snowstorm-mcp-server

An MCP server for querying SNOMED CT clinical terminology via Snowstorm and Snowstorm Lite backends.

SNOMED CT is the world's most comprehensive clinical terminology, used in electronic health records across 80+ countries. This server exposes SNOMED CT lookup, search, validation, hierarchy navigation, and value set expansion through the Model Context Protocol (MCP), enabling AI assistants to work with clinical terminology directly.

Supports all SNOMED CT editions available on the connected backend (International, US, UK, AU, etc.). No user account is required when connected to a public Snowstorm instance.

This repository supports two related but distinct usage modes:

1. Hosted remote connector: run a public HTTPS MCP endpoint and connect Claude to it via the custom connector / Connector Directory flow.

2. Self-hosted or local usage: run the server yourself against your own Snowstorm or Snowstorm Lite deployment, including Claude Desktop and future MCPB packaging scenarios.

If you are preparing a hosted connector for Claude web/desktop/mobile, start with Hosted remote connector. If you want to run the server yourself against your own terminology backend, start with Self-hosted and local usage.

Hosted remote connector

Use this mode when you are operating a public MCP endpoint, for example https://your-domain.example/mcp, and want Claude to connect to it from Anthropic's infrastructure.

Hosted deployment (Docker)

Build and run the container:

docker build -t snowstorm-mcp-server .
docker run -p 8000:8000 snowstorm-mcp-server

The server starts in Streamable HTTP mode on port 8000 using the bundled config.docker-snowstorm.yaml (expects a local Snowstorm at http://localhost:8080). Mount your own config at runtime:

docker run -p 8000:8000 \
  -v /path/to/your/config.yaml:/app/config.yaml \
  snowstorm-mcp-server

For production, deploy behind an HTTPS reverse proxy or on a platform with automatic TLS (Cloud Run, Fly.io, Railway, etc.). For public-facing deployments, configure rate limiting at both the reverse proxy (IP-based) and the application level (per-session) — see Performance guards below.

For remote MCP connector deployments intended for Claude web/desktop, the server enables CORS for https://claude.ai and https://claude.com on the Streamable HTTP endpoint by default. Override the allowed origin list with the SNOWSTORM_MCP_CORS_ALLOW_ORIGINS environment variable if needed using a comma-separated list.

Remote connector notes

• Anthropic connects to your hosted MCP endpoint from its cloud infrastructure.

• Anthropic does not configure your internal Snowstorm backend settings such as base_url, user_agent, or target auth. Those stay in your server config.

• manifest.json in this repo is for local packaging scenarios, not for the hosted remote connector flow.

Self-hosted and local usage

Use this mode when you want to run the MCP server yourself against your own Snowstorm or Snowstorm Lite backend, whether locally, on private infrastructure, or for Claude Desktop / MCPB-style packaging.

Development quick start

uv venv
uv pip install -e ".[dev]"
uv run pytest -q
./scripts/check.sh

For unit vs integration test workflows (including Docker stack setup and RF2 import), see docs/testing.md.

Docker integration stack (Snowstorm + Lite)

Start local containers for integration testing:

docker compose -f docker-compose.integration.yml up -d

Import a local RF2 archive into both Snowstorm and Snowstorm Lite:

dev/integration/import_snomed.sh \
  --rf2-zip ../SnomedCT_InternationalRF2_PRODUCTION_20251101T120000Z.zip

Run integration tests against each backend. Set SNOWSTORM_MCP_TEST_CONFIG in your .env to point at the relevant config, then:

uv run pytest -q tests/integration

Running the server locally

The server reads its config from a YAML file (see example-configs/config.local.yaml). Create a .env file in the project root to set the config path and any secrets (see .env.example):

cp .env.example .env
# edit .env to point at your config file

The server automatically loads .env from the current working directory at startup. Existing shell environment variables take precedence over .env values.

stdio (for Claude Desktop and most MCP clients):

uv run snowstorm-mcp-server --transport stdio

Use --log-level DEBUG|INFO|WARNING|ERROR to control verbosity (default: INFO). Logs go to stderr and are captured by Claude Desktop in mcp-server-snowstorm.log. The server prints the active guard configuration on startup so you can confirm settings are being loaded from the right config file.

SSE / Streamable HTTP (for HTTP-based MCP clients):

uv run snowstorm-mcp-server --transport sse
# or
uv run snowstorm-mcp-server --transport streamable-http

Claude Desktop config example (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "snowstorm": {
      "command": "uv",
      "args": [
        "run",
        "--project", "/path/to/snowstorm-mcp-server",
        "snowstorm-mcp-server",
        "--transport", "stdio"
      ]
    }
  }
}

Note: Claude Desktop runs uv from the project directory, so it picks up the .env file automatically. If you prefer explicit env vars, pass them via the "env" key in the Claude Desktop config.

