What is the key difference between Fhir MCP Server and Omop MCP?

Fhir MCP Server belongs to the Biology, Medicine and Bioinformatics category with local stdio execution, while Omop MCP belongs to the Biology, Medicine and Bioinformatics category with local stdio execution.

How do I install Fhir MCP Server or Omop MCP in Claude Desktop or Cursor?

Copy the mcpServers JSON configuration snippet provided on this page into your claude_desktop_config.json or ~/.cursor/mcp.json file and restart your AI client.

Are Fhir MCP Server and Omop MCP free or paid?

Fhir MCP Server operates under a BYOK (Pay Provider Direct) model (API Key required). Omop MCP operates under a BYOK (Pay Provider Direct) model (API Key required).

Which MCP server has more tools and community activity?

Fhir MCP Server lists 1 tools with 2 views and 100 GitHub stars. Omop MCP lists 5 tools with 2 views and 40 GitHub stars.

Can I use both Fhir MCP Server and Omop MCP together in the same MCP host?

Yes! MCP hosts like Claude Desktop, Cursor, Windsurf, Cline, and VS Code support configuring multiple servers under the mcpServers object simultaneously.

Side-by-Side Model Context Protocol Comparison

Fhir MCP Server vs Omop MCP

In-depth architectural comparison of the Fhir MCP Server and Omop MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

At a Glance & Executive Verdict

Fhir MCP Server

Biology, Medicine and Bioinformatics · Local stdio

Quality: 47/100 (Fair) | Auth: API Key required

Omop MCP

Biology, Medicine and Bioinformatics · Local stdio

Quality: 36/100 (Fair) | Auth: API Key required

Verdict Summary: Choose Fhir MCP Server if you need specialized Biology, Medicine and Bioinformatics tools running via a local process. Choose Omop MCP if your workspace requires Biology, Medicine and Bioinformatics integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.

Which MCP Server Should You Choose?

Choose Fhir MCP Server when:

You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: API Key required (BYOK (Pay Provider Direct)).
You have access to required keys: FHIR_SERVER_URL, FHIR_OAUTH_CLIENT_ID, FHIR_OAUTH_CLIENT_SECRET, FHIR_OAUTH_TOKEN_URL, PINECONE_API_KEY, LOINC_API_KEY.
Primary tools included: Security.

Explore Fhir MCP Server Details

Choose Omop MCP when:

You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: API Key required (BYOK (Pay Provider Direct)).
You have access to required keys: OMOPHUB_API_KEY, LLM_API_KEY.

Feature & Specification Comparison

Specification	Fhir MCP Server the-momentum Biology, Medicine and Bioinformatics	Omop MCP OHNLP Biology, Medicine and Bioinformatics
Summary	MCP Server that connects AI agents to FHIR servers. One example use case is querying patient history in natural language.	Map clinical terminology to OMOP concepts using LLMs for healthcare data standardization and interoperability.
Category & Scope	Biology, Medicine and Bioinformatics

Tools & Capabilities Breakdown

Fhir MCP Server Tools (1)

Security

OAuth2 authentication and proper access control for all operations

Omop MCP Tools (5)

Intelligent clinical terminology mapping to OMOP concepts

Direct OMOP vocabulary search via OMOPHub API

Batch mapping tool for CSV input

Automatic preferred vocabulary selection by domain

Live documentation access for OMOP CDM

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

Fhir MCP Server Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "the-momentum-fhir-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "the-momentum-fhir-mcp-server"
      ],
      "env": {
        "FHIR_SERVER_URL": "YOUR_FHIR_SERVER_URL_HERE",
        "FHIR_OAUTH_CLIENT_ID": "YOUR_FHIR_OAUTH_CLIENT_ID_HERE",
        "FHIR_OAUTH_CLIENT_SECRET": "YOUR_FHIR_OAUTH_CLIENT_SECRET_HERE",
        "FHIR_OAUTH_TOKEN_URL": "YOUR_FHIR_OAUTH_TOKEN_URL_HERE",
        "PINECONE_API_KEY": "YOUR_PINECONE_API_KEY_HERE",
        "LOINC_API_KEY": "YOUR_LOINC_API_KEY_HERE"
      }
    }
  }
}

Omop MCP Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "ohnlp-omop-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "ohnlp-omop-mcp"
      ],
      "env": {
        "OMOPHUB_API_KEY": "YOUR_OMOPHUB_API_KEY_HERE",
        "LLM_API_KEY": "YOUR_LLM_API_KEY_HERE"
      }
    }
  }
}

Frequently Asked Questions

Fhir MCP Server is categorized under Biology, Medicine and Bioinformatics and uses a local stdio subprocess. In contrast, Omop MCP belongs to Biology, Medicine and Bioinformatics using local stdio subprocess. Select Fhir MCP Server when you need capabilities focused on biology, medicine and bioinformatics and Omop MCP when you require tools for biology, medicine and bioinformatics.

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