Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: schwallergroup
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Size: 13.2 MB
Statistics
- Stars: 8
- Watchers: 0
- Forks: 1
- Open Issues: 3
- Releases: 2
Metadata Files
README.md
<!--
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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.
```python 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:
bash
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:
bash
$ 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
bibtex
@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](https://github.com/schwallergroup/ontorag/blob/master/.github/CONTRIBUTING.md) for more information on getting involved. ### Development Installation To install in development mode, use the following: ```bash $ 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: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/schwallergroup/ontorag/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ 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`](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`](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: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/OntoRAG/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/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.Owner
- Name: schwallergroup
- Login: schwallergroup
- Kind: organization
- Repositories: 1
- Profile: https://github.com/schwallergroup
Citation (CITATION.cff)
cff-version: 1.0.2 message: "If you use this software, please cite it as below." title: "OntoRAG" authors: - name: "Andres M Bran" version: 0.0.1 doi: url: "https://github.com/schwallergroup/ontorag"
GitHub Events
Total
- Watch event: 7
- Delete event: 1
- Issue comment event: 1
- Push event: 4
- Public event: 1
- Pull request event: 2
- Fork event: 1
Last Year
- Watch event: 7
- Delete event: 1
- Issue comment event: 1
- Push event: 4
- Public event: 1
- Pull request event: 2
- Fork event: 1
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite
- nougat-ocr *
- ollama *
- owlready2 *
- pymupdf *
- spacy *
- transformers ==4.44.2
- unidecode *
- anthropic *
- ollama *
- spacy *
- thinc *