Medical Terminologies MCP Server

Medical Terminologies MCP Server

A Model Context Protocol (MCP) server providing unified access to major global medical terminologies:

• ICD-11 - International Classification of Diseases (WHO)
• SNOMED CT - Systematized Nomenclature of Medicine (opt-in; requires self-hosted Snowstorm)
• LOINC - Logical Observation Identifiers Names and Codes
• RxNorm - Normalized names for clinical drugs (NIH)
• MeSH - Medical Subject Headings (NLM)
• ATC - Anatomical Therapeutic Chemical classification (WHO Collaborating Centre, served via NLM RxClass)
• CID-10 - Brazilian Portuguese translation of ICD-10 (DataSUS V2008, bundled)

Features

• 31 default tools (37 with SNOMED enabled) for medical terminology lookup
• 3 MCP Prompts that orchestrate tool calls into named workflows (find-medical-code, drug-info, cid10-portuguese-lookup) — clients render these as one-click user actions
• 4 MCP Resources for in-process reference content (info://server, info://cid10/chapters, info://licenses, info://stats) — sub-millisecond reads (except info://stats which round-trips to the StatsCounter Durable Object on the hosted endpoint)
• Multi-terminology support in a single server
• Cross-terminology mapping and search
• Built-in caching for improved performance
• Rate limiting to respect API limits
• Detailed responses with rich formatting
• Two transports: stdio (default; for Claude Desktop, IDE clients) and Streamable HTTP (for hosted deployments — runs on Cloudflare Workers at the edge by default, Smithery URL submission, or self-hosted Docker)

Who is this for?

This server is not a clinical-care decision tool — practicing clinicians have specialized assistants (UpToDate AI, OpenEvidence, EHR-integrated tools) for that. The actual audience is researchers, public-health analysts, clinical informatics developers, and educators who need programmatic access to authoritative terminology data.

Try the hosted instance (no install)

A public Cloudflare Workers deployment runs at:

https://medical-terminologies-mcp.sidneybissoli.workers.dev/mcp

Connect via the MCP Inspector or any Streamable HTTP MCP client:

npx @modelcontextprotocol/inspector --transport streamable-http \
  --server-url https://medical-terminologies-mcp.sidneybissoli.workers.dev/mcp

Or install via Smithery, which proxies the same endpoint through their gateway:

npx -y smithery mcp add sidneybissoli/medical-terminologies

The hosted instance has WHO credentials configured, so all 31 default tools work without any setup on your side. For your own deployment (e.g. corporate network, different region, custom WHO credentials), see the Installation and Hosted on Cloudflare Workers sections below.

Installation

Global Installation (Recommended)

npm install -g medical-terminologies-mcp

Local Installation

npm install medical-terminologies-mcp

Configuration

Claude Desktop

Add to your Claude Desktop configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "medical-terminologies": {
      "command": "npx",
      "args": ["-y", "medical-terminologies-mcp"],
      "env": {
        "WHO_CLIENT_ID": "your-who-client-id",
        "WHO_CLIENT_SECRET": "your-who-client-secret"
      }
    }
  }
}

Environment Variables

¹ Required for ICD-11 tools. Get credentials at: https://icd.who.int/icdapi.

² See SNOMED CT setup (advanced) below. LOINC, RxNorm, and MeSH need no configuration.

HTTP transport (hosted / shared deployments)

The server runs over stdio by default — that's what Claude Desktop and IDE clients expect. For hosted deployments (Cloudflare Workers, Smithery, your own Docker container), pass --http to switch to Streamable HTTP transport instead:

medical-terminologies-mcp --http --port 3000
# or, in Docker / containers:
medical-terminologies-mcp --http --host 0.0.0.0 --port 3000

Endpoints:

• POST /mcp — JSON-RPC over Streamable HTTP (the MCP protocol). Stateless mode: each request is independent, no session cookies.
• GET /health — liveness probe returning { status, name, version, tool_count } for load balancers and uptime monitors.
• CORS is permissive (*) so browser clients (e.g. the MCP Inspector web UI) can connect directly.

