oak-mcp
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@oak-mcpsearch for terms related to 'apoptosis' in GO"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
oak_mcp
A model context protocol (MCP) to help agents interact with ontologies and the ontology access kit
Quick Start
# Install dependencies and set up development environment
make dev
# Run the MCP server
make run-server
# Run tests
make testRelated MCP server: OWL MCP Server
Installation
Using uvx (Recommended)
# Install and run directly with uvx
uvx oak-mcpDevelopment Installation
# Install in development mode (includes dependencies)
make dev-installUsage
Testing MCP Protocol
make test-mcpIntegration with AI Tools
Claude Desktop
Add this to your Claude Desktop configuration file:
{
"mcpServers": {
"oak-mcp": {
"type": "stdio",
"command": "uvx",
"args": [
"oak-mcp"
],
"env": {}
}
}
}Claude Code
claude mcp add oak-mcp uvx oak-mcpGoose
goose session --with-extension "uvx oak-mcp"Development
# Full development setup
make dev
# Run tests
make test
# Check dependencies
make check-deps
# Clean build artifacts
make cleanLicense
BSD-3-Clause
This server cannot be deployed
Maintenance
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- AlicenseNot gradedqualityCmaintenanceEnables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.4 npmMIT