What topic do you wish to add?
Add national resource page for Switzerland.
Maybe copy paste from the Sandbox? https://elixir-belgium.github.io/infectious-diseases-toolkit-sandbox/national-resources/switzerland

What topic do you wish to add?
Quality control measures for human health and clinical data.

To which existing Infectious Diseases Toolkit page should the topic be added to?
Human clinical and health data > Quality control page

Context
Collect feedback from the baseline use case.

What topic do you wish to add?
Add national resource page for Sweden

Link to the page of interest
https://www.infectious-diseases-toolkit.org/contribute/working-with-git

Describe what you would like to change on the page
In the section "Run using Jekyll directly" , step 5 it says run bundle exec jekyll serve. If you're on Ruby 3.x I think you might run get an error like:

bundler: failed to load command: jekyll (/Users/cookm/.rbenv/versions/3.1.3/bin/jekyll)
/Users/cookm/.rbenv/versions/3.1.3/lib/ruby/gems/3.1.0/gems/jekyll-3.9.3/lib/jekyll/commands/serve/servlet.rb:3:in `require': cannot load such file -- webrick (LoadError)

See this issue: jekyll/jekyll#8523. As noted in the issue, the solution is to add webrick: bundle add webrick. So maybe we should add that in point 5: "If this command returns an error, try running bundle add webrick' before trying bundle exec jekyll serve again (see this issue)." @bedroesb I guess this is the "compatibility issue" mentioned in the introduction to this section of the page? Or maybe there are more issues!

This is a decision that has been agreed on in the editorial meeting

The Style guide page at /contribute/style_guide needs to be updated to remove RDMkit specific guidance.

What topic do you wish to add?
Linked Cohort Data page

Are there existing pages in the Infectious Diseases Toolkit website related to the requested page?
No - test page in sandbox. More work being done in the Google Doc.

Google, one of the main search engines, prefers hyphens instead of underscores in the url for better interpretation. With RDMkit we are to late in changing this, but with IDTk we are still in time, since the website is still under construction.

Do we go ahead and change this?

The Code of conduct page is a modification of the RDMkit code of conduct page.
It needs further adjustments to reflect the IDTk structure.

• Defining a new Code of Conduct group
• Creating an email to the [email protected]
• Define the resolution steps, including the procedure for when the CoC group does not reach a consensus within reasonable time

These urls are defined in the ELIXIR toolkit theme and should get an optional path parameter

We should update the workflow file so it does not try to run the update script and fail.

On the Code of Conduct page at /CODE_OF_CONDUCT.
Pending decision on who are the members of the Code of Conduct Group

There is currently no template for a Showcase page.
These pages are similar to a Tool Assembly page in RDMkit.

A nice description about what we our aim is and how we try to achieve it would be nice.

What topic do you wish to add?
Human clinical and health data sources

Resources
https://docs.google.com/document/d/1Hds3vxLINCjGaNBaIFqjW3ksJWcJv9sDDGKj6EC0f98/edit?usp=sharing

I notice there are a lot of empty pages. That makes me think of the old customer service cliché, "Always exceed customer expectations." If we promise content and make people click for it, then perhaps we need to fulfil that promise. This seems particularly cruel on landing pages (e.g. https://www.infectious-diseases-toolkit.org/pathogen_characterisation/), where we know there is no content behind the tiles, but we don't warn people before they click.

It's true there is the "Site under construction" message on the home page, but it's not clear how far the site is "complete". I guess all the links suggested to me I could click on them and find something. If there is no content, and we want the empty pages to be live, perhaps we could at least give people information on those pages about why the content is not there. We could just repeat the box on the home page, but this also seems like a an opportunity to engage people.

Is there a rough editorial timetable that we could link to, showing when different pages should be completed? Could the Twitter link be put there, if updates are announced on Twitter? If we can't/don't want to announce updates on Twitter, what about an RSS feed or a link to visualping (https://visualping.io/) so people can see when content is added? There are also browser addons that might be useful for people. It seems a shame to present people with a white wall! Just a thought, anyway.

What topic do you wish to add?
Socioeconomics data sources

Resources
https://docs.google.com/document/d/1GAljkcNYJqbJcrfvv7U00arj5seWpc2xYsuivltTy7Q/edit?usp=sharing

Add to the editor's checklist - what an editor should do when a page is updated? (check RDMKit for duplicit information, etc...)

I would like to report an issue on the Website overview page at /contribute/website-overview. Description of the issue:

Should all page IDs be made using - instead of _ ?

There have been optimizations to the documentation in RDMkit, like the docker code snippet elixir-europe/rdmkit#1071, we should apply it here too

One liner about the website

What topic do you wish to add?
Quality control measures for pathogen characterisation.

To which existing Infectious Diseases Toolkit page should the topic be added to?
Pathogen characterisation > Quality control page

Context
Collect feedback from the wastewater use case.

A Getting Started page would contain user journey like descriptions on how certain goals could be achieved on IDTk.
These might also appear as short descriptions on how to achieve the goals defined on some of the user stories.
User stories that require navigating through multiple pages of IDTk would have the focus here.

