omophub/omophub-mcp

6 stars 0 forks Quality 87 Trend 28MIT

Medical vocabularies for AI agents. Search, map, and navigate 11M+ OMOP concepts: SNOMED CT, ICD-10, RxNorm, LOINC, and more. Directly from Claude, Cursor, VS Code, or any MCP-compatible client.

Overview

Medical vocabularies for AI agents. Search, map, and navigate 11M+ OMOP concepts: SNOMED CT, ICD-10, RxNorm, LOINC, and more. Directly from Claude, Cursor, VS Code, or any MCP-compatible client. Quick Start · Tools · Examples · Docs · Website Working with medical vocabularies today means downloading multi-gigabyte CSV files, loading them into a local database, and writing SQL to find what you need. Every time. . No database setup, no CSV wrangling, no context switching. Just ask. - - Find OMOP concept IDs for clinical terms in seconds - - Map between ICD-10, SNOMED, RxNorm, LOINC, and 120+ vocabularies - - Explore ancestors and descendants for phenotype definitions - - Let your AI agent assemble complete concept sets for cohort definitions - - Verify medical codes and check their standard mappings Sign up at omophub.com → create an API key in your dashboard. Open Claude Desktop settings > "Developer" tab > "Edit Config". Add to claude_desktop_config.

README

OMOPHub MCP Server

Medical vocabularies for AI agents. Search, map, and navigate 11M+ OMOP concepts: SNOMED CT, ICD-10, RxNorm, LOINC, and more. Directly from Claude, Cursor, VS Code, or any MCP-compatible client.

Quick Start · Tools · Examples · Docs · Website

Why OMOPHub MCP?

Working with medical vocabularies today means downloading multi-gigabyte CSV files, loading them into a local database, and writing SQL to find what you need. Every time.

OMOPHub MCP Server gives your AI assistant instant access to the entire OHDSI ATHENA vocabulary. No database setup, no CSV wrangling, no context switching. Just ask.

You: "Map ICD-10 code E11.9 to SNOMED"

Claude: Found it - E11.9 (Type 2 diabetes mellitus without complications)
        maps to SNOMED concept 201826 (Type 2 diabetes mellitus)
        via standard 'Maps to' relationship.

Use cases:

Concept lookup - Find OMOP concept IDs for clinical terms in seconds
Cross-vocabulary mapping - Map between ICD-10, SNOMED, RxNorm, LOINC, and 120+ vocabularies
Hierarchy navigation - Explore ancestors and descendants for phenotype definitions
Concept set building - Let your AI agent assemble complete concept sets for cohort definitions
Code validation - Verify medical codes and check their standard mappings

Quick Start

1. Get an API Key

2. Add to Your AI Client

3. Start Asking

“What’s the OMOP concept ID for type 2 diabetes?”

“Map ICD-10 code E11.9 to SNOMED”

“Show me all descendants of Diabetes mellitus in SNOMED”

Available Tools

Tool	What it does
`search_concepts`	Search for medical concepts by name or clinical term across all vocabularies
`get_concept`	Get detailed info about a specific OMOP concept by `concept_id`
`get_concept_by_code`	Look up a concept using a vocabulary-specific code (e.g., ICD-10 `E11.9`)
`map_concept`	Map a concept to equivalent concepts in other vocabularies (paginated — see note below)
`get_hierarchy`	Navigate concept hierarchy - ancestors, descendants, or both
`list_vocabularies`	List available medical vocabularies with statistics
`semantic_search`	Search using natural language with neural embeddings (understands clinical meaning)
`find_similar_concepts`	Find concepts similar to a reference concept, name, or description
`explore_concept`	Get concept details, hierarchy, and cross-vocabulary mappings in one call
`fhir_resolve`	Resolve a FHIR coded value (incl. administrative codes via the HL7 FHIR-to-OMOP IG ConceptMaps) to its OMOP standard concept and CDM target table
`fhir_resolve_codeable_concept`	Resolve a FHIR CodeableConcept — best match by OHDSI vocabulary preference, honoring `userSelected`

Resources

URI	Description
`omophub://vocabularies`	Full vocabulary catalog with statistics
`omophub://vocabularies/{vocabulary_id}`	Details for a specific vocabulary

Prompts

Prompt	Description
`phenotype-concept-set`	Guided workflow to build a concept set for a clinical phenotype
`code-lookup`	Look up and validate a medical code with mappings and hierarchy

Example Prompts

Find a concept → search_concepts

“Search for metformin in RxNorm”

Cross-vocabulary mapping → map_concept

“I have SNOMED concept 201826 - what’s the ICD-10 code?”

