BrainKB MCP MCP server

An official Model Context Protocol server for the BrainKB neuroscience knowledge graph. It allows AI agents to interact with the knowledge base by ingesting RDF data, searching entities, executing vetted scientific questions, and tracing provenance for every change, all while maintaining per-caller identity and access control.

Endpoint and access

No sign-in: your client connects and lists tools immediately, with no account or key.

No sign-inEndpoint checked 2026-10-05Operated by BrainKB

MCP endpoint (Streamable HTTP)

https://mcp.brainkb.org/mcp

Vendor documentation

What you can do with it

Ingest RDF files into private or public workspaces
Search and read entities within the neuroscience knowledge graph
Execute ready-made questions about cells, markers, and phenotypes
Trace provenance history of graph changes and contributions

Tools advertised by the last live check:

brainkb_login
brainkb_globus_login
brainkb_finish_login
brainkb_logout
brainkb_whoami
brainkb_create_token
brainkb_list_tokens
brainkb_revoke_token
brainkb_use_token
brainkb_list_spaces
brainkb_create_space
brainkb_set_space_visibility
brainkb_add_space_member
brainkb_add_space_graph
brainkb_ingest_text
brainkb_list_uploads
brainkb_upload_status
brainkb_discard_upload
brainkb_ingest_upload
brainkb_ingest_files
brainkb_list_jobs
brainkb_job_status
brainkb_recover_job
brainkb_search
brainkb_read_space
brainkb_list_registered_graphs
brainkb_sparql
brainkb_qa_list
brainkb_qa_run
brainkb_provenance_job
brainkb_provenance_graph
brainkb_delta
brainkb_delta_history
brainkb_delta_compare
brainkb_capabilities
brainkb_grant_capability
brainkb_revoke_capability
brainkb_list_capabilities
brainkb_role_capabilities
brainkb_grant_role_capability
brainkb_revoke_role_capability
brainkb_list_access_rules
brainkb_add_access_rule
brainkb_remove_access_rule
brainkb_list_users
brainkb_available_roles
brainkb_create_role
brainkb_assign_role
brainkb_remove_role
brainkb_activate_user
brainkb_deactivate_user
brainkb_ban_user
brainkb_unban_user
brainkb_list_permissions
brainkb_create_permission

Connect from your client

Each snippet registers the same endpoint; pick the client you use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Claude Code

Run this once in a terminal. It registers a Streamable HTTP server. Use --scope project to write .mcp.json for the repo.

Claude Code configuration

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

Codex

Run this once. Codex stores MCP servers in ~/.codex/config.toml (or .codex/config.toml in a trusted project).

Codex configuration

codex mcp add brainkb-mcp --url https://mcp.brainkb.org/mcp

Cursor

Merge this server into .cursor/mcp.json in your project, then enable brainkb-mcp in your MCP settings.

Cursor configuration

{
  "mcpServers": {
    "brainkb-mcp": {
      "url": "https://mcp.brainkb.org/mcp"
    }
  }
}

Cline

Merge this into cline_mcp_settings.json (Cline → MCP Servers → Configure). The type must be streamableHttp for a remote HTTP server.

Cline configuration

{
  "mcpServers": {
    "brainkb-mcp": {
      "type": "streamableHttp",
      "url": "https://mcp.brainkb.org/mcp",
      "disabled": false
    }
  }
}

VS Code

Merge this server into .vscode/mcp.json. Use MCP: List Servers to start brainkb-mcp and inspect its tools.

VS Code configuration

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

Gemini CLI

Run this once. It writes .gemini/settings.json in the current project; pass --scope user for ~/.gemini/settings.json.

Gemini CLI configuration

gemini mcp add --transport http brainkb-mcp https://mcp.brainkb.org/mcp

Claude Desktop

Merge this into claude_desktop_config.json (macOS: ~/Library/Application Support/Claude/, Windows: %APPDATA%\Claude\), then restart Claude Desktop.

Claude Desktop configuration

{
  "mcpServers": {
    "brainkb-mcp": {
      "url": "https://mcp.brainkb.org/mcp"
    }
  }
}

Windsurf

Merge this into ~/.codeium/windsurf/mcp_config.json, then refresh MCP in Cascade. Windsurf remote servers use serverUrl, not url.

Windsurf configuration

{
  "mcpServers": {
    "brainkb-mcp": {
      "serverUrl": "https://mcp.brainkb.org/mcp"
    }
  }
}

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