This Dockerized python tool converts ontologies and data in RDF knowledge graphs to i2b2 simple databases.ontologies and data for the i2b2 common data model.
Given an ontology in RDF graph, it will output a complete ONT cell schema in CSV format.
Given a RDF graph of instances of observations based on 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 (with standard SQL loading script (not provided).
This was developed as a subproject at by the Clinical Data Science Group of the Lausanne University Hospital (CHUV) by Jules Fasquelle and Jean Louis Raisaro. , Switzerland as part of the Swiss Personalized Health Initiative (SPHN) https://sphn.ch/.
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
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