Open Biological and Biomedical Ontologies (OBO) Organized Knowledge (OBOOK)

The OBOOK is the main resource for OBOAcademy training materials for Semantic OBO Engineers.

• To get started with learning: https://oboacademy.github.io/obook/getting-started/
• To contribute: https://oboacademy.github.io/obook/contributing/

Running the website locally

Installing dependencies

# Create a virtual environment in the project folder
python -m venv .venv

# Activate the virtual environment
# in mac/linux
source .venv/bin/activate
# in Windows
.\.venv\Scripts\activate

# Install dependencies
pip install mkdocs
pip install mkdocs-material

Running the site locally

If you haven't, activate the local virtual environment

# in mac/linux
source .venv/bin/activate
# in Windows
.\.venv\Scripts\activate

Then run:

mkdocs serve

Go to http://127.0.0.1:8000/, you should see the site.

License

This content is available under the Creative Commons CC0 Public Domain Dedication.

Citation

The conference article describing the OBOOK can be cited with the following:

Nicole Vasilevsky, James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, & Nicolas Matentzoglu. (2022, August 3). OBO Academy: Training materials for bio-ontologists. 2022 ISMB Bio-Ontologies Community, Madison, WI. https://doi.org/10.5281/zenodo.6955490

Acknowledgements

Critical Path Institute

Critical Path Institute (CPI) is an independent, nonprofit organisation dedicated to bringing together experts from regulatory agencies, industry, and academia to collaborate and improve the medical product development process.

In April 2021, the CPI has commissioned the first version of this OBO course, contributing not only funding for the preparation and delivery of the materials, but also valuable feedback about the course contents and data for the practical exercises. We thank the CPI for contributing significantly to the OBO community and open science!

https://c-path.org/