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Ncbi Eutils

Searches and retrieves records across NCBI Entrez databases through MCP tools or a local stdio package.

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Install Ncbi Eutils

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "ncbi-eutils": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-eutils"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

We couldn’t confirm it starts correctly

The install command started, but didn't respond the way we expected when we tried to talk to it.

npx -y @pipeworx/mcp-ncbi-eutils

initialize succeeded but no response to tools/list.

This is an experimental automated check and can have false negatives — missing environment variables, a slow cold install, etc. It doesn’t necessarily mean something’s wrong. Last checked 6d ago.

Overview

The Ncbi Eutils MCP server searches and retrieves records across NCBI Entrez databases, including PubMed, Gene, Nucleotide, Protein, Taxonomy, ClinVar, dbSNP, OMIM, BioProject, BioSample, and SRA. It exposes database inspection, search, summary, full-record fetch, cross-database linking, and global query tools through MCP. Use the hosted gateway for a remote connection, or run the npm package locally over stdio without a Pipeworx account. It is suitable for agents that need structured access to NCBI data without managing an API key.

Use cases

  • Search PubMed for records matching a research term
  • Inspect fields available in an NCBI database
  • Fetch full gene, sequence, or protein records
  • Link records across NCBI databases
  • Run a global query across Entrez databases

Key features

  • Federated search across NCBI Entrez databases
  • Database metadata and field inspection
  • Summary and full-record retrieval
  • Cross-database record linking
  • Global Entrez queries
  • Hosted HTTP and local stdio access

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 2d ago

Recent health check succeeded.

7/7 checks healthy over the last 40d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 14d ago via OSV.dev · @pipeworx/mcp-ncbi-eutils (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

npm downloads665Package downloads in the last 30 days.
Last commit14d agoMost recent push to the default branch.
Install checkInconclusiveStarted but did not complete the MCP handshake in our test.
Directory activity3 viewsConfig copies, upvotes, and views on AllMCPs.

How Ncbi Eutils works

What Ncbi Eutils does

The Ncbi Eutils MCP server gives MCP-compatible agents access to NCBI E-utilities at eutils.ncbi.nlm.nih.gov/entrez/eutils/.

The server supports the normal progression from discovery to retrieval. An agent can inspect a database and its fields, search for matching records, request summaries for returned identifiers, fetch complete records, follow links between databases, or run a query across all NCBI databases. This makes it useful for workflows such as finding PubMed records, retrieving gene or sequence entries, and moving from one NCBI record type to related data.

Tools and capabilities

The available pack-specific tools are:

  • einfo(db?) for database metadata and field lists.
  • esearch(db, term, retmax?, retstart?, sort?) for returning matching UID values.
  • esummary(db, ids, retstart?) for summary records associated with UIDs.
  • efetch(db, ids, rettype?, retmode?) for complete records in the requested format.
  • elink(dbfrom, dbto, ids, linkname?) for finding relationships between databases.
  • egquery(term) for searching across the NCBI database set.

The hosted pack endpoint also exposes shared Pipeworx gateway tools in addition to these six tools. The exact tool list is reported during MCP initialization and can change, so clients should treat that response as authoritative. The shared tools include routing and discovery functions such as ask_pipeworx, discover_tools, search_within, remember, and recall.

Setup and configuration

The Ncbi Eutils MCP server can be added remotely with the hosted MCP URL https://gateway.pipeworx.io/ncbi-eutils/mcp. The full gateway is also available at https://gateway.pipeworx.io/mcp; both URLs use the same gateway and underlying data sources, but the pack URL lists this pack's tools directly.

For a local connection, run npx -y @pipeworx/mcp-ncbi-eutils as an MCP stdio process. A client can configure the package as the command with the same npm argument. The local process responds to initialize, tools/list, and tools/call, and lists only the pack-specific tools rather than the gateway's shared tools.

The tools can also be called over HTTP. For example, a JSON POST to https://gateway.pipeworx.io/v1/tools/einfo can request information about a database. The source states that no account is needed for the first calls. NCBI access is keyless, with a stated limit of three requests per second without a key.

Limitations and notes

The hosted pack endpoint is not limited to the six NCBI tools: shared gateway schemas appear alongside them. There is currently no documented option to mount the pack endpoint without those shared tools. If that additional context is undesirable, the local npm process exposes only the NCBI pack, while the full gateway exposes all catalog packs directly.

The local and hosted modes use the same source and pack tools, but only the hosted gateway provides ask_pipeworx routing across the broader catalog. The material does not describe environment variables or an NCBI API-key configuration for this package.

Read the full README View source on GitHub

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Frequently Asked Questions about Ncbi Eutils

Ncbi Eutils is an MCP server that connects AI agents to NCBI E-utilities and Entrez databases such as PubMed, Gene, Nucleotide, Protein, Taxonomy, ClinVar, and SRA. Its main tools inspect databases, search records, retrieve summaries or full records, link related entries, and run global Entrez queries.

Install it locally by configuring your MCP client to run `npx -y @pipeworx/mcp-ncbi-eutils`. The package communicates over stdin and stdout and does not require a Pipeworx account. You can alternatively add the hosted MCP URL `https://gateway.pipeworx.io/ncbi-eutils/mcp`.

Yes, Cursor is listed as a supported example client. Add the hosted MCP URL to Cursor, or configure the local npm command for a stdio connection.

It also states that no account is needed for the first hosted gateway calls.

Yes, the hosted gateway provides HTTP tool endpoints under `https://gateway.pipeworx.io/v1/tools/`. Send a JSON POST request to a tool endpoint such as `/v1/tools/einfo` with the required arguments.

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