Deploying Openmed MCP

What it does

When your agent uses it

• The user wants to add OpenMed to an agents MCP config
• Expose de-id/NER as MCP tools
• Run an MCP server over stdio
• Streamable HTTP

Example prompts

• “/deploying-openmed-mcp”

Requirements

• Python 3
• Docker

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1Install + launch. pip install "openmed[mcp]", then
2. 2Configure the runtime via the ServiceRuntime env vars (profile,
3. 3Register with the client. Add the mcpServers entry (stdio command, or
4. 4Front HTTP with auth/TLS if remote — the server has none built in; keep
5. 5Let the agent call tools (openmed_deidentify before sharing a snippet,
6. 6Manage memory with openmed_loaded_models / openmed_unload_model.

What it can do on your machine

Read from SKILL.md and the folder at commit 34d7b8c. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • python
  • pip

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • modelcontextprotocol.io
  • docs.anthropic.com

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Deploying Openmed MCP loads about 1.9k tokens when it runs. Until then it costs about 189 tokens; SKILL.md has 655 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~189

When it runs · the whole SKILL.md, loaded when a task matches

~1.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from maziyarpanahi/openmed at commit 34d7b8c, republished under its Apache-2.0 licence (© maziyarpanahi). 655 words, ~1,944 tokens.

name

deploying-openmed-mcp

description

Run OpenMed's Model Context Protocol (MCP) server so coding agents (Claude Code, Codex) and chat clients can call clinical NER, PII extraction, and de-identification as tools, on-device. Use when the user wants to add OpenMed to an agent's MCP config, expose de-id/NER as MCP tools, run an MCP server over stdio or Streamable HTTP, give Claude/Codex access to OpenMed, or containerize the MCP server. Covers the mcp extra, create_mcp_server, the 7 tools (openmed_analyze_text, openmed_extract_pii, openmed_deidentify, openmed_list_models, openmed_list_pii_languages, openmed_loaded_models, openmed_unload_model), the resources and prompts, stdio vs streamable-http transports, ServiceRuntime env config, and MCP client config snippets.

license

Apache-2.0

metadata.project

OpenMed

metadata.category

deployment-ops

metadata.pairs

adjacent

metadata.version

1.0

pip install "openmed[mcp]"                 # FastMCP / MCP SDK

# stdio transport (what coding agents spawn): default
python -m openmed.mcp.server

# Streamable HTTP transport (network-reachable):
python -m openmed.mcp.server --transport streamable-http --host 127.0.0.1 --port 8081

# Or embed it:
from openmed.mcp.server import create_mcp_server
server = create_mcp_server()              # FastMCP("OpenMed", ...) with tools+resources+prompts
server.run(transport="stdio")             # or "streamable-http"

// Claude Code: .mcp.json (or ~/.claude.json) — stdio transport
{
  "mcpServers": {
    "openmed": {
      "command": "python",
      "args": ["-m", "openmed.mcp.server"],
      "env": { "OPENMED_PROFILE": "prod" }
    }
  }
}

FROM python:3.11-slim
RUN pip install --no-cache-dir "openmed[mcp]"
ENV OPENMED_MCP_TRANSPORT=streamable-http \
    OPENMED_MCP_HOST=0.0.0.0 OPENMED_MCP_PORT=8081 \
    OPENMED_SERVICE_PRELOAD_MODELS="OpenMed/OpenMed-PII-SuperClinical-Small-44M-v1"
EXPOSE 8081
CMD ["python", "-m", "openmed.mcp.server"]

© maziyarpanahi, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/deploying-openmed-mcp of maziyarpanahi/openmed.

Open the folder on GitHubat commit 34d7b8c