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Tools and resources table

One of the themes key features is the support for a central tool and resource table. This means that tools that are mentioned at multiple places on the website, can be described centrally, and these descriptions/metadata fields can be used to automatically populate a tools and resources table at the bottom of the page.

Way of working

The all_tools_and_resources list is based on the yaml file in the _data directory. Tools and resources can be manually linked to FAIRsharing.org, Bio.tools and TeSS and EuroPMC.

Prerequisites

  • The main yaml file describing the tools is called tool_and_resource_list.yml located in /_data and is using the correct YAML syntax
  • Make sure MarkDown pages where you want to mention the tools have a page_id in their frontmatter, see metadata documentation.
  • When making use of the new way of tagging tools:
    • gem "elixir-toolkit-theme-plugins" is added to the /Gemfile
    • - elixir-toolkit-theme-plugins is added to the plugins block in the _config.yml file
  • GitHub Actions is used to deploy the website. See instructions).

The main yaml file

Each tool or resource mentioned in the text has metadata stored in the main yaml file. The metadata block for each tool consists of 5 attributes:

  • id: The ID of a tool, in kebab-case, lowercase with hyphens.
  • name: The name of the tool or resource
  • url: URL to the main page of the tool or resource, make sure to let the URL start with https://
  • description: A short description of the tool or resource. Try to not use the characters " or '
  • registry: 3 registries are supported: Bio.tools, FAIRsharing.org, TeSS and EuroPMC. The keywords you can use respectively are: biotools, fairsharing, fairsharing-coll, tess and europmc, specifying the id or query with a colon. FAIRsharing collections have an ID that follows the pattern bsg-s000XXX. List registries under the registry attribute as key: value pairs.
  • related_pages: List of page_ids (Deprecated, This is replaced by the {% tool "tool_id" %} snippet in the text)
  • how_to_access: This is free text feels that describes the accessibility of the tool or resource.

Example:

- id: github
  name: GitHub
  url: https://github.com
  description:
    Versioning system, used for sharing code, as well as for sharing of
    small data
  registry:
    tess: GitHub

What tool or resource can be added to the table

Tools and resources specifically mentioned in the text of the pages should be present in the main table.

Adding new tools

  1. Make sure the tool you want to add is not yet already described in the yaml file. If yes,go to step 3, if not, go follow the next step.

  2. Click on the pencil icon seen on the GitHub view of the main yaml file as described in our GitHub Guide. Add your tool or resource at the bottom of the file following the structure described in the The main yaml file section of this page. Make sure the indentation follows the one of the previous listed items. Copy the content of the yaml file and paste in in an online yaml validator in case of doubt.

  3. Copy the tool_id of the tool or resource

  4. Add the tool in the text by mentioning it using following syntax:

        
     {% tool "tool_id" %}
        
    

    Examples:

        
     {% tool "zenodo" %} is a powerful data publication service, which is supported by the European commission and focused on research data, including supplemental material like software, tables, figures or slides.
        
    

    Will give:

    Zenodo is a powerful data publication service, which is supported by the European commission and focused on research data, including supplemental material like software, tables, figures or slides.

        
     {% tool "beacon" %} is a GA4GH standard which enables standardised querying across multiple sources.
        
    

    Will give:

    Beacon v2 is a GA4GH standard which enables standardised querying across multiple sources.

Listing all resources

By default, the table at the bottom of the page will appear when tools are mentioned in the text/tagged with the correct page_id as seen at the bottom of this page under the “Tools and resources on this page” heading. To list manually all tools and resources that are described in your website, use following snippet:


{% include resource-table-all.html %}

Skip tool table

Tool or resource Description Related pages Registry
Beacon v2 API framework and data model for cross-cohort searching. Standards/Databases Publication
Bioconda Bioconda is a bioinformatics channel for the Conda package manager Template example General page example 2 Tool info Training
Bitbucket Git based code hosting and collaboration tool, built for teams. General page example 2
GitHub Versioning system, used for sharing code, as well as for sharing of small data
Template example Standards/Databases Training
GitLab GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider. Template example Training
Zenodo Generalist research data repository built and developed by OpenAIRE and CERN Standards/Databases Training
Resource name

A general description about the resource

GitHub
General page example 3 Template example General page example 2 Tool info Training
Resource name 2

A general description about the resource

General page example 3
Resource name 3

A general description about the resource

Tools and resources on this page

Skip tool table
Tool or resource Description Related pages Registry
Beacon v2 API framework and data model for cross-cohort searching. Standards/Databases Publication
Zenodo Generalist research data repository built and developed by OpenAIRE and CERN Standards/Databases Training