Breaking Barriers for Interoperability: A Reference Implementation of CSV-FHIR Transformation Using Open-Source Tools

FHIR is a widely accepted interoperability standard for exchanging medical data, but data transformation from the primary health information systems into FHIR is usually challenging and requires advanced technical skills and infrastructure. There is a critical need for low-cost solutions, and using Mirth Connect as an open-source tool provides this opportunity. We developed a reference implementation to transform data from CSV (the most common data format) into FHIR resources using Mirth Connect without any advanced technical resources or programming skills. This reference implementation is tested successfully for both quality and performance, and it enables reproducing and improving the implemented approach by healthcare providers to transform raw data into FHIR resources. For ensuring replicability, the used channel, mapping, and templates are available publicly on GitHub (https://github.com/alkarkoukly/CSV-FHIR-Transformer).

Knowledge bases and software support for variant interpretation in precision oncology

Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.