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Connect with Claude

This guide covers how to connect Alien Intelligence connectors to Anthropic's Claude across all supported interfaces: claude.ai, Claude Code, and Claude Desktop.

For general MCP concepts and available tools, see AI Agent Integration. For MCP server deployment, see Deploy MCP.

Prerequisites​

  • For public research connectors (OpenAIRE, bioRxiv, medRxiv): No setup required beyond a Claude account. You can add the connector URL directly in claude.ai or install the openscience plugin in Claude Code (see Alien Marketplace).
  • For your own data cluster: A deployed MCP server (see Deploy MCP) and an API token or OAuth credentials for authentication.

Connect via claude.ai​

The claude.ai web interface supports MCP connectors natively. You add a connector once and it becomes available in all your conversations.

Adding a Custom Connector​

  1. Go to claude.ai/customize.
  2. Click Connectors in the left sidebar.
  3. Click the + button next to the "Connectors" heading.
  4. Select Add custom connector from the dropdown. (The other option, "Browse connectors", opens the official connectors directory.)
  5. In the dialog, fill in:
    • Name: A short label for the connector, e.g. openaire-alpha
    • Remote MCP server URL: The MCP endpoint, e.g. https://openaire.mcp.alpha.alien.club/mcp
    • Advanced settings (optional): OAuth Client ID and Client Secret for pre-registered clients. Leave these blank to use dynamic client registration.
  6. Click Add.
  7. The connector appears under the "Web" section with a CUSTOM badge.

Reviewing Tool Permissions​

Click the connector to open its details panel. You will see:

  • The server URL you configured.
  • A Tool permissions panel listing all discovered tools, grouped as "Read-only tools" with a count (e.g. 29 tools for the OpenAIRE connector).
  • Each tool has three permission modes: auto-allow, needs approval, and block. Adjust these to control which tools Claude can invoke without asking.

Tool annotations published by the MCP server — such as title and readOnlyHint — are reflected in this permissions UI.

Adding a Skill​

Skills provide Claude with domain-specific instructions. They are independent from connectors: a skill supplies context and guidance, but is not linked to any particular set of tools.

  1. Click Skills in the Customize sidebar.
  2. Click the + button. Three options appear: "Create with Claude", "Write skill instructions", and "Upload a skill".
  3. Select Upload a skill.
  4. The upload dialog accepts:
    • A .md file with YAML frontmatter containing name and description fields.
    • A .zip or .skill file containing a SKILL.md file.
  5. After upload, the skill appears under Personal skills (separate from Anthropic's example skills).
  6. Each skill displays: name, "Added by: User", "Last updated" date, "Invoked by: User or Claude", description text, and the full rendered markdown content.

How Connectors Work on claude.ai​

  • Connectors are global. Once added, a connector is available in every conversation — there is no per-conversation or per-project toggle.
  • OAuth is deferred. Authentication is not triggered when you add the connector. It triggers on the first tool call in a conversation.
  • MCP instructions are injected automatically. If the MCP server returns an instructions field, Claude receives it as system context.
  • Resources and prompts are not surfaced. The claude.ai web interface does not expose MCP resources or prompts — only tools.
  • Projects can scope workflows. Claude Projects let you combine specific connectors with uploaded files and custom instructions for a focused workflow.

Connect via Claude Code​

Claude Code supports MCP servers through the plugin system and through manual .mcp.json configuration.

Using the Alien Marketplace Plugin​

The fastest way to get started is to install a plugin from the Alien Marketplace. For public research connectors (OpenAIRE, bioRxiv, medRxiv):

/plugin marketplace add the-alien-club/claude-marketplace#main
/plugin install openscience@alien
/reload-plugins

This registers the OpenAIRE, bioRxiv, and medRxiv MCP servers automatically and loads the research skills. No manual configuration is needed — see Alien Marketplace for details on what the plugin provides.

Using .mcp.json for Your Own Data Cluster​

If you have your own data cluster on the Alien Intelligence platform, create a .mcp.json file in your project root:

{
  "mcpServers": {
    "my-data-cluster": {
      "type": "http",
      "url": "https://your-cluster.mcp.alien.club/mcp",
      "headers": {
        "Authorization": "Bearer oat_YOUR_API_TOKEN"
      }
    }
  }
}

Claude Code automatically detects and connects to MCP servers defined in .mcp.json when you open the project.

Verify the Connection​

In Claude Code, ask:

"What MCP tools are available?"

Claude will list the tools from all connected MCP servers. You should see tools like datacluster_keyword_search, datacluster_vector_search_chunks, and (if the openscience plugin is installed) search_research_products.

