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.

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'