Local packaging / MCPB installs

If you install the server from a Connector Directory entry, the manifest prompts for a config file path and passes it as --config at startup. Choose one of the YAML files in example-configs/ for local development, or provide the path to your own Snowstorm/Snowstorm Lite deployment config.

Configuration

See example-configs/config.local.yaml (Snowstorm at http://localhost:8080).

Backend type restriction

A single configuration must use either Snowstorm or Snowstorm Lite targets — mixing both in the same config is not supported. The server_mode field must match the target type ("snowstorm" for Snowstorm targets, "lite" for Lite targets).

Multiple Snowstorm Lite instances are supported (one per SNOMED edition).

Multi-edition Lite config example

server_mode: "lite"
default_terminology: snomedct
response_limits:
  max_expand_contains: 100
  max_search_hits: 50
  max_synonyms: 25

# Guards — all values shown are defaults. Omit the block to use defaults.
# For public-facing deployments, set per_session_rate_limit_calls.
# guards:
#   rate_limit_calls: 10
#   rate_limit_window_seconds: 60
#   max_concurrent_requests: 3
#   max_count_per_call: 500
#   large_result_threshold: 1000
#   max_children_calls_per_minute: 5
#   per_session_rate_limit_calls: null   # set an integer to enable
#   block_zero_cardinality_on_large_sets: false  # set true to block [0..0] on top-level roots
#   enable_expansion_size_guard: false   # preflight summary check for any non-summary expansion
#   expansion_count_threshold: 20000     # block if total concepts exceeds this value
#   size_cache_ttl_seconds: 86400

targets:
  lite-int:
    base_url: "http://localhost:8081"
    mode: "lite"
    terminology_name: "snomedct"
    fhir_path: "/fhir"
    auth:
      mode: "none"

  lite-us:
    base_url: "http://localhost:8082"
    mode: "lite"
    terminology_name: "snomedct-us"
    fhir_path: "/fhir"
    auth:
      mode: "bearer"
      token: "${SNOWSTORM_LITE_TOKEN}"

Terminology-based routing

This server routes requests by terminology (SNOMED edition), not by backend target.

• Snowstorm: Terminologies are auto-discovered from GET /codesystems. Each code system's shortName (lowercased) becomes the terminology name (e.g., snomedct, snomedct-us). The branch path is used automatically for native Snowstorm operations.

• Snowstorm Lite: Each instance serves one terminology. Configure terminology_name in the target config.

Default terminology

Set default_terminology in config to allow callers to omit the terminology parameter. If only one terminology is available, it becomes the default automatically.

Available MCP tools

All tools accept an optional terminology parameter (e.g., "snomedct-us"). Most tools also accept optional target to constrain routing/disambiguate target selection. If omitted, the default terminology is used.

Env secret overrides

Secrets can be injected at runtime using env vars instead of committing values:

• Placeholder interpolation in config: ${ENV_VAR} or ${ENV_VAR:-default}

• Target auth secret override variables:

  • SNOWSTORM_MCP_TARGETS__<TARGET_NAME_UPPER>__AUTH__PASSWORD

  • SNOWSTORM_MCP_TARGETS__<TARGET_NAME_UPPER>__AUTH__TOKEN

Sample MCP tool calls

list_terminologies:

{}

Expected response shape:

{
  "terminologies": [
    {"name": "snomedct", "backend_type": "snowstorm", "branch_path": "MAIN"},
    {"name": "snomedct-us", "backend_type": "lite", "branch_path": null}
  ],
  "default_terminology": "snomedct"
}

server_capabilities (default terminology):

{}

Expected response shape:

{
  "terminology": "snomedct",
  "backend_type": "snowstorm",
  "reachable": true,
  "fhir_base_url": "http://localhost:8080/fhir",
  "capabilities": {"has_fhir": true, "has_native_api": true, "has_lite_load_package": false},
  "fhir_metadata_summary": {"resourceType": "CapabilityStatement", "fhirVersion": "4.0.1"}
}

fhir_metadata summary-only mode (omit raw CapabilityStatement body):

{"terminology": "snomedct", "include_raw": false}

Expected response shape:

{
  "terminology": "snomedct",
  "fhir_base_url": "http://localhost:8080/fhir",
  "summary": {"resourceType": "CapabilityStatement", "fhirVersion": "4.0.1"}
}

snomed_lookup:

{"code": "404684003", "terminology": "snomedct"}

Expected response shape:

{
  "terminology": "snomedct",
  "code": "404684003",
  "display": "Clinical finding",
  "system": "http://snomed.info/sct"
}

snowstorm_search_concepts (Snowstorm only):

{"terminology": "snomedct", "term": "myocardial infarction", "limit": 5}

Expected response shape:

{
  "terminology": "snomedct",
  "term": "myocardial infarction",
  "branch": "MAIN",
  "returned": 5,
  "hits": [{"concept_id": "22298006", "pt": "Myocardial infarction"}]
}

Usage examples

These examples show how an AI assistant uses the server's tools in response to natural language questions.