An easy and obvious way to reach the Getting Started page would be already found on the main landing page. A suggestion given during the 2022 hackathon was to have it right below the search box and above the tiles of the website sections.

Over the next few weeks I will try to identify relevant content from the PaRI project that could be used to inspire content for some of the sections.

• Project summary slides
• Partners’ guide to SARS-CoV-2 genome data sharing
• Schematic overview of research documentation and data outputs
• PaRI Data Dictionaries and Data Mappings
• PaRI Galaxy, data flows, etc.

To further help gathering user stories at this stage of the development, the spreadsheet could be linked under the Ways of contributing of the Contribute page.

Further along in development, we would remove the link.

Update Contribute section with the latest version of the RDMkit Contribute section. The text of RDMkit Contribute section has to be pasted into IDTk Contribute section.

In the Text section, there are instructions for "Headings" and "Titles", both includes information about capitalisation, in Titles mentions acronyms.

https://www.infectious-diseases-toolkit.org/contribute/style_guide

Pathogen Characterisation - data description
Need to finalise the pathogen characterisation data description page that was started at the IDTk contentathon.

Are there existing pages in the Infectious Diseases Toolkit website related to the requested page?
Initiation of new topic page

Resources
Use Google doc that in our BY-COVID folder (link not shared here).

I would like to report an issue on the Contributors page at /about/contributors. Description of the issue:
The link for join us leads to the wrong url.
It should point to: https://www.infectious-diseases-toolkit.org/contribute/

What topic do you wish to add?
New page human biomolecular data - Quality control

Resources
https://docs.google.com/document/d/1bsp4bmsC7dfzFzdzc3BtPX6ySREFYBRhjsVDg_4xV6Q/edit?usp=sharing

@ainajene

Issue related to: Under 'Human clinical and health data' there is the topic 'regulatory considerations'.
When talking about data access, the common term often used is 'governance'. Depending on what you would like to cover, I would suggest to generalize the topic 'regulatory' to ELSI (ethical legal and sociological implications). Or split the topic up to the respective topics: Ethical implications, Data access governance ect.

I would like to report an issue on the News page at /about/news. Description of the issue:

Clicking on the "propose changes..." pencil icon leads to a 404 page on GitHub with the following message:
The 'elixir-europe/infectious-diseases-toolkit' repository doesn't contain the '_data/news.yaml' path in 'main'.

What topic do you wish to add?
Human biomolecular data - Data analysis

Resources
https://docs.google.com/document/d/14_HAQZEXF9Ua_G_Bxli5n_8pvvC4rADuHWo0XiZH-Q0/edit?usp=sharing

@solcos

In order to link towards pages and tag tools, we need a page_id for every page

On the Support page at /about/support.

A more clear distinction between what is based on RDMkit and comes from the use of the same Jekyll theme as RDMkit might make it easier for the readers to not conflate RDMkit and IDTk.

What topic do you wish to add?
Quality control measures for human biomolecular data.

To which existing Infectious Diseases Toolkit page should the topic be added to?
Human biomolecular data > Quality control page

Context
Collect feedback from the disease map use case.

What topic do you wish to add?
Human biomolecular data sources

Resources
https://docs.google.com/document/d/12mxv8P75m6Um1hBN01K41gOjvBw1DafBpmxrNTAS6sM/edit?usp=sharing

I would like to report an issue on the Page metadata page at /contribute/page_metadata. Description of the issue:

The Related pages paragraph still uses RDMkit nomenclature for the sections. These should instead be the IDTk sections.

@bedroesb Add quick suggestion form to contribute and make sure that form entries end up in IDTk editors mailing list.

In cell B1 there is a link to overview that leads to RDMkit
It should lead to the corresponding page in IDTk
The corresponding page in IDTk is not available yet.
Spreadsheet link here

Link to the page of interest
https://www.infectious-diseases-toolkit.org/human-clinical-and-health-data/provenance

Describe what you would like to change on the page
Adding a link to the Data provenance page of RDMkit to the IDTk page metadata

List the tool(s)or resource(s) that are missing on the page (if applicable)

• Name: RDMkit Data provenance page
• Link: https://rdmkit.elixir-europe.org/data_provenance

It has been raised that Socioeconomic data is a more fitting and recognizable title for the currently named Social and economic impact.

When there is agreement, update:

• rename category
• /sidebars/main.yml
• page_ids to reflect new name. From sei to sed
• /_config.yml
• showcase/TEMPLATE_showcase.md
• /TEMPLATE_page.md
• social_and_economic_impact/index.md
• /CODEOWNERS
• contribute/markdown_cheat_sheet.md
• contribute/page_metadata.md
• contribute/editorial_board_guide.md
• metadata of all pages
• GitHub issue label

This file will basically make editors responsible for certain directories/files. This means that a change against these directories/files will add the responsible editor as reviewer so he can review the changes.

Instead of the gradient in the headings we could also have this:

Using

h1:after {
    content: " ";
    display: block;
    height: 4px;
    border-radius: 2px;
    background-image: $color-gradient;
    margin-top: 5px;
  }