How do I install the omophub mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

What credentials does it need?

It reads `OMOPHUB_API_KEY`, `OMOPHUB_BASE_URL` from the environment. Store these in your client's env block or a secrets manager — never commit them to a repository — and grant the narrowest scope that still covers your use case.

SSyncDev

Start a project

Omophub MCP Server

Search, lookup, map, and navigate OMOP medical vocabularies via AI agents

Remote serverstreamable-httpPython

What is the Omophub MCP Server?

Search, lookup, map, and navigate OMOP medical vocabularies via AI agents

The short version

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

Concept lookup — - Find OMOP concept IDs for clinical terms in seconds
Cross-vocabulary mapping — - Map between ICD-10, SNOMED, RxNorm, LOINC, and 100+ 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

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

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
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

How to install the Omophub MCP Server

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

Configuration as documented by the project. Restart the client after saving.

Configuration

Variable	Description	Required
OMOPHUB_API_KEY	Credential the server authenticates with.	Yes
OMOPHUB_BASE_URL	Endpoint or connection string the server talks to.	Yes

Example prompts to try

“Use Omophub to search concepts.”
“Use Omophub to get concept.”
“Use Omophub to get concept by code.”

Frequently asked questions

Search, lookup, map, and navigate OMOP medical vocabularies via AI agents Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.

Alternatives to the Omophub MCP Server

Ctgov

Enables analysis of clinical trial data from the AACT database, tracking development trends, and generating analysis memos.

Databases★ 9

Academic

Scholarly search: OpenAlex, Crossref, arXiv, OpenCitations and PubMed in one endpoint.

Research & Scientific ComputingRemote

Bioportal

BioPortal — NCBO's biomedical ontology repository (data.bioontology.org).

Healthcare & Life SciencesRemote

Azure Fhir

A Model Context Protocol (MCP) server implementation for Azure Health Data Services FHIR (Fast Healthcare Interoperability Resources). This service

Cloud & DevOpsPython

Mosaic Pre-Clinical Intelligence

Pre-clinical drug-target intelligence as an MCP server: target profiles, compounds, literature, structure, clinical pipeline, validation precedent and whitespace analysis — 11 tools, 5 free and 6…

Healthcare & Life Sciences

MedAdapt Content Server

A specialized MCP server for Claude Desktop that enhances AI-assisted medical learning

Developer ToolsPython