FHIR MCP Server

The FHIR MCP Server is a purpose‑built Model Context Protocol (MCP) backend that bridges large language model agents with FHIR‑compliant clinical data stores. By exposing a rich set of MCP tools, it allows assistants such as Claude to perform full CRUD operations on key FHIR resources—patients, conditions, medications, encounters—and to retrieve or update information using natural‑language prompts. This eliminates the need for developers to write custom API wrappers, enabling rapid integration of clinical data into conversational workflows.

At its core, the server is built on FastMCP, a high‑performance framework that delivers low‑latency MCP interactions. It ships with dedicated tools for each major FHIR resource type, while a generic tool covers any remaining resources. Authentication is handled through OAuth2 token management, ensuring that all requests to the underlying FHIR server are securely authorized. The modular architecture includes a FHIR Server Client for API communication, a RAG Service that ingests documents (TXT, CSV, JSON, PDF) and generates embeddings via Pinecone, and a LOINC Client that resolves and validates standardized medical terminology.

Beyond simple data retrieval, the server supports semantic search across ingested documents. By storing embeddings in Pinecone, it enables retrieval‑augmented generation (RAG) pipelines where an assistant can pull in contextually relevant documents to answer complex queries. For example, a user might ask whether a patient’s current symptoms could be linked to previously diagnosed conditions; the assistant can automatically invoke and then enrich the response with relevant lab results or clinical notes retrieved through semantic search.

Real‑world scenarios include clinical decision support, patient record exploration, and automated report generation. Developers can embed the server into existing healthcare platforms or deploy it via Docker for scalable, container‑native operations. Its extensive configuration allows fine‑grained control over authentication, vector store settings, and resource permissions, making it adaptable to diverse regulatory environments.

In summary, the FHIR MCP Server turns a standard FHIR API into an intelligent, agent‑ready interface. It abstracts away authentication, resource handling, and semantic retrieval, giving developers a single point of integration for building conversational healthcare applications that are both powerful and compliant.