biocypher 0.4.5

A unifying framework for biomedical research knowledge graphs

BioCypher

📖 Documentation

Tutorial and developer docs at https://biocypher.org. For a quickstart into your own pipeline, you can refer to our project template, and for an overview of existing and planned adapters for resources and outputs, as well as other features, visit our GitHub Project Board.

❓ Description

This is the development repository for BioCypher, our proposal for a unifying framework to create knowledge graph databases for systems biomedicine. For an overview, usage notes, and a tutorial, read the docs here.

⚙️ Usage

BioCypher is currently in prototype stage. Installation instructions can be found here.

Exemplary usage of BioCypher to build a graph database is shown in various adapters we have created. For instance, interested users can refer to the migration of the Clinical Knowledge Graph, or the adapters created for the CROssBAR project. As the project evolves, more of these examples will be directly included in the documentation.

🤝 Getting involved

We are very happy about contributions from the community, large and small! If you would like to contribute to BioCypher development, please refer to our contribution guidelines. :)

If you want to ask informal questions, talk about dev things, or just chat, please join our community at https://biocypher.zulipchat.com!

Imposter syndrome disclaimer: We want your help. No, really. There may be a little voice inside your head that is telling you that you're not ready, that you aren't skilled enough to contribute. We assure you that the little voice in your head is wrong. Most importantly, there are many valuable ways to contribute besides writing code.

This disclaimer was adapted from the Pooch project.

✍️ Citation

The BioCypher paper is available as a preprint at https://arxiv.org/abs/2212.13543.

Acknowledgements

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 965193 for DECIDER and No 116030 for TransQST.