OMOPHub MCP MCP Server

About OMOPHub MCP

OMOPHub gives healthcare data teams instant API access to the OHDSI standardized vocabularies: 11M+ concepts across 120+ vocabularies, including SNOMED CT, ICD-10, LOINC and RxNorm. It offers semantic and multilingual search, cross-vocabulary mappings, hierarchy navigation, FHIR-to-OMOP resolution, a FHIR terminology service, Python/R/Node SDKs and an MCP server for AI agents. Hosted remote endpoint with 11 tools; local via npx -y @omophub/omophub-mcp. Auth: OMOPHub API key (free tier, 3,000 calls/month).

OMOPHub MCP tools (11)

Read from the live server on Oct 26, 2026. These are the tools your AI assistant can call once connected.

search_concepts

Search for medical concepts across OHDSI standardized vocabularies by name, synonym, or clinical term. Returns matching concepts with IDs, names, vocabulary, domain, and standard status. Use this when you need to find the OMOP concept ID fo

semantic_search

Search for medical concepts using natural language with neural embeddings. Unlike keyword search, semantic search understands clinical meaning — 'heart attack' finds 'Myocardial infarction', 'high blood sugar' finds 'Hyperglycemia'. Returns

find_similar_concepts

Find medical concepts similar to a reference concept, name, or natural language query. Supports three algorithms: 'semantic' (neural embeddings — best for meaning, and the default), 'lexical' (text matching — best for typos), 'hybrid' (comb

get_concept

Get detailed information about a specific OMOP concept by its numeric concept_id. Returns the concept name, vocabulary, domain, concept class, standard status, valid dates, and synonyms. Use this when you already have a concept_id and need

get_concept_by_code

Look up an OMOP concept using a vocabulary-specific code and vocabulary ID. Both parameters are required to avoid ambiguity - the same code can exist in multiple vocabularies (e.g., 'E11' exists in both ICD10CM and ICD10). If multiple conce

explore_concept

Get a comprehensive view of a medical concept in one call: detailed info, ancestors/descendants hierarchy, and cross-vocabulary mappings. Use this instead of calling get_concept + get_hierarchy + map_concept separately. Ideal for understand

map_concept

Find mappings FROM a source concept TO equivalent concepts in other vocabularies. The concept_id you provide is always the SOURCE — results show what it maps TO. Returns cross-vocabulary mappings with relationship types and mapping quality.

get_hierarchy

Navigate the vocabulary hierarchy for a concept. Use direction='up' for ancestors (broader terms like 'Diabetes mellitus' → 'Metabolic disease'), direction='down' for descendants (narrower terms, essential for building concept sets in pheno

list_vocabularies

List all available medical vocabularies in the OMOP standardized vocabulary system with concept counts and metadata. Use this to understand what terminology systems are available (SNOMED CT, ICD-10-CM, RxNorm, LOINC, etc.) and their scope.

fhir_resolve

Resolve a FHIR coded value (system URI + code) to its OMOP standard concept and CDM target table. Supports text-only input via semantic search fallback and optional Phoebe recommendations. Examples: system='http://snomed.info/sct' code='440

fhir_resolve_codeable_concept

Resolve a FHIR CodeableConcept with multiple codings. Picks the best match per OHDSI vocabulary preference (SNOMED > RxNorm > LOINC > CVX > ICD-10). Falls back to the text field via semantic search if no coding resolves.

How to connect OMOPHub MCP to Claude, Cursor or VS Code

OMOPHub MCP runs as a hosted remote MCP server at https://mcp.omophub.com. Add that URL to your MCP client's config (Claude Code, Cursor, Windsurf or VS Code) and the tools appear immediately, no install required.

{
  "mcpServers": {
    "omophub-mcp": {
      "url": "https://mcp.omophub.com"
    }
  }
}

Claude Code: claude mcp add --transport http omophub-mcp https://mcp.omophub.com. Servers that require OAuth or an API key will prompt on first use.