Synapse MCP Server

A Model Context Protocol (MCP) server that enables AI agent access to Synapse entities (Datasets, Projects, Folders, Files, Tables, and more).

You (your AI agent) can:

• Retrieve entities by ID
• Get entity annotations
• List entity children
• Search Synapse entities with path and type filters
• Inspect provenance/activity recorded for an entity version

Available Tools

Available Resources

Resources provide ready-to-present context that clients can pull without extra parameters. When you need to search or compute derived results, prefer tools instead.

⚠️ Terms of Service Compliance Notice

Important: When using this MCP server with external AI services (such as Claude, ChatGPT, or other cloud-based models), please be aware that:

• You will use your personal Synapse access token to retrieve data
• Data sent to external AI services may be stored, logged, or used for model training
• The Synapse Terms of Service prohibit redistribution of data, which may include storage or use by third-party AI providers

Recommended Safe Usage:

• ✅ Use with enterprise AI deployments with data residency guarantees
• ✅ Use with local/self-hosted AI models
• ✅ Leverage responsible AI use training if provided
• ❌ Avoid use with consumer AI services that may store or train on your data

You are responsible for ensuring your usage complies with the Synapse Terms of Service.

Usage

This guide provides typical user instructions for connecting to the Synapse MCP server. For contributor setup, please see DEVELOPMENT.md.

Authentication

The Synapse MCP server supports two authentication methods:

1. OAuth2 (Default): This is the primary and recommended authentication method. It provides a secure, browser-based login flow. When your AI agent needs to access protected resources, it will prompt you to log in to Synapse in your browser. This method is used by default for both local and remote servers.

2. Personal Access Token (PAT): This method is available for local development or in environments where a browser-based login is not feasible. It requires you to provide a Synapse Personal Access Token to the server.

MCP Server setup

Remote Server

Use this URL in your client: 🔌 https://mcp.synapse.org/mcp

Claude Desktop Instructions

Go to Settings > Connectors > Add custom connector

Claude Code

claude mcp add --transport http synapse -- https://mcp.synapse.org/mcp

Local Server

For running local server, see DEVELOPMENT.md

Example Prompts

See usage examples

Contributing

Contributions are welcome! Please see our Development Guide for instructions on setting up a development environment, running tests, and more.

License

MIT

Contact

For issues, please file an issue. For other contact, see https://sagebionetworks.org/contact.