MCP Server × PostgreSQL on MIMIC‑IV

by ambakick

224 downloads

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Database

Description

# MCP Server × PostgreSQL on MIMIC‑IV > **Project goal:** Evaluate whether a Model Context Protocol (MCP) Server layered on Azure Database for PostgreSQL can match—or outperform—direct SQL while reducing developer effort for large‑scale clinical analytics. --- ## 1. Problem…

About

Details

Author: ambakick
Downloads: 224
Categories: Database

- MCP‑based abstraction over Azure Database for PostgreSQL.
- Designed for clinical dataset MIMIC‑IV (millions of rows, hundreds of attributes).
- Supports both password and Microsoft Entra authentication.
- Includes benchmark scripts to compare performance with direct SQL.
- Example benchmarks show up to 33% faster query execution for COUNT(*) on EMAR data.
- Reduces lines of code (LOC) by 66% compared to raw SQL for a sample workload.

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name MCP Server × PostgreSQL on MIMIC‑IV

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

From the repository

Install Python 3.10+ and required libraries (psycopg, mcp[cli], azure‑identity, etc.). Load MIMIC‑IV data into an Azure Database for PostgreSQL Flexible Server using the provided SQL scripts and bulk copy script. Start the MCP server by running python azure_postgresql_mcp.py with environment variables PGHOST, PGUSER, PGPASSWORD, PGDATABASE set (or use Microsoft Entra authentication by setting AZURE_USE_AAD=True). Benchmarks can be run with python benchmarks/run_sql.py --query <name> for direct SQL or python benchmarks/run_mcp.py --query <name> for the MCP server.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "mcp server \u00d7 postgresql on mimic\u2011iv": {
            "mimic-mcp-server": {
                "command": "python",
                "args": [
                    "02_bulk_copy.py",
                    "--csv-root",
                    "/path/to/mimic-iv"
                ]
            }
        }
    }
}

McpServers

{
    "mimic-mcp-server": {
        "command": "python",
        "args": [
            "02_bulk_copy.py",
            "--csv-root",
            "/path/to/mimic-iv"
        ]
    }
}

MCP Server × PostgreSQL on MIMIC‑IV

> Project goal: Evaluate whether a Model Context Protocol (MCP) Server layered on Azure Database for PostgreSQL can match—or outperform—direct SQL while reducing developer effort for large‑scale clinical analytics.

---

1. Problem Statement

Clinical datasets such as MIMIC‑IV contain tens of millions of rows and hundreds of attributes. Writing and maintaining raw SQL against such breadth is error‑prone and slow. We ask:

_Can an MCP‑based abstraction simultaneously improve developer productivity and sustain (or enhance) runtime efficiency compared with traditional SQL‑only workflows?_

To answer this we compare direct SQL against an MCP Server → Postgres path on identical workloads—ranging from a simple COUNT(*) on mimiciv_hosp.emar_detail (≈ 87 M rows) to multi‑table note aggregations.

---

2. Repository Layout

.
├── mimic-postgres/          # Scripts to create schemas & ingest MIMIC‑IV CSVs
├── src/            # Fork of azure_postgresql_mcp with env configs
└── README.md              # This file

---

3. Prerequisites

- Python 3.10+
- Node 18+ (optional, for additional MCP tooling)
- Azure Database for PostgreSQL – Flexible Server (Standard_D4s v5 or larger)
- MIMIC‑IV credential & data download permission

```bash

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Description

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

MCP Server × PostgreSQL on MIMIC‑IV

1. Problem Statement

2. Repository Layout

3. Prerequisites

Install

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