OntoRAG

Ontology-based RAG for Scientific Discovery

🔥 Usage

OntoRAG lets you define a Q&A system that is grounded to predefined ontologies of specific fields.

from OntoRAG.ontorag import OntoRAG

# Initialize OntoRAG with your ontology
orag = OntoRAG(
    ontology_path="path/to/your/ontology",
)

# Ask a question (in the domain of the ontology)
question = "What's the difference between DNA and RNA"
answer = orag.forward(question)
print(answer)

You'll need to set up your OpenAI API key in your environment:

export OPENAI_API_KEY='your-api-key-here'

Or use a .env file:

OPENAI_API_KEY=your-api-key-here

👩‍💻 Installation

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/schwallergroup/ontorag.git

📂 OntoGen: Ontogen package

The OntoGen package is a tool for generating ontologies from a set of text documents. Ontogen is located in src/OntoGen directory.

For more details see the OntoGen README.

✅ Citation

Andres M Bran. et al. OntoRAG - Ontology-based RAG for Scientific Discovery

@Misc{ontorag_bran2025,
    author = {Bran, Andres M and Oarga, Alexandru and Hart, Matthew and Lederbauer, Magdalena and Schwaller, Philippe},
    title = {OntoRAG - Ontology-based RAG for Scientific Discovery},
    howpublished = {Github},
    year = {2025},
    url = {https://github.com/schwallergroup/ontorag}
}

🛠️ For Developers

See developer instructions

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

Development Installation

To install in development mode, use the following:

$ git clone git+https://github.com/schwallergroup/ontorag.git
$ cd ontorag
$ pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+https://github.com/schwallergroup/ontorag.git
$ cd ontorag
$ tox -e docs
$ open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the setup.cfg. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the setup.cfg, src/OntoRAG/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using build
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion -- minor after.