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)

Instructions

Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.

This server publishes no instructions, or was last inspected before Glama recorded them.

Capabilities

Features and capabilities supported by this server

Protocol revision2025-11-25

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
Instructions
Capabilities
Tools
Prompts
Resources

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