BrAPI MCP Server

The BrAPI MCP Server provides LLMs with tools to search and retrieve data from BrAPI v2 Compatible Servers.

Jerry Yu, Akarsh Eathamukkala, Jay Shah, Benjamin Maza, Jerome Maleski

🛠️ Tools Overview

This server provides 10 powerful tools for accessing and analyzing plant breeding data from BrAPI-compatible servers:

Tool Name	Description
Core BrAPI Access
describe_server_capabilities	Returns a list of accesible endpoints and searchable filters for the BrAPI compliant server you are connected to.
brapi_get	Fetches data from any BrAPI GET endpoint. Supports filtering by Database ID (DbID) and pagination.
brapi_search	Performs advanced searches using BrAPI POST search endpoints.
get_search_parameters	Gets valid search parameters for a specific service. Use before brapi_search to see available filters.
get_image_search_parameters	Retrieves valid filters for the image search endpoint.
download_images	Downloads images from the BrAPI server to the local directory based on search criteria.
Data Processing & Management (Mostly for the Model)
get_result_summary	Provides a summary of a saved result (columns, row count, size) without loading the full data.
load_result	Loads a saved result (or a specific subset) into the conversation context for analysis. Supports pagination and column selection.
get_download_instructions	Generates URLs and instructions for downloading a csv of saved results via HTTP.
quick_download_link	Returns a direct download URL for a saved result, ideal for quick access.

You can access some example workflows in the Examples folder. Conversational_Workflow.md and Covington_MetaAnalysis_EDA.md show some workflows that incorporate some complex interactive filtering. VS Code Copilot with Claude Sonnet/Haiku 4.5 were used to for the workflows.

Examples

brapi_get

Download data from most BrAPI compatible servers. Generally use it to fetch data for subsequent searches.

Example Use Cases:

• "Where are all the locations that sweetpotatoes have been trialed on?"
• "For the variantset with the dbID =5, what were the possible genotype calls?"

More examples here.

brapi_search

Search and discover breeding data using advanced filters. Supports all search terms compatible with BrAPI.

Example Use Cases:

• "Find all studies in 'Mozambique' with 'Advanced Yield Trial' type."
• "Please download all data For the Advanced Yield Trial run at NCSU research station 1 during spring 2018."

More examples here.

download_images

Download images from BrAPI servers with optional search filters.

Example Use Cases:

• "Download 10 images from the database."
• "Download all images with height greater than 300 pixels."
• "Get images associated with observation unit 12345."

More examples here.

Getting Started

• The server supports two modes: STDIO and HTTP.
  • STDIO: Best for personal use. The server runs directly on your machine, and files are saved to your local disk. It is easier to configure and more secure for single users.
  • HTTP: Under active development. Best for hosting the server for multiple users or on a cloud instance. It exposes a web endpoint that MCP clients can connect to over the network.

Configuration

1. Clone the Repository

git clone https://github.com/Plant-Phenomics-Lab/Breedbase-Client

2. Create UV Environment. You must have uv installed to run the MCP server locally.

cd Breedbase-Client
uv venv
.venv\Scripts\activate
uv sync

3. Configure the enviroment variables. You can set these in a .env file, pass them via your MCP client config, or use Docker environment variables. You must configure BASE_URL for your server to work.

Key Variables

Variable	Default	Description
BASE_URL	https://sweetpotatobase.org/brapi/v2	The BrAPI server URL. You must set a base url. Set it at root of the BRAPI server endpoints (ends in /brapi/v2)
BRAPI_USERNAME	None	Your login username.
BRAPI_PASSWORD	None	Your login password.
MODE	stdio	stdio for local apps, http for remote.

👉 See CONFIGURATION.md for full details and examples.

Example with Editing .env.

# Copy the .env example file
cd Breedbase-Client
cp .env.example .env
# Then edit the file with your favorite text editor. 

4. Configure the server.

For STDIO, can can just add this command to your MCP Client Configuration file (ex claude.json).

{
  "mcpServers": {
    "brapiserver": {
      "command": "uv",
      "args": [
        "run",
        "--directory",
        "/path/to/Breedbase-Client",
        "src/main.py"
      ]
    }
  }
}

For HTTP You need to run the server and then connect your server to the MCP client. Thus:

# Run the Sever, assume you're in the Breedbase-Client folder. 
docker compose up -d

Then connect the server. Remember to use the port you configured.

{
  "mcpServers": {
    "brapiserver": {
			"url": "http://127.0.0.1:8000/mcp",
			"type": "http"
		}
  }
}

Dependencies

• UV version 0.4.0 or higher for running locally with STDIO.
• Docker for running HTTP.

Features:

• Python Client: A robust Python client for calling Breedbase that handles pagination automatically
• FastMCP Implementation: Simple FastMCP implementation with tool uses that can call Breedbase and save data locally as CSV or JSON

Compatability

• A List of Server the MCP was tested against.

Server	Auth Type	Works?	Base Get	Search	Images
Cassavabase	SGN	✅	✅	✅	✅
Solgenomics	SGN	✅	✅	✅	✅
Sweetpotatobase	SGN	✅	✅	✅	✅
Yambase	SGN	✅	✅	✅	✅
Musabase	SGN	✅	✅	✅	No Images
CitrusBase	SGN	Not Tested	Not Tested	Not Tested	Not Tested
sugarcane.sgn.cornell.edu	SGN	Not Tested	Not Tested	Not Tested	Not Tested
BrAPI Test Server	None	✅	✅	✅	✅
T3 (Wheat Oat, Barley)	None	✅	✅	✅	✅
Gigwa	None	✅	✅	✅	No Images
MGIS	None	✅	✅	No Images	✅
Musa Acuminata GWAS Panel1 - GBS - genome V1	None	✅	✅	✅	No Images
Musa Acuminata GWAS Panel - GBS - genome V2	None	✅	✅	✅	No Images
Musa Germplasm Information System v5	None	✅	✅	✅	No Images
Crop Ontology	None	❌	❌	❌	❌
EU-SOL Tomato collection	None	❌	❌	❌	❌
TERRA-REF BrAPI implementation	None	❌	❌	❌	❌
URGI GnpIS Information System	None	❌	❌	❌	❌

Contributing

This project is under active development. Contributions and feedback are welcome!

• The current branch is main. Feel free to ignore everything else :).