Example 1 — Looking up a clinical concept

User: "What is SNOMED CT concept 22298006?"

The assistant calls snomed_lookup with {"code": "22298006"} and receives the concept's preferred term ("Myocardial infarction"), its SNOMED CT system URI, and any associated properties. The assistant can then explain the concept to the user in plain language, including its clinical meaning.

Example 2 — Checking a hierarchical relationship

User: "Is type 2 diabetes mellitus a kind of endocrine disorder in SNOMED CT?"

The assistant calls snomed_subsumes with {"code_a": "362969004", "code_b": "44054006"} (Endocrine disorder and Type 2 diabetes mellitus respectively). The response indicates whether code_a subsumes code_b, confirming or denying the IS-A relationship.

Example 3 — Finding concepts by clinical term

User: "Find SNOMED CT concepts related to 'atrial fibrillation'."

The assistant calls snomed_expand with {"filter": "atrial fibrillation", "count": 10} to search across the terminology. The response returns matching concepts with their IDs, preferred terms, and whether they are active, allowing the assistant to present a concise list of clinically relevant matches.

FHIR operations and multi-edition Snowstorm

For native Snowstorm operations (search, concept detail), the terminology's branch path is used automatically to select the correct edition.

For FHIR operations ($lookup, $validate-code, $subsumes), the terminology routes to the correct backend server. On a multi-edition Snowstorm instance, you may additionally need to specify the FHIR version parameter for precise edition targeting, as FHIR edition selection is governed by the system/version parameters rather than branch paths.

Additional backend capability notes and v0.1 scope boundaries are documented in docs/v0.1-capability-matrix.md. Release tagging/smoke steps are in docs/release-v0.1-checklist.md.

Performance guards

All tools that make backend HTTP calls share a common set of guards to protect the Snowstorm instance from overload. These apply regardless of which tool is called — server_health, server_capabilities, fhir_metadata, snomed_expand, snomed_lookup, snomed_validate_code, snomed_subsumes, all hierarchy tools, and all snowstorm_* native tools.

Guards that are always active:

Per-process only. Guards use in-memory state. If you run multiple server processes behind a load balancer, each process enforces its own independent limits. For shared limits across processes, a Redis-backed implementation is needed.

Per-session rate limiting

By default, the global rate limit is shared across all connected sessions. One active session can exhaust the budget for everyone else. For public-facing deployments, enable per-session limiting:

guards:
  rate_limit_calls: 30            # global ceiling across all sessions
  rate_limit_window_seconds: 60
  per_session_rate_limit_calls: 8 # no single session can exhaust the global budget

When per_session_rate_limit_calls is set, each MCP session gets its own independent rolling window using the same rate_limit_window_seconds. Sessions are tracked by object identity and are dropped automatically when the underlying session object is garbage-collected.

This limits the blast radius of a single heavy user but does not prevent abuse via repeated reconnects. For that, add IP-based rate limiting at your reverse proxy (Nginx limit_req, Caddy rate_limit, Cloudflare, etc.).

Unguarded tools

In-memory tools that do not call the Snowstorm backend are intentionally left unguarded: list_terminologies.

Snowstorm native search constraint (important)

The MCP tool snowstorm_search_concepts calls Snowstorm's native description search endpoint (GET /browser/{branch}/descriptions), which may reject very short queries (for example AD, B2) with HTTP 400.

Practical guidance:

• Use at least 3 searchable characters (letters/digits).

• For short acronyms, include context (for example use a longer phrase instead of AD).

The MCP server validates this early and returns a clear error message before calling Snowstorm.

Privacy policy

This server acts as a stateless proxy between an MCP client and a configured SNOMED CT backend (Snowstorm or Snowstorm Lite). It does not collect, store, or process personal data and does not send data to any third party beyond the configured backend. All query content is forwarded to the backend and discarded after the response is delivered. When per-session rate limiting is enabled, the server holds in-memory call timestamps per session purely for rate enforcement; this state contains no PII and is automatically discarded when the session ends.

Responses contain SNOMED CT terminology content subject to SNOMED International licensing terms. When deployed as a hosted service, standard web server access logs (IP address, timestamp, request path) may be retained by the hosting infrastructure for operational purposes.

For the full privacy policy, see PRIVACY.md.

Support

• Issues and bug reports: GitHub Issues

• SNOMED CT licensing and content: SNOMED International

• General enquiries: info@snomed.org

License

This project is licensed under Apache 2.0.