Democratising Knowledge Representation with BioCypher
Author(s): Sebastian Lobentanzer,Julio Saez-Rodriguez
Affiliation(s): Institute for Computational Biomedicine, University Hospital Heidelberg, Germany
Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a modular and accessible framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Flexibly mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from conversion of maintenance- to task-oriented knowledge stores, to interoperability between biomedical domains, to synchronisation of task-specific knowledge graphs for federated learning. By its streamlined design, our framework (https://biocypher.org) frees up valuable developer time; we encourage further development and usage by the community.