Enhancing Clinical Decision Support and EHR Insights through LLMs and the Model Context Protocol: An Open-Source MCP-FHIR Framework

Abstract

Enhancing clinical decision support (CDS), reducing documentation burdens, and improving patient health literacy remain persistent challenges in digital health. This paper presents an open-source, agent-based framework that integrates Large Language Models (LLMs) with HL7 FHIR data via the Model Context Protocol (MCP) for dynamic extraction and reasoning over electronic health records (EHRs). Built on the established MCP-FHIR implementation, the framework enables declarative access to diverse FHIR resources through JSON-based configurations, supporting real-time summarization, interpretation, and personalized communication across multiple user personas, including clinicians, caregivers, and patients. To ensure privacy and reproducibility, the framework is evaluated using synthetic EHR data from the SMART Health IT sandbox (https://r4.smarthealthit.org/), which conforms to the FHIR R4 standard. Unlike traditional approaches that rely on hardcoded retrieval and static workflows, the proposed method delivers scalable, explainable, and interoperable AI-powered EHR applications. The agentic architecture further supports multiple FHIR formats, laying a robust foundation for advancing personalized digital health solutions.

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