MCP Server Healthcare

A Model Context Protocol (MCP) server for an NHS clinical coding workflow — suggesting ICD-10-CM/OPCS-4/HCC codes for a clinical note, tracking SAR/FOI information-governance requests, running DSAR mapping-repository requests through classification and clinical review, batch coding, and reading/ writing patient data via a Cerner FHIR R4 sandbox.

Any MCP client (Claude Desktop, Claude Code, Copilot Studio's MCP connector, etc.) can call these tools directly — no REST API layer required.

Originally built as part of bobbynoble/clinical-coding-bot; this repo is the standalone MCP server, with its own copy of the business logic it wraps so it has no dependency on that repo.

Tools

cerner_post_condition, cerner_post_procedure and cerner_writeback_episode perform real writes against whatever Cerner environment is configured (a non-production sandbox by default — see app/fhir_cerner.py).

Related MCP server: fhir-synthetic-mcp

Setup

pip install -r requirements.txt
cp .env.example .env   # fill in Azure OpenAI / Search / Cerner credentials as needed

Every tool loads regardless of which credentials are set, but suggest_clinical_codes needs Azure OpenAI + Azure AI Search configured, and the cerner_* tools need CERNER_CLIENT_ID/CERNER_CLIENT_SECRET — calling one without the matching credentials fails with a clear error rather than crashing the server.

Running

Stdio (Claude Desktop, Claude Code, most local MCP clients):

python -m MCP_Server_Healthcare

Example Claude Desktop config (claude_desktop_config.json):

{
  "mcpServers": {
    "clinical-coding-bot": {
      "command": "python",
      "args": ["-m", "MCP_Server_Healthcare"],
      "cwd": "/absolute/path/to/mcp_server_healthcare"
    }
  }
}

Streamable HTTP (remote access, e.g. from Copilot Studio or a hosted MCP client):

python -m MCP_Server_Healthcare --transport http --port 8010

The HTTP transport requires CODING_API_KEY to be set in .env — every request must carry a matching X-API-Key header, or it's rejected with 401 (fails closed). It listens on 127.0.0.1 by default; set MCP_HOST=0.0.0.0 (and put it behind TLS/a reverse proxy) to expose it beyond localhost.

Repository layout

MCP_Server_Healthcare/   the MCP server itself (server.py has the tool
                         definitions; __main__.py the stdio/http entry point;
                         auth.py the HTTP transport's API-key gate)
app/                     business logic each tool wraps — coder.py (RAG
                         coding), sar_foi.py, dsar.py, batch.py,
                         fhir_cerner.py. Each stores its state in a SQLite
                         file created alongside it on first run.

Notes

• Blocking network calls (Azure OpenAI/Search, Cerner FHIR) are offloaded with asyncio.to_thread so one slow call doesn't stall other tool calls on the same server.

• SQLite files (app/sar_foi.db, app/batch.db, app/dsar.db) are created automatically on first run and are gitignored.