This is the GitHub organisation of the biocypher project, an ecosystem to facilitate building and using biomedical knowledge graphs and Large Language Models (LLMs). We are an inclusive and multi-cultural team interested in making knowledge graph creation more effective and accessible. Find us at https://biocypher.org and https://biochatter.org, including docs and tutorials.

The main projects in the ecosystem are BioCypher itself, a modular framework for knowledge graph creation, and BioChatter, a similarly modular framework for the connection of knowledge graphs and bioinformatics methods to Large Language Models and their related technologies. A demonstration of the ecosystem's capabilities can be seen in our web apps BioChatter Light and BioChatter Next, which are available online. You can also experiment with a local integration of a BioCypher knowledge graph with the BioChatter Light app using the POLE dataset demo repository.

One of our aims is to facilitate implementation of the FAIR and TRUST principles in the workflows related to the building of knowledge graphs and using LLMs in biomedical tasks. We aim to do so by providing modular architectures, allowing extensions in the areas of input (representing knowledge resources), ontology (for harmonisation and machine readability), output (to allow adoption of the most effective format for each task), language models, and auxiliary strategies for task facilitation.

You can find an overview of our adapters and pipelines on the Components Project Board. For more convenient browsing, you can also check out the meta-graph). If you create something yourself, or are planning to, please get in touch, so we can keep this board updated for everyone! If you have an adapter ready, you can use our issue form to make sure that all relevant information is recorded.

We welcome all contributions of any kind. Please check out 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.

• BioCypher
  • Preprint on arXiv
  • Peer-reviewed in Nature Biotechnology
  • Self-archived version on Zenodo
  • Read online here
• BioChatter
  • Preprint on arXiv
  • Peer-reviewed in Nature Biotechnology

We are fortunate to be funded by several organisations with focus on open science and software sustainability.

• DECIDER, a Horizon 2020 EU Project with the aim of improving ovarian cancer care, https://www.deciderproject.eu
• DFG528753569, in the context of a call on research software sustainability, https://dfg.de/
• OTAR3088, a project with the aim of modernising automated knowledge management in the Open Targets Platform, https://www.opentargets.org