genkopieantal, CSV fil.](https://raw.githubusercontent.com/ScilifelabDataCentre/covid-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data finns tillgängligt från vecka 38 2020 och uppdateras veckovis. +**Ladda ner data:** [Genkopieantal av luftvägsvirus normaliserat mot PMMoV-genkopieantal, CSV fil.](https://raw.githubusercontent.com/ScilifelabDataCentre/pathogens-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data finns tillgängligt från vecka 38 2020 och uppdateras veckovis. **Citera datasetet:** diff --git a/content/svenska/dashboards/wastewater/enteric_quantification/_index.md b/content/svenska/dashboards/wastewater/enteric_quantification/_index.md index 2610b4235..6a817b2fc 100644 --- a/content/svenska/dashboards/wastewater/enteric_quantification/_index.md +++ b/content/svenska/dashboards/wastewater/enteric_quantification/_index.md @@ -40,7 +40,7 @@ Vänligen se [avsnittet med sammanfattande information om virusen](#grundläggan
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/enteric_graph_gu.json" height="550px" >}}
-**Källkod som avvänts för att generera visualiseringar:** [Källskod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/enteric_viruses_gu.py). +**Källkod som avvänts för att generera visualiseringar:** [Källskod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/enteric_viruses_gu.py). ## Kommentarer från forsksargruppen diff --git a/content/svenska/dashboards/wastewater/influenza_quantification/_index.md b/content/svenska/dashboards/wastewater/influenza_quantification/_index.md index e20f7b798..c93f8f946 100644 --- a/content/svenska/dashboards/wastewater/influenza_quantification/_index.md +++ b/content/svenska/dashboards/wastewater/influenza_quantification/_index.md @@ -40,7 +40,7 @@ SLU-SEEC samlar in och analyserar prover för kvantifiering av nivåerna av infl
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infA.json" height="600px" >}}
-**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_influenza_a.py). +**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_influenza_a.py). ### Influensa B @@ -52,7 +52,7 @@ SLU-SEEC samlar in och analyserar prover för kvantifiering av nivåerna av infl
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infB.json" height="600px" >}}
-**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_influenza_b.py). +**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_influenza_b.py). ## Kommentarer från forskargruppen @@ -68,7 +68,7 @@ Forskargruppen tillhandahåller en rapport som sammanfattar information från de **Kontakt:** and -**Ladda ner data:** [Genkopieantal för luftvägsvirus normaliserat mot PMMoV-genkopieantal.CSV fil](https://raw.githubusercontent.com/ScilifelabDataCentre/covid-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data finns tillgänglig för influensa A-virus från vecka 42 2022 och för influensa B-virus från vecka 12 2023, uppdateras veckovis. +**Ladda ner data:** [Genkopieantal för luftvägsvirus normaliserat mot PMMoV-genkopieantal.CSV fil](https://raw.githubusercontent.com/ScilifelabDataCentre/pathogens-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data finns tillgänglig för influensa A-virus från vecka 42 2022 och för influensa B-virus från vecka 12 2023, uppdateras veckovis. **Citera data:** diff --git a/content/svenska/partners.md b/content/svenska/partners.md index 8fe07c877..5ea777513 100644 --- a/content/svenska/partners.md +++ b/content/svenska/partners.md @@ -9,7 +9,7 @@ menu: Patogens Portal Sverige lanserades ursprungligen som den 'svenska Covid-19 dataportalen. Portalen var den första nationella noden av den [Europeiska COVID-19 dataportalen](https://covid19dataportal.org/); en europeisk plattform som möjliggör för forskare att dela, får åtkomst till och analysera Covid-19-relaterade data. [Europeiska COVID-19 dataportalen](https://covid19dataportal.org/) finansieras av den Europeiska kommissionen och drivs av European Biobinformatics Institute (EBI) som är en del av Europeiska molekylärbiologiska laboratoriet (EMBL). -Ett nätverk av nationella dataportaler växte sedan fram då ett antal andra länder lanserade egna nationella Covid-19 dataportaler. Många av dessa har använt [vår källkod](https://github.com/ScilifelabDataCentre/covid-portal) för att starta! Nedan är en lista över de andra nationella COVID-19-dataportalerna: +Ett nätverk av nationella dataportaler växte sedan fram då ett antal andra länder lanserade egna nationella Covid-19 dataportaler. Många av dessa har använt [vår källkod](https://github.com/ScilifelabDataCentre/pathogens-portal) för att starta! Nedan är en lista över de andra nationella COVID-19-dataportalerna: - [COVID-19 Data Portal Estland](https://covid19dataportal.ee) - [COVID-19 Data Portal Grekland](https://www.covid19dataportal.gr) diff --git a/content/svenska/projects/dashboard.md b/content/svenska/projects/dashboard.md index cc5533723..42241d5c1 100644 --- a/content/svenska/projects/dashboard.md +++ b/content/svenska/projects/dashboard.md @@ -5,7 +5,7 @@ plotly: true --- Visualiseringarna på denna sida återspeglar hur produktionen av vetenskapliga forskningsartiklar kopplade till covid-19 och SARS-CoV-2 utvecklas över tid. Vi har valt att presentera en sammanställning av publicerade vetenskapliga artiklar och preprint där minst en författare är affilierad till ett svenskt lärosäte. Den svenska covid-19 publikationsdatabasen [nås här](/sv/publications/). Observera att sammanställningen görs manuellt och kan därför inte kan anses komplett. Den fullständiga sammanställningen av publikationer som visas på denna sida finns tillgänglig för nedladdning och användning för andra ändamål, se [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014). -All källkod som används för att göra visualiseringarna på denna sidan finns tillgängliga på [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Källkod som används är länkad under respektive visualisering. +All källkod som används för att göra visualiseringarna på denna sidan finns tillgängliga på [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations). Källkod som används är länkad under respektive visualisering. ## Antal nya publikationer @@ -15,7 +15,7 @@ Diagrammet visar antal publikationer (vilket inkluderar vetenskapliga artiklar o {{< publications_per_month >}} -**Källkod som används för att skapa grafen:** [Källkod som används för att skapa visualisering](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Count_publications/count_publications.py). +**Källkod som används för att skapa grafen:** [Källkod som används för att skapa visualisering](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Count_publications/count_publications.py). ## De senast publicerade publikationerna (tio senaste) @@ -29,7 +29,7 @@ Tabellen visar de tio senaste publikationerna (inkluderar både tidskriftsartikl Detta ordmoln visar de vanligaste orden eller fraserna som förekommer i publikationernas titlar. Observera att vi har filtrerat bort funktionella ord (som 'the', 'a', 'this', etc.) samt 'COVID-19' och 'SARS-CoV-2' eftersom alla titlar innehöll dessa ord. Alla ordmoln uppdateras veckovis. -**Källkod som används för att skapa ordmoln:** [Källkod som används för att skapa visualiseringarna](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +**Källkod som används för att skapa ordmoln:** [Källkod som används för att skapa visualiseringarna](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). #### Alla publikationer @@ -45,7 +45,7 @@ Vi visar endast anslagsgivare där vi identifierat minst 20 publikationer i publ Ordmolnen visar de vanligaste förekommande orden eller fraserna från abstrakten (inkl. både preprint och vetenskapliga artiklar). Observera att vi har filtrerat bort funktionella ord (som 'the', 'a', 'this', etc.) samt 'COVID-19' och 'SARS-CoV-2' eftersom alla abstrakt innehöll dessa ord. Alla ordmoln uppdateras veckovis. -**Källkod som används för att skapa ordmoln:** [Källkod som används för att skapa visualiseringarna](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud). +**Källkod som används för att skapa ordmoln:** [Källkod som används för att skapa visualiseringarna](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Wordcloud). #### Alla publikationer diff --git a/content/svenska/publications/_index.md b/content/svenska/publications/_index.md index 7918e4660..2a6d72888 100644 --- a/content/svenska/publications/_index.md +++ b/content/svenska/publications/_index.md @@ -2,7 +2,7 @@ title: Publikationer om covid-19 och SARS-CoV-2 --- -I denna sektion presenteras en sammanställd kurerad lista över publicerade vetenskapliga artiklar och preprint rörande covid-19 och SARS-CoV-2. Minst en författare är affilierad till ett svenskt lärosäte. Sammanställningen görs manuellt och kan därför inte anses komplett. Observera att vi från maj 2023 började använda Europe PMC REST API för att identifiera publikationer. Källkoden vi använder för att göra detta är [tillgänglig på GitHub](https://github.com/ScilifelabDataCentre/covid-portal-scripts/tree/main/All_publications) och kan återanvändas med andra patogener. +I denna sektion presenteras en sammanställd kurerad lista över publicerade vetenskapliga artiklar och preprint rörande covid-19 och SARS-CoV-2. Minst en författare är affilierad till ett svenskt lärosäte. Sammanställningen görs manuellt och kan därför inte anses komplett. Observera att vi från maj 2023 började använda Europe PMC REST API för att identifiera publikationer. Källkoden vi använder för att göra detta är [tillgänglig på GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-scripts/tree/main/All_publications) och kan återanvändas med andra patogener. Om du saknar din vetenskapliga artikel eller vill förändra din vetenskapliga artikels sortering [kontakta vänligen oss](/sv/contact/). Vi har även en [sida med visualiseringar av publikationerna i denna databas](/dashboards/covid_publications/). diff --git a/layouts/datasets/single.html b/layouts/datasets/single.html index 1db0044d4..5d4492a3d 100644 --- a/layouts/datasets/single.html +++ b/layouts/datasets/single.html @@ -9,7 +9,7 @@

