openEHR Mapper - A Tool to Fuse Clinical and Genomic Data Using the openEHR Standard

Precision medicine is an emerging and important field for health care. Molecular tumor boards use a combination of clinical and molecular data, such as somatic tumor mutations to decide on personalized therapies for patients who have run out of standard treatment options. Personalized treatment decisions require clinical data from the hospital information system and mutation data to be accessible in a structured way. Here we introduce an open data platform to meet these requirements. We use the openEHR standard to create an expert-curated data model that is stored in a vendor-neutral format. Clinical and molecular patient data is integrated into cBioPortal, a warehousing solution for cancer genomic studies that is extended for use in clinical routine for molecular tumor boards. For data integration, we developed openEHR Mapper, a tool that allows to (i) process input data, (ii) communicate with the openEHR repository, and (iii) export the data to cBioPortal. We benchmarked the mapper performance using XML and JSON as serialization format and added caching capabilities as well as multi-threading to the openEHR Mapper.