README.md

pheno-docs

This repository contains the documentation of the Human Phenotype Project (HPP) for researchers. It is published under the Pheno Knowledgebase website.

• Updates should be made via a PR.
• Please separate commits for changes to the source files from the rendering of the docs.

How to build the docs

1. Ensure quarto is installed.
2. Install the JupyterLab extension for Quarto. This is required to render the Jupyter Notebooks properly.

python3 -m pip install jupyterlab-quarto

3. Go to the pheno_knowledge_base folder.
4. Run quarto render to build the docs.
5. Run quarto preview to preview the docs before publishing.

How to update the publications list

1. Run the src/create_publications.ipynb notebook.
2. Build the docs (see above).

How to update the datasets introduction

1. Update the corresponding markdown file in the markdowns-expanded folder.
2. Run the python ../pheno-examples/src/tools/add_intro.py pheno_knowledge_base/datasets command to update the introduction to the datasets.
3. Build the docs (see above).