This repo contains the files for the Bioschemas website. The website is deployed on GitHub using Jekyll.

Feel free to propose changes to the Bioschemas website! This can be done by opening an issue on our specifications repo or by forking this repository and making a pull request. The content of this website is built using a combination of Markdown and HTML.

Since the website uses GitHub pages for its deployment, it is possible to create live previews to inspect your changes. Go to your fork -> settings tab -> pages and select the branch you are working on to activate GitHub pages. GitHub will do the rest and will tell you at which url the website will be served.

It is possible to preview the website locally to preview changes. You need a Ruby installation in order to do so. Ruby version 2.7.* works out of the box well with Jekyll, more recent versions will need bundle add webrick to make it work. If you already have the correct Ruby installed on your machine, then the following files will allow you to get started by installing the relevant dependencies:

• Install Jekyll and Dependencies: gem install jekyll bundler and gem install jekyll-sitemap jekyll-sitemap jekyll-gist jekyll-redirect-from
• Clone the repository: git clone https://github.com/Bioschemas/bioschemas.github.io.git
• Run the website: jekyll serve

If you need more help with installing Jekyll, then see their installation instructions for full details.

Note, if you use the GitHub pages documentation, then you will need a Gemfile with the following contents (Gemfile):

source 'https://rubygems.org'
gem 'github-pages', group: :jekyll_plugins

The website uses a series of collections that are configured in the _config.yml file. There are collections in the pages directory for:

• About: _about
• Community: _community
• Groups: _groups
• Meetings: _meetings
• News: _news
• People: _people
• Profiles: _profiles
• Stories: _stories
• Tutorials: _tutorials
• Types: _types
• Use Cases: _useCases

The list of live deployments is maintained in the JSON-LD file _data/live_deployments.json. The file conforms to the JSON-Schema defined in _data/live_deployments_schema.json. Upon pushing to GitHub, an action checks the live deployments data file conforms to the schema file.

A resource listing in the live deployments file consists of the following JSON keys (optional properties denoted with a ?, + indicates one or more required:

• name
• description?
• keywords?: ["CDR", "DDR", "RIR"]
• url
• nodes?: ELIXIR node two letter code
• sitemap?
• profiles+:
  • profileName: Valid profile name
  • conformsTo
  • exampleURL
  • highlight?

The status of specification files, i.e. latest draft, release, or deprecated, is controlled by the following data files:

• Profiles: _data/profile_version.yaml
• Types: _data/type_version.yaml

There should be an entry in each file for each profile/type respectively.

The values of the latest_publication and latest_release keys should be the corresponding filename (without extension) in the _profile or _type folder. The latest_publication field captures the latest publication (draft or release) of a specification, while the latest_release key captures the most recent release. The latest_release key may be empty if there has not been a release.

The status value is used to distinguish between 'active' specifications, and those that have been 'deprecated'. Deprecated specifications must have a deprecated_date value.