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arXiv · 2509.03828

An Agentic Model Context Protocol Framework for Medical Concept Standardization

Jaerong Ahn·Andrew Wen·Nan Wang·Heling Jia·Zhiyi Yue·Sunyang Fu·Hongfang Liu
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Abstract

The Observational Medical Outcomes Partnership (OMOP) common data model (CDM) provides a standardized representation of heterogeneous health data to support large-scale, multi-institutional research. One critical step in data standardization using OMOP CDM is the mapping of source medical terms to OMOP standard concepts, a procedure that is resource-intensive and error-prone. While large language models (LLMs) have the potential to facilitate this process, their tendency toward hallucination makes them unsuitable for clinical deployment without training and expert validation. Here, we developed a zero-training, hallucination-preventive mapping system based on the Model Context Protocol (MCP), a standardized and secure framework allowing LLMs to interact with external resources and tools. The system enables explainable mapping and significantly improves efficiency and accuracy with minimal effort. It provides real-time vocabulary lookups and structured reasoning outputs suitable for immediate use in both exploratory and production environments.

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Jaerong Ahn, Andrew Wen, Nan Wang, Heling Jia, Zhiyi Yue, Sunyang Fu, Hongfang Liu. 2025-09-04. An Agentic Model Context Protocol Framework for Medical Concept Standardization. https://arxiv.org/abs/2509.03828

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