OmopHub MCP
A medical code reference for your agent: search, map and navigate SNOMED CT, ICD-10, RxNorm and LOINC concepts across vocabularies
Extended access
Why this level
- Queries with terms and codes go to OMOPHub servers in both the hosted setup and the npx run
- The key spends your plan's call limit, so bulk paging can quickly use up the free 3,000 calls
- The server returns reference data, but patient details pasted into queries would also reach the vendor
Install
- Works in
Manual install
claude mcp add omophub --transport http -H "Authorization: Bearer oh_your_key_here" https://mcp.omophub.comThe hosted server with no installation. Replace oh_your_key_here with your key from the OMOPHub dashboard.
Access and checks
How we reviewExtended accessThe tool runs code or makes network calls and only reads external data.
- Queries with terms and codes go to OMOPHub servers in both the hosted setup and the npx run
- The key spends your plan's call limit, so bulk paging can quickly use up the free 3,000 calls
- The server returns reference data, but patient details pasted into queries would also reach the vendor
This is third-party code. Review the repository files before installing.
What it does
OmopHub MCP gives an agent a reference for OHDSI medical terminology. Given a name or a code, the agent finds an OMOP concept, translates it into a code from another vocabulary and walks up or down the hierarchy. The vocabularies include SNOMED CT, ICD-10, RxNorm, LOINC and more; the developer puts the total at 11 million concepts across more than 120 vocabularies. The server exposes 11 tools. Concepts can be searched by name or synonym with search_concepts and by meaning with semantic_search, where a plain-language query finds a clinical term. find_similar_concepts suggests related concepts, and get_concept and get_concept_by_code return a record by identifier or by vocabulary code. map_concept translates a concept into other vocabularies, get_hierarchy shows ancestors and descendants, explore_concept gathers the record, hierarchy and mappings in one call, and list_vocabularies lists what is available. The pair fhir_resolve and fhir_resolve_codeable_concept resolves a FHIR value to a standard OMOP concept and the target table of the CDM model. This is a reference for development work. The server returns codes, names and links between vocabularies; it holds no patient data and makes no clinical decisions.
Who it is for. For data engineers, analysts and developers who build ETL into the OMOP model, assemble concept sets for cohorts or check codes in Claude Code, Cursor, VS Code and Windsurf.
Good fit when
- You need the OMOP concept identifier for a clinical term, such as a diagnosis, a drug or a lab measurement
- An ICD-10 code has to be translated to SNOMED CT or back, and you want to see which mapping is the standard one
- A phenotype definition needs a concept set that includes every descendant of a chosen condition
- When moving data from FHIR to OMOP you need the standard concept and the CDM table for a coded value
- A list of codes from an extract has to be checked for validity and you want to see where each one maps
Not a fit when
- You want advice on a diagnosis, treatment or dosage: the server returns codes and vocabulary links, with no medical recommendations
- You need to search the records of specific patients: the server works with reference vocabularies, not medical charts
- You need a complete code list for reporting: map_concept and search return data in pages, and without paging through them the set will be incomplete
- You need a fully local run with no calls to an outside service: the npx package also calls the OMOPHub API and requires a key
Example request
Find the OMOP concept for type 2 diabetes, show every descendant in SNOMED CT, map the codes to ICD-10 and assemble them into a concept set for a cohortMCP
- Transport
- http, stdio
- Authentication
- API key
Environment variables
OMOPHUB_API_KEYrequired, secret- API key from the OMOPHub dashboard, required for the local npx run
OMOPHUB_ANALYTICS_OPTOUT- Set to true to disable the package's analytics headers
Limitations
OmopHub MCP suits terminology work in development and does not replace clinical expertise: its answers must not drive treatment decisions for a specific person.
You need an API key from the OMOPHub dashboard. Both connection methods send requests to OMOPHub servers: the hosted server mcp.omophub.com takes the key in a header, and the npx package calls api.omophub.com by default. Keep patient personal data out of your queries. The call volume is capped by your plan, and the package's analytics headers are switched off with the OMOPHUB_ANALYTICS_OPTOUT variable.
map_concept returns one page per call, so for a complete code list keep requesting until has_more is false. The Custom Connectors screen in Claude Desktop accepts only OAuth and does not send a key header, so that client needs the npx setup. Availability of the service from Russia has not been verified.
How to disable. Remove the omophub server from the agent's settings: in Claude Code with claude mcp remove omophub, in other clients by deleting the omophub block in the configuration file. Also delete the key from the configuration and from the OMOPHUB_API_KEY variable, and remove the key you no longer need in the OMOPHub dashboard.
FAQ
How do I connect OmopHub MCP to Claude Code?
Create a key in the OMOPHub dashboard and pick a method. Hosted: claude mcp add omophub --transport http -H "Authorization: Bearer <key>" https://mcp.omophub.com. Local: claude mcp add omophub -- npx -y @omophub/omophub-mcp, then set the OMOPHUB_API_KEY variable. Check that it works by calling list_vocabularies.
Do I need a key and a paid plan for OmopHub MCP?
A key is always required: without one the server lists its tools, and calling any of them ends with an AUTH_FAILED error. According to the pricing page on October 28, 2026, the Free plan costs 0 dollars and includes 3,000 calls a month, Pro costs 39 dollars for 50,000 calls, and Scale and Business sit above it. Semantic search is basic on the free plan, and the full version starts with Pro.
Does OmopHub MCP work in Claude Desktop?
It works through npx. The Custom Connectors section in Claude Desktop accepts only OAuth and does not send a key header, so the hosted address cannot be added there. Add the npx command with the arguments -y and @omophub/omophub-mcp, plus the key in env, to claude_desktop_config.json.
How is the hosted server different from running it through npx?
Hosted needs no installation: the client connects to https://mcp.omophub.com and sends the key in a header. The @omophub/omophub-mcp package runs on your machine in stdio mode and reads the key from OMOPHUB_API_KEY. Both methods use OMOPHub data. The same package can also run as a local HTTP server with the --transport=http flag or in Docker.
How do I get the full concept set when map_concept returns one page at a time?
map_concept returns 1 to 200 mappings per call, 100 by default. A common drug can have over a thousand NDC codes alone, so a single call is a sample. Increase the page number until the server returns no more mappings. find_similar_concepts does not fit this job: it ranks by similarity of meaning and does not know whether a concept belongs to a set.
Discussion
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Comparison with similar tools
Entries that share the main search query, and how they differ.
| Entry | Official | Authentication | Repository stars | Main difference |
|---|---|---|---|---|
| OmopHub MCP (this entry) | yes | API key | ||
| BioMCP | no | not required | 668 | one command line over 70 biomedical sources such as PubMed and ClinVar, while OmopHub covers only OMOP vocabularies and codes |
| ToolUniverse | no | not required | 1,764 | more than 1000 scientific tools for biology, chemistry and medicine, while OmopHub is a single narrow terminology reference |
README in short
The documentation leads from a key in the dashboard to client setup: Claude Desktop, Claude Code, Cursor, VS Code, the hosted address, local HTTP and Docker. Next come a table of tools and example queries, from searching and mapping codes to building a concept set. The server also exposes the omophub://vocabularies resource and two ready prompts, phenotype-concept-set and code-lookup.