Data available from research groups in Sweden

began to use a script to query the Europe PMC database (making use of their API) in order to locate relevant publications. We only include data from publications about COVID-19/SARS-CoV-2 that BOTH involve at least one author affiliated with a Swedish research institution AND openly share reusable data and/or - code. The code + code. The code used for the query is written in Python and, as with all of our code, it is openly available in GitHub. We welcome others to reuse it and to repurpose it for other pathogens.

The lists of available data may not be exhaustive as the script used to generate it does not search for every diff --git a/layouts/partials/footer.html b/layouts/partials/footer.html index 18fd2afdb..9cc983d49 100644 --- a/layouts/partials/footer.html +++ b/layouts/partials/footer.html @@ -73,7 +73,7 @@

{{ if eq $.Site.Language.Language {{ $code_version := cond (strings.HasPrefix $git_sha "v") $git_sha (substr $git_sha 0 7) }}
+ href="https://github.com/ScilifelabDataCentre/pathogens-portal{{ with $code_version }}/tree/{{ $code_version }}{{ end }}"> {{ if eq $.Site.Language.LanguageName "Svenska" }}Källkod finns tillgänglig på GitHub{{ else }}Website code is available on Github{{ end }} {{ with $code_version }}({{ $code_version }}){{ end }} diff --git a/static/img/site_logo/CV19DP_logo_square_SWE.svg b/static/img/site_logo/CV19DP_logo_square_SWE.svg index 7289e998e..1363297c5 100644 --- a/static/img/site_logo/CV19DP_logo_square_SWE.svg +++ b/static/img/site_logo/CV19DP_logo_square_SWE.svg @@ -60,7 +60,7 @@