Building a knowledge graph for biomedical tasks usually takes months or years. What if you could do it in weeks or days? We created BioCypher to make the process of creating a biomedical knowledge graph easier than ever, but still flexible and transparent. BioCypher is built around the concept of a “trifold modularity”: modularity of data sources, modularity of structure-giving ontology, and modularity of output formats (see the graphical abstract below). This design allows for a high degree of flexibility and reusability, rationalising efforts by leveraging the biomedical community.

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Preconfigured project with BioCypher as a dependency, including docker integration


BioCypher is an inclusive community-driven project. If you have any questions, specific needs, or want to contribute to the project, please contact us over on our Zulip channel, on GitHub or via email at sebastian.lobentanzer (at) uni-heidelberg.de.

BioCypher graphical abstract

BioCypher uses a collection of reusable “adapters” for the different sources of biomedical knowledge, which can be flexibly recombined to fit various demands, thus reducing redundant maintenance work through quasi-standardisation. Integrating the controlled vocabularies of ontologies into the process helps to harmonise the data from individual resources and yields a consistent semantic basis for downstream analyses. Through unambiguous and simple “low-code” configuration, a reproducible knowledge graph can be created and shared for every specific task.