MedixHub Model Context Protocol (MCP) Server

By profliuhao GitHub

MedixHub - A Model Context Protocol (MCP) server with a collection of medical and healthcare APIs and tools.

Overview

what is MedixHub?

MedixHub is a Model Context Protocol (MCP) server that provides a collection of medical and healthcare APIs and tools for developers.

how to use MedixHub?

To use MedixHub, clone the repository, install dependencies, configure environment variables, and start the server. You can then access various API endpoints to execute functions or retrieve medical data.

key features of MedixHub?

Pure JavaScript implementation
Standardized MCP metadata for function exposure
Parameter validation for function execution
Integration with LLMs like Ollama
Secure API endpoints with authentication
Support for streaming responses

use cases of MedixHub?

Executing GraphQL queries against the OpenTarget API for disease and drug information.
Retrieving drug information from the FDA database.
Searching for biomedical entities and their associations in the Monarch database.

FAQ from MedixHub?

What programming language is MedixHub built with?

MedixHub is built using JavaScript.

How do I authenticate with the MedixHub API?

You can authenticate using API keys or JWT tokens.

Is there documentation available for the API?

Yes, full API documentation is available at the /functions/medixhub endpoint.

Content

MedixHub Model Context Protocol (MCP) Server

A Model Context Protocol (MCP) server with integrated medical and healthcare API access through MedixHub.

Features

Pure JavaScript implementation
Exposes functions with standardized MCP metadata
Executes functions with parameter validation
Seamlessly integrates with LLMs like Ollama
Secure API endpoints with authentication
Supports streaming responses

Implemented Functions

The server includes JavaScript implementations of these functions:

executeOpenTargetQuery - Executes GraphQL queries against the OpenTarget API
FDADrugLabelSearch - Retrieves drug information from the FDA database
get_drug_generic_name - Maps between generic and brand drug names
MonarchSearch - Searches the Monarch database for genes, diseases, or phenotypes
MonarchDiseasesForMultiplePhenotypes - Finds diseases matching multiple phenotypes

OpenTarget Functions

Disease information lookup
Drug details and associations
Target (gene/protein) information
Disease-target associations
Drug-disease relationships

FDA Drug Label Functions

Drug information search
Generic and brand name mapping
Adverse reactions lookup
Drug interactions search

Monarch Database Functions

Biomedical entity search
Disease-phenotype associations
Gene-phenotype relationships
Multi-phenotype disease finder

Getting Started

Prerequisites

Node.js 14 or later
npm or yarn

Installation

Clone the repository

git clone https://github.com/yourusername/medixhub-mcp-server.git
cd medixhub-mcp-server

Install dependencies

npm install

Configure environment variables

cp .env.example .env
# Edit .env with your settings

Start the server

npm start

For development with auto-reload:

npm run dev

Usage

Execute API

Use the /execute endpoint to run any registered MedixHub function:

POST /execute
Content-Type: application/json

{
  "name": "queryFDADrugLabel",
  "parameters": {
    "searchFields": {
      "drug_name": ["openfda.brand_name", "openfda.generic_name"]
    },
    "returnFields": ["openfda.generic_name", "warnings"],
    "arguments": {
      "drug_name": "ibuprofen",
      "limit": 1
    }
  }
}

Direct MedixHub API

Use the /medixhub endpoints for direct API access:

/medixhub/opentargets
/medixhub/opentargets-genetics
/medixhub/drug-by-name
/medixhub/fda-drug-label
/medixhub/drug-generic-name
/medixhub/monarch
/medixhub/diseases-for-phenotypes

Function Metadata

Get information about available functions:

/functions - All available functions
/functions/medixhub - MedixHub-specific functions
/functions/category/:category - Functions by category

API Documentation

Full API documentation is available at /functions/medixhub

Development

Project Structure

medixhub-mcp-server/
├── server.js                   # Main server file
├── src/
│   ├── medixhub/               # MedixHub integration
│   ├── middleware/             # Middleware
│   ├── routes/                 # Route handlers
│   └── services/               # Services
├── examples/                   # Usage examples
└── tests/                      # Test suite

Adding New Functions

To add a new function to the registry:

const { registerFunction } = require('./src/services/functionRegistry');

registerFunction('myNewFunction', {
  name: 'myNewFunction',
  description: 'Description of what this function does',
  parameters: {
    // Parameter schema
  },
  function: async (params) => {
    // Implementation
    return result;
  }
});

Running Tests

npm test

Authentication

The server supports two authentication methods:

API Keys: Simple key-based authentication
JWT Tokens: More granular access control

In production mode, authentication is required for all endpoints except function discovery.

Environment Variables

Configure the server through the following environment variables:

PORT: Server port (default: 3000)
NODE_ENV: Environment ('development' or 'production')
OLLAMA_API_URL: URL for Ollama API
API_KEYS: Comma-separated list of valid API keys
FDA_API_KEY: API key for FDA drug database

See .env.example for all available options.

Performance Considerations

The server uses asynchronous processing for all API calls
Rate limiting is enabled to prevent abuse
Timeout handling prevents hanging requests
Memory usage is optimized by processing streams efficiently

License

This project is licensed under the MIT License - see the LICENSE file for details.

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