io.github.pipeworx-io/ncbi-eutils

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by pipeworx-io · TypeScript

Ncbi Eutils

NCBI E-utilities — federated Entrez search/fetch (PubMed/Gene/Nucleotide/…)

Federated search and fetch across NCBI databases including PubMed, genes, and sequences.

Topics

mcpmcp-servermodel-context-protocolpipeworxncbi-eutils

README.md1 KBView on GitHub

mcp-ncbi-eutils

NCBI E-utilities MCP — federated Entrez search/fetch.

Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.

Tools

Tool	Description
`einfo`	Database info / field list.
`esearch`	Search a database → uid list.
`esummary`	Summary records by uid.
`efetch`	Full records. Returns text (XML/GenBank/FASTA/…) per rettype.
`elink`	Links across databases.
`egquery`	Global query across all Entrez databases.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

json

{
  "mcpServers": {
    "ncbi-eutils": {
      "url": "https://gateway.pipeworx.io/ncbi-eutils/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 673+ data sources:

json

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

code

ask_pipeworx({ question: "your question about Ncbi Eutils data" })

The gateway picks the right tool and fills the arguments automatically.

License

MIT

Install

claude_desktop_config.json

{
  "mcpServers": {
    "ncbi-eutils": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "https://gateway.pipeworx.io/ncbi-eutils/mcp"
      ]
    }
  }
}

Desktop config is stdio-only; this bridges via mcp-remote. Native remote: Settings > Connectors.