phenotype-concept-set

MCP tool from Omophub MCP by OMOPHub

Guided workflow to build a concept set for a clinical phenotype

How to use it

phenotype-concept-set is exposed by the Omophub MCP MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the phenotype-concept-set tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.

Install Omophub MCP

$npx -y @omophub/omophub-mcp

FULL OMOPHUB MCP LISTING

Other tools in Omophub MCP (12)

code-lookup

Look up and validate a medical code with mappings and hierarchy

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

find_similar_concepts

Find concepts similar to a reference concept, name, or description

get_concept

Get detailed info about a specific OMOP concept by conceptid

get_concept_by_code

Look up a concept using a vocabulary-specific code (e.g., ICD-10 E11.9)

get_hierarchy

Navigate concept hierarchy - ancestors, descendants, or both

list_vocabularies

List available medical vocabularies with statistics

map_concept

Map a concept to equivalent concepts in other vocabularies (paginated — see note below)

search_concepts

Search for medical concepts by name or clinical term across all vocabularies

semantic_search

Search using natural language with neural embeddings (understands clinical meaning)