Schema | OMOP MCP Server

OMOP MCP Server

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Server Configuration

Describes the environment variables required to run the server.

Name	Required	Description	Default
`OMOPHUB_API_KEY`	Yes	API key for OMOP HUB vocabulary lookups (obtain from omophub.com)

Capabilities

Features and capabilities supported by this server

Capability	Details
`tools`	{ "listChanged": false }
`prompts`	{ "listChanged": false }
`resources`	{ "subscribe": false, "listChanged": false }
`experimental`	{}

Tools

Functions exposed to the LLM to take actions

Name Description

Name	Description
find_omop_conceptB	`Find OMOP concepts for a given keyword, table, and field. Returns multiple candidates for LLM to choose from based on context. Args: keyword: The clinical term to map omop_table: The OMOP CDM table name omop_field: The concept ID field name max_results: Maximum number of candidate concepts to return Returns: Dict containing candidate concepts or error information if no results found.`
batch_map_concepts_from_csvC	Process a CSV file of keywords, mapping each row and returning a CSV with mapping results appended as new columns.

find_omop_conceptB

Find OMOP concepts for a given keyword, table, and field.
Returns multiple candidates for LLM to choose from based on context.

Args:
    keyword: The clinical term to map
    omop_table: The OMOP CDM table name
    omop_field: The concept ID field name
    max_results: Maximum number of candidate concepts to return

Returns:
    Dict containing candidate concepts or error information if no results found.

batch_map_concepts_from_csvC

Process a CSV file of keywords, mapping each row and returning a CSV with mapping results appended as new columns.

Prompts

Interactive templates invoked by user choice

Name	Description
`map_clinical_concept`	Create a prompt for mapping clinical concepts.

Resources

Contextual data attached and managed by the client

Name	Description
`omop://tables`
`omop://documentation`
`omop://preferred_vocabularies`

Server Configuration
Capabilities
Tools
Prompts
Resources

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