Connect Open WebUI to SciSure Research

SciSure MCP: Overview · ChatGPT (OpenAI) · Claude · LM Studio · Open WebUI · Other MCP applications

Add SciSure Research as an MCP tool in Open WebUI, secure the connection with OAuth 2.1, and start working with the research data you are already authorized to access.

What you’ll need

MCP requires a Private Cloud or On-Premises SciSure Research environment — it isn't available on the shared Cloud.

The setup joins three parts: your Open WebUI installation, an OAuth client in SciSure Research, and the MCP endpoint on your SciSure tenant.

• Open WebUI admin access — You need access to the Admin Panel and the public URL users use to reach Open WebUI.
• SciSure group settings — You need permission to create an OAuth2 client and choose its read scopes.
• Your tenant URL — Have the base URL for the SciSure Research environment you want to connect.

How the connection works: Open WebUI → OAuth 2.1 → SciSure Research MCP

1. Start with an existing Open WebUI installation

This tutorial expects Open WebUI to be installed, running, and reachable on your network.

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WEBUI_SECRET_KEY is required

A persistent WEBUI_SECRET_KEY must already be defined for the Open WebUI installation. Without it, Open WebUI does not allow an MCP connection to be configured. If you do not manage the installation, ask your Open WebUI administrator to confirm this before continuing.

services:
  openwebui:
    image: ghcr.io/open-webui/open-webui:main-slim
    container_name: open-webui
    ports:
      - "3000:8080"
    volumes:
      - open-webui:/app/backend/data
    environment:
      - WEBUI_SECRET_KEY=your_random_secret_here

volumes:
  open-webui:

2. Build the exact callback URL

The Open WebUI connection ID becomes part of the OAuth callback URL. For this guide, use SciSure-MCP and keep the spelling and capitalization consistent.

OAuth redirect URI

https://<your-openwebui-host>/oauth/clients/mcp:SciSure-MCP/callback

Replace <your-openwebui-host> with the hostname users actually use to open Open WebUI. Include a non-default port if your public URL uses one.

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Connection ID vs. Client ID

The Open WebUI connection ID and the OAuth Client ID are different values. SciSure-MCP identifies the connection inside Open WebUI; the OAuth Client ID is created in SciSure and entered as a credential in step 4.

3. Register Open WebUI in SciSure Research

In SciSure Research, go to Group Settings → OAuth2 Clients and add a new application.

• Enter a recognizable Application name and Client ID.
• Paste the redirect URI from step 2 into Redirect URIs.
• Select the required scopes. Use Read only when the connection only needs to retrieve data.
• Create the application and retain the Client ID and Client Secret for step 4.

Add the callback URI and select the read scopes the Open WebUI connection needs.

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Copy the callback URL exactly

A redirect URI mismatch stops authentication. Check the protocol, hostname, optional port, and the mcp:SciSure-MCP segment character for character.

4. Configure the connection in Open WebUI

In Open WebUI, go to Admin Panel → Settings → Integrations → External Tool Servers, then select Add (+). Change the type from OpenAPI to MCP Streamable HTTP.

Your MCP endpoint: Replace <your-instance> with the base URL you use to sign in to your SciSure Research environment (for example acme.elabnext.com, acme.elabjournal.com, or a custom domain for self-hosted deployments). Your instance also publishes its configuration at <your-instance>/.well-known/oauth-authorization-server.

The completed SciSure Research connection before client registration.

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Experimental-feature warning

Open WebUI may display a warning that MCP support is experimental. The warning itself does not mean the connection has failed.

5. Verify the endpoint and register the client

Complete the connection in this order so Open WebUI can discover the endpoint and bind it to the OAuth client.

1. Select Verify Connection — the refresh icon next to the URL.
2. Select Register Client.
3. Confirm that the status changes to Registered.
4. Select Save.

The green Registered state confirms client registration. Keep your own connection ID set to SciSure-MCP, as configured in step 4.

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Client registered

When the status is Registered and the connection is saved, the SciSure MCP tool is ready to be enabled in a chat.

6. Authenticate from a new chat

Start a new Open WebUI chat, enable SciSure MCP for that chat, and approve the requested access in SciSure Research.

Open the integrations menu

In the prompt bar, select the integrations icon next to the plus button.

Select the integrations icon in the prompt bar.

Choose Tools

In the integrations menu, select Tools.

Open Tools from the integrations menu.

Enable SciSure MCP

Switch SciSure MCP on. The authentication flow should start automatically.

Enable SciSure MCP for the current chat.

Approve access in SciSure Research

After signing in if prompted, review the application name and requested permissions. If they match the OAuth client created in step 3, select Allow Access.

The application name in your environment may differ from this example. Verify the name and permissions before selecting Allow Access.

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Check before you allow access

Only grant access when you recognize the application and the listed permissions match the scopes selected for your OAuth client.

• Return to the Open WebUI chat after authorization completes.
• Ask a question that uses your authorized SciSure Research data.

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Connected

You are connected. Requests run through the SciSure MCP endpoint using the scopes and access granted to the authenticated user.

Common connection issues

Check these items before recreating the connection.