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Installation and Usage Notes

The Biolink Model is defined as a YAML. Any changes or edits are to be made to this YAML.

We make use of linkML library to generate various artifacts from the YAML.


The generation of Biolink Model artifacts requires Python 3.7+ because it makes extensive use of Python dataclasses library.

The standard approach is to install Python 3.7+ on your machine (see: for details).

Generate artifacts

All artifact generation is driven by the Makefile:

make all

Generate Python dataclasses

To generate Python dataclasses,

make python

Generate ShEx

To generate Shape Expressions,

make shex

Generate JSON-LD context

To generate Biolink Model JSON-LD context,

make context.jsonld

Build GitHub Pages documentation

To build the documentation site,

Switch to gh-pages branch

First ensure that you are on gh-pages branch,

git checkout gh-pages

Merge master

Now, merge master branch to get the latest changes,

git merge master

Note: Ensure there is no merge conflicts and that the merge was successful.

Generate markdown

Now regenerate the markdown,

make jekyll-docs

This should regenerate all the Jekyll formatted markdown in /docs folder.

Commit all the changes

Now add the /docs folder, commit and push.

git add docs
git commit -m "Update docs"
git push origin gh-pages

This push operation should trigger GitHub Pages to rebuild the documentation site with the latest changes.