BioThings MCP vs Memory (Knowledge Graph)

A side-by-side comparison of two AI, Data & Knowledge servers — tools, transport, auth, maintenance, and copy-paste config for each.

	BioThings MCP Query genes, variants, chemicals, and taxa from BioThings.io (mygene, myvariant, mychem) in your AI client. Unverified stdio (local) No auth Stale Python	Memory (Knowledge Graph) Official MCP server providing persistent, file-backed knowledge-graph memory across sessions. Verified stdio (local) No auth TypeScript
Category	AI, Data & Knowledge	AI, Data & Knowledge
Language	Python	TypeScript
Transport	stdio (local)	stdio (local)
Auth	None	None
GitHub stars	32	74k
Last commit	7 months ago	5 months ago
Verified
Actively maintained
Install	`uvx biothings-mcp`	`npx -y @modelcontextprotocol/server-memory`
Repo	Open	Open

Verdict

Pick BioThings MCP if you prefer its approach (query genes, variants, chemicals, and taxa from biothings.io (mygene, myvariant, mychem) in your ai client).

Pick Memory (Knowledge Graph) if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option.

Add BioThings MCP

Install / run

uvx biothings-mcp

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "biothings-mcp": {
      "command": "uvx",
      "args": [
        "--from",
        "biothings-mcp",
        "stdio"
      ]
    }
  }
}

Requires `uv` (the Python package runner). Install it from https://docs.astral.sh/uv/ if `uvx` is not found.

Add Memory (Knowledge Graph)

Install / run

npx -y @modelcontextprotocol/server-memory

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "memory-knowledge-graph": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-memory"
      ],
      "env": {
        "MEMORY_FILE_PATH": "/absolute/path/to/memory.jsonl"
      }
    }
  }
}

FAQ

BioThings MCP or Memory (Knowledge Graph) — which is better?

Pick BioThings MCP if you prefer its approach (query genes, variants, chemicals, and taxa from biothings.io (mygene, myvariant, mychem) in your ai client). Pick Memory (Knowledge Graph) if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option.

Can I use both BioThings MCP and Memory (Knowledge Graph)?

Yes — MCP clients let you enable multiple servers at once. Add both configs to your client's mcpServers and use whichever tool fits the task.

Do BioThings MCP and Memory (Knowledge Graph) work with Claude, Cursor and Windsurf?

Both do. Copy the per-client config below into Claude Desktop, Cursor, or Windsurf.

View BioThings MCP →View Memory (Knowledge Graph) →More comparisons →