Synapse MCP Server

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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

Tool	Friendly Name	Description
`get_entity(entity_id)`	Fetch Entity	Fetch core metadata for a Synapse entity by ID.
`get_entity_annotations(entity_id)`	Fetch Entity Annotations	Return custom annotations associated with an entity.
`get_entity_provenance(entity_id, version=None)`	Fetch Entity Provenance	Retrieve provenance (activity) metadata for an entity, optionally scoped to a specific version.
`get_entity_children(entity_id)`	List Entity Children	List children for container entities such as projects and folders.
`search_synapse(query_term=None, ...)`	Search Synapse	Search Synapse entities by keyword with optional name/type/parent filters. Results are provided by Synapse as data custodian; attribution and licensing follow the source entity metadata.

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.

Resource	Friendly Name	Description
`synapse://feeds/blog`	Sage Blog RSS	Live RSS XML for the latest Sage Bionetworks publication posts.

⚠️ 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:

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.
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

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

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