addbioschemas

Adding bioschemas to mkdocs

A small markdown extension to add bioschemas to mkdocs. It requires a yaml or json file with bioschemas markup, and adds it to the rendered html.

addbioschemas is a plain Python-Markdown extension, so it also works with Zensical, the static site generator built by the Material for MkDocs team. Zensical reads mkdocs.yml directly and runs Python-Markdown extensions unchanged, so everything below applies to Zensical projects as-is — no separate configuration is needed.

Installation

pip install addbioschemas

To use the plugin simply add addbioschemas to the list of plugins in mkdocs.yml:

markdown_extensions:
  - addbioschemas

Usage

Option 1: add the bioschemas file name to the markdown file

Simply add [add-bioschemas file='path/to/yaml/metadata.yaml'] to the markdown file where you want to add the bioschemas. This method supports multiple metadata files.

A markdown snippet of a page where you want to add bioschemas to:

# awesome title
[add-bioschemas file='path/to/yaml/metadata.yaml']
I started with some YAML and turned it into JSON-LD

Important: If you are using mkdocs-material, make sure there is markdown before the insertion of [add-bioschemas]. Otherwise, other plugins will add incorrect tags to the json-LD chunk.

The contents of path/to/yaml/metadata.yaml use the bioschemas properties:

"@context": https://schema.org/
"@type": LearningResource
"@id": https://elixir-europe-training.github.io/ELIXIR-TrP-LessonTemplate-MkDocs/
http://purl.org/dc/terms/conformsTo:
  "@type": CreativeWork
  "@id": https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE
description: Template for ELIXIR lessons
keywords: FAIR, OPEN, Bioinformatics, Teaching
name: ELIXIR Training Lesson template
# lookup at https://spdx.org/licenses/
license: CC-BY-4.0
author:
- "@type": Person
  name: Geert van Geest
  email: geert.vangeest@sib.swiss
  github: GeertvanGeest
  orcid: 0000-0002-1561-078X
- "@type": Person
  name: Elin Kronander
  github: elinkronander
  orcid: 0000-0003-0280-6318

addbioschemas also supports the json format.

Option 2: add the bioschemas file name to mkdocs.yml

Specify the path to the yaml file in mkdocs.yml. This method only supports one metadata file.

Add to mkdocs.yml:

markdown_extensions:
  - addbioschemas:
      metadata: 'path/to/yaml/metadata.yaml'

A markdown snippet of a page where you want to add bioschemas to:

# awesome title
[add-bioschemas]
I started with some YAML and turned it into JSON-LD

Important: If you are using mkdocs-material, make sure there is markdown before the insertion of [add-bioschemas]. Otherwise, other plugins will add incorrect tags to the json-LD chunk.

Using with Zensical

Zensical can read an existing mkdocs.yml file directly, and runs the same Python-Markdown extensions without changes, so both options above work in a Zensical project without modification — just install addbioschemas and keep your mkdocs.yml as is.

If you migrate a project to Zensical's native zensical.toml configuration instead, configure addbioschemas under its markdown_extensions setting the same way you would for any other Python-Markdown extension; see the Zensical documentation for the exact syntax.