Quick smoke test from another terminal:

curl -sS http://localhost:3000/health
# {"status":"ok","name":"medical-terminologies-mcp","version":"1.5.0","tool_count":31}

# Inspector via HTTP
npx @modelcontextprotocol/inspector --transport streamable-http --server-url http://localhost:3000/mcp

Hosted on Cloudflare Workers (primary)

The production deployment is a Cloudflare Worker. Source lives in src/worker.ts, config in wrangler.toml, and CI deploy in .github/workflows/deploy-worker.yml (auto-runs on every push to main).

To deploy your own instance:

npm ci
npm run build:worker
npx wrangler login         # one-time, browser flow
npx wrangler deploy        # publishes to <name>.<account>.workers.dev
# Set ICD-11 secrets so those 5 tools work:
npx wrangler secret put WHO_CLIENT_ID
npx wrangler secret put WHO_CLIENT_SECRET

The public endpoint is POST https://<name>.<account>.workers.dev/mcp. CORS is permissive so the MCP Inspector web UI connects directly. /health returns { status, name, version, tool_count, uptime_s }.

Why Workers: zero cold start at the edge, $5/mo flat for 10M requests (free tier covers up to 100k req/day), and no VMs to size or restart. Stage-1 deploy uses per-isolate cache + rate-limiter — fine for moderate traffic; under sustained high load, swap in Workers KV cache and a Durable Object rate limiter (tracked as PROGRESS.md Phase 11.9 Stage 2 follow-up).

Listing on Smithery

After your Worker is live, register the URL on Smithery:

1. Visit https://smithery.ai → Publish → MCP (or https://smithery.ai/new).
2. Pick the URL submission path (Smithery deprecated container hosting in 2024 — URL is the supported flow now).
3. Paste https://<your-worker>.workers.dev/mcp. Smithery's gateway scans for compliance and proxies traffic.

Self-hosted Docker (alternative)

If you'd rather run the server in your own infrastructure (private deployment, internal compliance constraints, on-prem), the repo includes a Dockerfile:

docker build -t medical-terminologies-mcp .
docker run --rm -p 3000:3000 \
  -e PORT=3000 \
  -e WHO_CLIENT_ID=... -e WHO_CLIENT_SECRET=... \
  medical-terminologies-mcp

Multi-stage build (~150 MB), runs node dist/index.js --http, binds 0.0.0.0:$PORT. Same MCP endpoints as the Workers deployment.

Available Tools (31 by default, 37 with SNOMED enabled)

ICD-11 Tools (5)

LOINC Tools (4)

RxNorm Tools (5)

MeSH Tools (4)

SNOMED CT Tools (5, disabled by default)

These are only registered when ENABLE_SNOMED_TOOLS=true. See SNOMED CT setup (advanced).

Crosswalk Tools (5 — map_snomed_to_icd10 requires SNOMED)

ATC Tools (3)

WHO Anatomical Therapeutic Chemical classification, served through NLM RxClass (free, no auth). The WHOCC base itself requires a paid subscription, but RxClass envelopes the same code/name pairs.

CID-10 Tools (4)

Brazilian Portuguese translation of ICD-10 (DataSUS V2008). Bundled as a static dataset — no HTTP calls. The Brazilian SUS uses CID-10 V2008 operationally; for the international ICD-11 (current WHO revision), use the ICD-11 tools above.

Versioning Tools (2)

Surface what version of each terminology this server queries against today — useful when running batch validation against a pinned release or when investigating an unexpected lookup miss after an upstream update.

