The Synapse MCP Server enables AI agents to access and interact with Synapse entities including Datasets, Projects, Folders, Files, Tables, and more.
• Retrieve entities by ID: Get detailed information about specific Synapse entities using their unique identifiers • Get entity annotations: Access metadata and annotations associated with Synapse entities • Get entity children: List child entities contained within container entities (like folders or projects) • Search entities: Find entities using search terms with optional filters for parent ID and entity type • Query entities: Search entities based on various criteria including name, parent ID, annotations, and entity type • Query tables: Execute queries against Synapse tables to retrieve structured data • Access public datasets: Get public datasets in Croissant metadata format for standardized data access
Enables cloning the source code repository from GitHub for installation and development.
Allows installing the Synapse MCP server package directly from PyPI repository.
Supports running tests for the Synapse MCP server using the pytest framework.
Provides integration with Sage Bionetworks' Synapse platform, allowing access to Synapse entities (Datasets, Projects, Folders, Files, Tables) and their annotations through a RESTful API.
Click on "Install 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., "@Synapse MCP Serversearch for datasets related to Alzheimer's disease"
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.
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
Tool | Friendly Name | Description |
| Fetch Entity | Fetch core metadata for a Synapse entity by ID. |
| Fetch Entity Annotations | Return custom annotations associated with an entity. |
| Fetch Entity Provenance | Retrieve provenance (activity) metadata for an entity, optionally scoped to a specific version. |
| List Entity Children | List children for container entities such as projects and folders. |
| 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. |
Related MCP server: SourceSync.ai MCP Server
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 |
| 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
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
For issues, please file an issue. For other contact, see https://sagebionetworks.org/contact.