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.
Installation
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: http://python.org/ 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.