This Dockerized python tool converts RDF knowledge graphs to i2b2 simple databases.
Given an ontology RDF graph, it will output a complete ONT cell schema in CSV format.
Given a RDF graph of instances of the former ontology graph, it will output a complete CRC cell schema in CSV format.
All CSV tables should then be pushed to your i2b2 database (loading script not provided).

This was developed as a subproject at Lausanne University Hospital (CHUV) by Jules Fasquelle and Jean Louis Raisaro.
It was published at the MIE2022 conference : https://pubmed.ncbi.nlm.nih.gov/35612099/

Full user documentation

and run instructions are available at https://rdf-to-i2b2-converter.readthedocs.io/en/latest/

Docker files - Ontology converter - https://github.com/CHUV-DS/docker-ontology-converter
Docker files -

Data samples converter - https://github.com/CHUV-DS/docker-data-converter

Source python files - https://github.com/CHUV-DS/RDF-i2b2-converter