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](https://www.synapse.org/TrustCenter:TermsOfService).

Getting Started

The Synapse MCP server can be used as a remote hosted server (recommended) or installed locally from source. Choose the approach that fits your needs.

Remote Server (Recommended)

The hosted server is available at:

https://mcp.synapse.org/mcp

Authentication uses OAuth2 -- your MCP client will open a browser window for you to log in to Synapse. No API keys or tokens to manage.

Below are setup instructions for popular AI clients. If your client is not listed, use the generic JSON config.

#### Generic MCP JSON Config

Most MCP-compatible clients accept a JSON configuration block. Add the following to your client's MCP config file:

{
  "mcpServers": {
    "synapse": {
      "url": "https://mcp.synapse.org/mcp",
      "type": "http"
    }
  }
}

#### Claude Desktop

Go to Settings > Connectors > Add custom connector and enter the URL https://mcp.synapse.org/mcp.

<img width="664" height="146" alt="Claude Desktop connector setup" src="https://github.com/user-attachments/assets/fcfe54ba-1c1c-4fa8-9bae-c198cffff6ce" />

#### Claude Code (CLI)

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

#### VS Code / GitHub Copilot

VS Code's MCP client does not yet fully support OAuth Dynamic Client Registration (DCR). To connect to the remote server, follow these steps:

Step 1: Register a client

Run this command once to register an OAuth client with the MCP server:

curl -X POST https://mcp.synapse.org/register \
  -H "Content-Type: application/json" \
  -d '{
    "client_name": "vscode-synapse",
    "redirect_uris": ["http://127.0.0.1"],
    "grant_types": ["authorization_code", "refresh_token"],
    "response_types": ["code"],
    "token_endpoint_auth_method": "none"
  }'

Save the client_id from the response (e.g., c3dfaf80-126c-4f46-80ab-114747fcc3b3).

Step 2: Configure VS Code

Create or edit .vscode/mcp.json in your workspace:

{
  "servers": {
    "synapse": {
      "url": "https://mcp.synapse.org/mcp",
      "type": "http"
    }
  }
}

Step 3: Complete the OAuth flow

When you start the server, VS Code will open a browser to an authorization URL. Replace the client_id value in the URL with your registered client_id from Step 1, then press Enter to continue the Synapse login flow.

For example, change client_id=100441 to client_id=YOUR_CLIENT_ID in the browser address bar.

Alternatively, you can use the Local Server setup with a Personal Access Token, which does not require OAuth.

#### Cursor

Add to Cursor Settings > MCP > + Add new global MCP server, or add to your project's .cursor/mcp.json:

{
  "mcpServers": {
    "synapse": {
      "url": "https://mcp.synapse.org/mcp",
      "type": "http"
    }
  }
}

Local Server

Run the server locally for development, self-hosting, or offline use. The local server uses stdio transport by default, which is what most MCP clients expect for command-based servers.

Note: synapse-mcp is not currently published on PyPI. You must install from source.

#### Install

git clone https://github.com/Sage-Bionetworks/synapse-mcp.git
cd synapse-mcp
python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate
pip install -e .

After installation, the synapse-mcp command is available in your virtual environment.

#### Authentication for Local Server

For local use, authenticate with a Synapse Personal Access Token (PAT) by setting the SYNAPSE_PAT environment variable:

export SYNAPSE_PAT="your_synapse_pat_here"

To create a PAT, visit your Synapse Personal Access Tokens page.

#### MCP Client Configuration (Local)

Important: The synapse-mcp command must be on your PATH. If you installed in a virtual environment, either activate it first or use the full path to the binary (e.g., /path/to/.venv/bin/synapse-mcp).

Generic JSON config (stdio):

{
  "mcpServers": {
    "synapse": {
      "command": "/path/to/.venv/bin/synapse-mcp",
      "env": {
        "SYNAPSE_PAT": "your_synapse_pat_here"
      }
    }
  }
}

Claude Code (local):

claude mcp add synapse -e SYNAPSE_PAT=your_synapse_pat_here -- /path/to/.venv/bin/synapse-mcp

VS Code / GitHub Copilot (local):

In .vscode/mcp.json:

{
  "servers": {
    "synapse": {
      "command": "/path/to/.venv/bin/synapse-mcp",
      "env": {
        "SYNAPSE_PAT": "your_synapse_pat_here"
      }
    }
  }
}

Cursor (local):

{
  "mcpServers": {
    "synapse": {
      "command": "/path/to/.venv/bin/synapse-mcp",
      "env": {
        "SYNAPSE_PAT": "your_synapse_pat_here"
      }
    }
  }
}

Configuration

#### Environment Selection

You can configure which Synapse platform instance to connect to by setting the SYNAPSE_ENV environment variable:

• prod (default) -- Production instance at synapse.org
• staging -- Staging instance at staging.synapse.org
• dev -- Development instance at dev.synapse.org

If not set, the server defaults to prod.

Authentication

For contributor/development setup details, 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.