Search, lookup, map, and navigate OMOP medical vocabularies via AI agents
Most developer tooling work still happens through a UI a human drives. Omophub MCP server moves it into the conversation instead. Search, lookup, map, and navigate OMOP medical vocabularies via AI agents.
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.
The server publishes 13 tools. What each one is for:
search_concepts — Search for medical concepts by name or clinical term across all vocabulariesget_concept — Get detailed info about a specific OMOP concept by concept_idget_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 vocabulariesget_hierarchy — Navigate concept hierarchy - ancestors, descendants, or bothlist_vocabularies — List available medical vocabularies with statisticssemantic_search — Search using natural language with neural embeddings (understands clinical meaning)find_similar_concepts — Find concepts similar to a reference concept, name, or descriptionexplore_concept — Get concept details, hierarchy, and cross-vocabulary mappings in one callfhir_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 tablefhir_resolve_codeable_concept — Resolve a FHIR CodeableConcept — best match by OHDSI vocabulary preference, honoring userSelectedResources — The Resources tool exposed by this serverBecause this one is hosted, setup is mostly authentication — you point your client at the endpoint and approve access. Nothing runs on your machine, so there is no runtime to keep patched.
Configuration is passed through the environment: OMOPHUB_API_KEY, OMOPHUB_BASE_URL. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.
Among the developer tooling options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. Omophub's toolset — search_concepts, get_concept, get_concept_by_code and 10 more — is a fair guide to whether it matches your workflow. It is maintained by OMOPHub; worth a glance at recent repository activity before you build anything load-bearing on it.
This entry was verified against Omophub's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| 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 |
| Resources | The Resources tool exposed by this server. |
| Prompts | The Prompts tool exposed by this 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.
| Variable | Description | Required |
|---|---|---|
| OMOPHUB_API_KEY | Credential the server authenticates with. | Yes |
| OMOPHUB_BASE_URL | Endpoint or connection string the server talks to. | Yes |
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