Build a concept set → search_concepts → get_hierarchy → map_concept

“Help me build a concept set for Type 2 diabetes including all descendants”

Completeness matters here. map_concept returns one page at a time (page_size 1-200, default 100). A widely-used drug ingredient can have well over a thousand NDC mappings, so a single call is a sample, not the answer. Check has_more in the response and keep incrementing page until it is false — otherwise the concept set looks complete while silently missing codes.

Use find_similar_concepts for exploration, not for this: it is ranked embedding similarity, so it has no notion of set membership and cannot be exhaustive no matter how large page_size is.

Validate a code → get_concept_by_code → map_concept

“Is ICD-10 code E11.9 valid? What does it map to in SNOMED?”

Semantic search → semantic_search

“Find concepts related to ‘heart attack’”

Explore a concept → explore_concept

“Give me everything about SNOMED concept 201826”

FHIR-to-OMOP resolution → fhir_resolve

“Resolve FHIR SNOMED code 44054006 to OMOP — what table does it go in?”

CodeableConcept → fhir_resolve_codeable_concept

“This CodeableConcept has both SNOMED 44054006 and ICD-10 E11.9 — which should I use for OMOP?”

Find similar → find_similar_concepts

“What concepts are similar to ‘Type 2 diabetes mellitus’?”

Configuration

Environment Variables

Variable	Required	Description
`OMOPHUB_API_KEY`	✅	Your OMOPHub API key
`OMOPHUB_BASE_URL`		Custom API base URL (default: `https://api.omophub.com/v1`)
`OMOPHUB_LOG_LEVEL`		`debug` · `info` · `warn` · `error` (default: `info`)
`OMOPHUB_ANALYTICS_OPTOUT`		Set to `true` to disable analytics headers
`OMOPHUB_USER_AGENT_SUFFIX`		Optional deployment identifier appended to `omophub-mcp/` (default: none)
`MCP_TRANSPORT`		`stdio` (default) or `http`
`MCP_PORT`		HTTP server port (default: `3100`, only used with `http` transport)
`HEALTH_PORT`		Port for standalone health endpoint in stdio mode (default: disabled)

CLI Arguments

# Stdio mode (default)
npx @omophub/omophub-mcp --api-key=oh_your_key --base-url=https://custom.api.com/v1

# HTTP mode
npx @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key

# Stdio mode with standalone health endpoint
npx @omophub/omophub-mcp --api-key=oh_your_key --health-port=8080

Health Endpoint (Docker / Kubernetes)

In HTTP mode, the health endpoint is available at /health on the same port as the MCP endpoint:

npx @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key
curl http://localhost:3100/health
# → {"status":"ok","version":"1.5.0","uptime_seconds":42}

In stdio mode, use --health-port for a standalone health endpoint:

HEALTH_PORT=8080 OMOPHUB_API_KEY=oh_your_key npx @omophub/omophub-mcp
curl http://localhost:8080/health

The Docker image defaults to HTTP mode on port 3100 with health checks built in.

Development

git clone https://github.com/OMOPHub/omophub-mcp.git
cd omophub-mcp
npm install
npm run build
npm test

Run locally:

OMOPHUB_API_KEY=oh_your_key npx tsx src/index.ts

Troubleshooting

Error	Solution
`API key required`	Set `OMOPHUB_API_KEY` in your environment or MCP config
`Authentication failed`	API key may be invalid or expired - generate a new one
`Rate limit exceeded`	Automatic retries are built in. For higher limits, upgrade your plan
Tools not appearing	Restart your AI client, verify `npx @omophub/omophub-mcp` runs without errors, check config path

License

MIT - see LICENSE

View the full README on GitHub

Install

npx -y @omophub/omophub-mcp

New to MCP? Start with the mcpskill.org guide →

Configuration

{
  "mcpServers": {
    "omophub": {
      "command": "npx",
      "args": ["-y", "@omophub/omophub-mcp"],
      "env": {
        "OMOPHUB_API_KEY": "oh_your_key_here"
      }
    }
  }
}

omophub/omophub-mcp

Overview

README

Why OMOPHub MCP?

Quick Start

1. Get an API Key

2. Add to Your AI Client

3. Start Asking

Available Tools

Resources

Prompts

Example Prompts

Configuration

Environment Variables

CLI Arguments

Health Endpoint (Docker / Kubernetes)

Development

Troubleshooting

Links

License

Install

Configuration