Connect via Claude Desktop​

Plugin Integration Coming Soon

Alien Marketplace plugin support for Claude Desktop is planned. Once available, you will be able to install research connectors with the same ease as in Claude Code. For now, connect MCP servers manually using the configuration below.

Claude Desktop supports MCP servers natively. You configure connections in a JSON configuration file.

Step 1: Add the Configuration​

  1. Open Claude Desktop.
  2. Go to Settings > MCP Servers.
  3. Add your MCP server configuration:
{
  "mcpServers": {
    "my-data-cluster": {
      "type": "http",
      "url": "https://your-cluster.mcp.alien.club/mcp",
      "headers": {
        "Authorization": "Bearer oat_YOUR_API_TOKEN"
      }
    }
  }
}
  1. Save the settings. Claude Desktop will connect to the MCP server automatically.

Step 2: Verify the Connection​

Start a new conversation and ask Claude something like:

"List the datasets available in my data cluster."

Claude should call the datacluster_list_datasets tool and return the available datasets. If you see results, the connection is working.

Using OAuth Instead of API Token​

If you prefer interactive authentication rather than embedding an API token:

  1. Remove the headers section from the configuration, keeping only type and url.
  2. When Claude Desktop connects to the MCP server, it will initiate the OAuth flow.
  3. A browser window will open where you authenticate with your Alien Intelligence credentials.
  4. After authentication, Claude Desktop receives a short-lived token and the connection proceeds.
{
  "mcpServers": {
    "my-data-cluster": {
      "type": "http",
      "url": "https://your-cluster.mcp.alien.club/mcp"
    }
  }
}
tip

OAuth authentication requires that the MCP server has OAuth properly configured. The server exposes a /.well-known/oauth-authorization-server endpoint for OAuth discovery. API token authentication is generally simpler for getting started.

Platform-Managed MCP Servers​

If you have your own data cluster on the Alien Intelligence platform, the dashboard provides ready-made connection snippets. See Deploy MCP for the full deployment guide.

  1. In the Alien Intelligence dashboard, navigate to MCP in the left sidebar.
  2. Expand the row for your data cluster.
  3. Copy the connection snippet from the connection card — the dashboard provides both the raw MCP server URL and a pre-filled claude_desktop_config.json block with your API token embedded.

Use the URL in any of the methods above: paste it into the claude.ai custom connector dialog, add it to .mcp.json for Claude Code, or drop the JSON snippet into Claude Desktop settings.

OAuth Flow Walkthrough​

When using OAuth authentication (without an API token), the following flow occurs:

Key points about the OAuth flow:

  • Tokens are short-lived. Access tokens expire after a set period. Claude will re-authenticate automatically when needed.
  • Permissions are inherited. The AI agent can only access data that you have permission to see in your organization.
  • No credentials are stored by Claude. Only the short-lived access token is held in memory during the session.

Troubleshooting​

"Connection refused" or "Failed to connect"​

  • Verify the MCP server URL is correct. Copy it fresh from the platform dashboard.
  • Check that your data cluster is in an Active state.
  • Confirm the MCP server is deployed and shows Running status in the dashboard.
  • Try visiting https://your-cluster.mcp.alien.club/health in a browser — you should see a 200 OK response.

"Unauthorized" or "403 Forbidden"​

  • If using an API token: verify the token has not expired and belongs to the correct organization.
  • If using OAuth: try disconnecting and reconnecting the MCP server to trigger a fresh OAuth flow.
  • Ensure your token has at least CLUSTER_READ and DATASET_READ abilities.

Claude Does Not Use the MCP Tools​

  • On claude.ai, open the Customize page and confirm the connector shows under "Web" with a CUSTOM badge. Click it to verify tools are discovered.
  • In Claude Desktop, check Settings > MCP Servers to verify the server shows as connected.
  • In Claude Code, run /mcp to see the status of connected MCP servers.
  • Try explicitly asking Claude to use a specific tool: "Use the datacluster_keyword_search tool to search for..."
  • If using the openscience plugin in Claude Code, make sure you ran /reload-plugins after installation.

OAuth Window Does Not Appear​

  • Ensure you removed the headers section from the configuration (OAuth is skipped when an API token is provided).
  • On claude.ai, OAuth triggers on the first tool call, not when the connector is added — start a conversation and invoke a tool.
  • Check that your browser allows popups from Claude Desktop.
  • Try restarting Claude Desktop and reconnecting.

Tools Appear But Return Errors​

  • Check that your data cluster has at least one dataset with processed entries.
  • Verify you have the correct role in your organization (Viewer or higher for read operations).
  • Check status.alien.club for any service disruptions.

Next Steps​