Example Outputs

The samples below are the actual formatted output the tools produce — the text body of the CallToolResult. Tools also return a structuredContent object matching each tool's outputSchema for programmatic consumers.

loinc_search — query: "glucose", max_results: 3

## LOINC Search Results for "glucose"

Found 1024 total results (showing 3):

1. **74790-7** - Glucose challenge (hydrogen breath test) panel - Exhaled gas
   Component: Glucose challenge panel | Method: -

2. **104708-3** - Deprecated Estimated average glucose [Moles/volume] in Blood
   Component: Estimated average glucose | Property: SCnc

3. **97510-2** - Glucose measurements in range out of Total glucose measurements during reporting period
   Component: Glucose measurements in range/Total glucose measurements | Property: NFr | Method: Calculated

total_count (1024) reflects every match in the NLM Clinical Tables index, not just the page returned. Bump max_results (max 50) to see canonical codes like 2339-0 (Glucose [Mass/volume] in Blood); the API's relevance ranking puts panels and derived measurements above plain blood-glucose at small page sizes.

rxnorm_ingredients — rxcui: "6809" (metformin)

# Ingredients for RxCUI 6809

Found 18 ingredient(s):

| RxCUI | Name | Type |
|-------|------|------|
| 6809 | metformin | Single Ingredient |
| 1007411 | chlorpropamide / metformin | Multiple Ingredient |
| 1043562 | metformin / saxagliptin | Multiple Ingredient |
| 1243019 | linagliptin / metformin | Multiple Ingredient |
| 1486436 | dapagliflozin / metformin | Multiple Ingredient |
| 1545149 | canagliflozin / metformin | Multiple Ingredient |
| 1664314 | empagliflozin / metformin | Multiple Ingredient |
| 729717  | metformin / sitagliptin | Multiple Ingredient |
| ...     | (10 more combinations)   | Multiple Ingredient |

For an RxCUI that is itself an ingredient (TTY=IN), the tool returns that ingredient plus every multi-ingredient (TTY=MIN) concept that includes it. Use this to enumerate combination products built around a substance.

mesh_descriptor — mesh_id: "D006973" (Hypertension)

# Hypertension
MeSH ID: D006973

## Scope Note

Persistently high systemic arterial BLOOD PRESSURE. Based on multiple readings (BLOOD PRESSURE DETERMINATION), hypertension is currently defined as when SYSTOLIC PRESSURE is consistently greater than 140 mm Hg or when DIASTOLIC PRESSURE is consistently 90 mm Hg or more.

## Tree Numbers

- C14.907.489

## Concepts

- Hypertension *(preferred)*

## Allowed Qualifiers

35 qualifier(s) allowed. Use mesh_qualifiers for details.

The scope note comes from the descriptor's preferred concept, not its annotation field (which is an indexer-facing note). Tree numbers are the navigable path into MeSH's controlled hierarchy — C14.907.489 places Hypertension under Cardiovascular Diseases → Vascular Diseases.

Common Workflows

• ICD-11 lookup: icd11_search with a clinical term → pick the result → icd11_lookup with the code for full details, or icd11_hierarchy to walk parents/children.
• Drug pipeline: rxnorm_search for a brand or generic name → rxnorm_concept for the canonical record → rxnorm_ingredients and rxnorm_classes for downstream analysis.
• Cross-terminology scaffolding: find_equivalent with a clinical term searches ICD-11, LOINC, RxNorm, MeSH, and (when enabled) SNOMED in one call. Use it to bootstrap mappings; the pairwise map_* tools refine them.
• ICD-10 → ICD-11 (text search, not authoritative): map_icd10_to_icd11 does honest text search against WHO ICD-11. Real WHO transition tables are tracked in PROGRESS.md Phase 13.1.

SNOMED CT setup (advanced)

The 5 SNOMED tools (snomed_search, snomed_concept, snomed_hierarchy, snomed_descriptions, snomed_ecl) plus the SNOMED-dependent crosswalk tool (map_snomed_to_icd10) are disabled by default. With them disabled, the server registers 31 tools instead of 37; find_equivalent still works and skips the SNOMED branch with an explanatory note.

