OntoPortal MCP Server

An MCP (Model Context Protocol) server that integrates with AgroPortal and the broader OntoPortal ecosystem.

This server provides AI agents with tools to search, explore, and interact with the ontologies, vocabularies, and semantic resources available on AgroPortal.

Features

• Search Ontologies: Search for terms and classes across all or specific ontologies. Supports advanced filtering like language, obsolete classes, precise matches, and properties.
• List Ontologies: Retrieve a list of all available ontologies in AgroPortal.
• Get Versions: Fetch the history and versions of a specific ontology.
• Changelogs: Access changelog/diff data between ontology versions.
• Text Annotation: Annotate plain text to extract semantic entities and link them to AgroPortal ontologies.

Requirements

• Python 3.12+
• uv (Recommended for dependency management)

Installation

This project uses mcp and fastmcp.

1. Clone the repository:

   git clone https://github.com/your-username/ontoportal_mcp.git
   cd ontoportal_mcp
   

2. Set up the environment and install dependencies using uv:

   uv sync
   

3. Configure your API key. Create a .env file in the root directory:

   # .env
   AGROPORTAL_API_KEY=your_api_key_here
   

Usage

You can run the MCP server directly setup for your AI agent of choice (like Claude Desktop or any other MCP-compatible client).

uv run mcp run src/main.py

Adding to Claude Desktop

Add the following to your claude_desktop_config.json:

{
  "mcpServers": {
    "ontoportal": {
      "command": "uv",
      "args": [
        "run",
        "--directory",
        "/absolute/path/to/ontoportal_mcp",
        "mcp",
        "run",
        "src/main.py"
      ],
      "env": {
        "AGROPORTAL_API_KEY": "your_api_key_here"
      }
    }
  }
}

Development

The project is structured as follows:

• src/main.py - The MCP server entry point.
• src/config.py - Configuration and environment variable handling.
• src/clients/ontoportal_client.py - Client wrapper for interacting with the AgroPortal API.
• src/tools/ontoportal_tools.py - Registration and definitions of the MCP tools exposed to the LLM.

License

MIT License