The reason: as of 2026-05-08, the public IHTSDO Snowstorm endpoint that this project historically called (https://browser.ihtsdotools.org/snowstorm/snomed-ct/...) returns HTTP 410 Gone for every path. Without a working backend, registering these tools surfaces 6 guaranteed-broken tools to every client.

To enable the SNOMED tools:

1. Confirm your SNOMED CT license. SNOMED CT use requires an SNOMED International (IHTSDO) license. Member country residents typically have one through their national release center; non-members can obtain an Affiliate license. See https://www.snomed.org/snomed-ct/get-snomed.

2. Run a Snowstorm instance. SNOMED International publishes Snowstorm as open source (IHTSDO/snowstorm) and as a Docker image (snomedinternational/snowstorm). Self-hosting requires importing an RF2 release file (provided to license holders).

3. Configure this server:

   {
     "mcpServers": {
       "medical-terminologies": {
         "command": "npx",
         "args": ["-y", "medical-terminologies-mcp"],
         "env": {
           "WHO_CLIENT_ID": "...",
           "WHO_CLIENT_SECRET": "...",
           "ENABLE_SNOMED_TOOLS": "true",
           "SNOMED_BASE_URL": "https://my-snowstorm.example.com/snowstorm/snomed-ct",
           "SNOMED_LANGUAGE": "en"
         }
       }
     }
   }
   

   SNOMED_BASE_URL should point at the base under which Snowstorm exposes its /MAIN/concepts and related endpoints. SNOMED_LANGUAGE accepts standard Accept-Language tags (e.g. pt, es, pt-BR,en;q=0.8) — Snowstorm returns localized terms when the branch has them and falls back to English otherwise.

4. Restart the MCP client so the server picks up the env vars.

If you set ENABLE_SNOMED_TOOLS=true without configuring a working Snowstorm, the SNOMED tools will register but every call will fail at the network layer.

Terminology Licenses

ICD-11 (WHO)

ICD-11 content is provided under the Creative Commons Attribution-NoDerivatives 3.0 IGO license (CC BY-ND 3.0 IGO).

• You must attribute WHO as the source
• You may not create derivative works
• API access requires registration at https://icd.who.int/icdapi

SNOMED CT

SNOMED CT use requires an IHTSDO (SNOMED International) license. The SNOMED tools in this server are disabled by default and only enabled by operators with a valid license and a self-hosted Snowstorm instance — see SNOMED CT setup (advanced).

• Member countries have national licenses
• Affiliate licenses available for others
• More info: https://www.snomed.org/snomed-ct/get-snomed

LOINC

LOINC content is provided under the LOINC License.

• Free for most uses
• Attribution required
• Registration recommended

RxNorm

RxNorm is produced by the U.S. National Library of Medicine and is freely available.

• No license required for use
• Attribution appreciated

MeSH

MeSH is produced by the U.S. National Library of Medicine and is freely available.

• No license required for use
• Attribution appreciated

API Rate Limits

This server implements rate limiting to respect API providers:

Development

Building from source

git clone https://github.com/SidneyBissoli/medical-terminologies-mcp.git
cd medical-terminologies-mcp
npm install
npm run build

Running locally

npm start

Testing with MCP Inspector

npx @modelcontextprotocol/inspector node dist/index.js

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

Author

Sidney Bissoli

• GitHub: @SidneyBissoli

License

This project is licensed under the MIT License - see the LICENSE file for details.

Note: While this software is MIT licensed, the medical terminologies accessed through it have their own licenses (see Terminology Licenses above).

Acknowledgments

• WHO for the ICD-11 API
• Regenstrief Institute for LOINC
• U.S. National Library of Medicine for RxNorm and MeSH
• SNOMED International for SNOMED CT
• Anthropic for the Model Context Protocol

Support

If you encounter any issues or have questions:

• Open an issue on GitHub
• Check existing issues for solutions

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Made with love for the medical informatics community