MCP server

Ncbi Datasets

io.github.pipeworx-io/ncbi-datasets

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

NCBI Datasets — the US National Library of Medicine's genome, gene and taxonomy reference service…

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,378 tokens per request once connected45 tools

https://gateway.pipeworx.io/ncbi-datasets/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 45
Token cost: About 27,378 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http ncbi-datasets https://gateway.pipeworx.io/ncbi-datasets/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ncbi-datasets]
url = "https://gateway.pipeworx.io/ncbi-datasets/mcp"

Gemini CLI

{"mcpServers":{"ncbi-datasets":{"httpUrl":"https://gateway.pipeworx.io/ncbi-datasets/mcp"}}}

Cursor

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

VS Code

{"servers":{"ncbi-datasets":{"type":"http","url":"https://gateway.pipeworx.io/ncbi-datasets/mcp"}}}

Antigravity

agy mcp add ncbi-datasets https://gateway.pipeworx.io/ncbi-datasets/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ncbi-datasets","server_url":"https://gateway.pipeworx.io/ncbi-datasets/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ncbi-datasets","server_url":"https://gateway.pipeworx.io/ncbi-datasets/mcp"}

ncbi_gene_by_symbol ~328 tokens
Look up one or more genes by symbol in a given organism and get NCBI's authoritative record: Entrez gene id, official description, biotype, chromosome and orientation, RefSeqGene coordinates, and the cross-references that let you join to other databases — HGNC id, Ensembl gene ids, UniProt/Swiss-Pro
ncbi_genome_reports ~471 tokens
List the genome assemblies NCBI holds for an organism (or fetch one by accession), with assembly level, total length, contig and scaffold N50, GC percent, submitter, release date, BioProject, and the paired RefSeq/GenBank accession. AUTHORITATIVE for "what is the reference genome for X and how good
ncbi_taxonomy ~276 tokens
Resolve organisms in the NCBI Taxonomy — the naming authority GenBank, ENA and DDBJ all classify against — from a tax id, scientific name or common name, returning the full ancestor lineage as tax ids, the immediate children, the taxonomic rank, every name the organism goes by, and live counts of ho

Pubtator
PubTator 3 MCP — biomedical entity search, literature search with entity
Ncbi Variation
dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI…
Seqbench Workbench
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
String Db
STRING-DB MCP — protein-protein interaction networks.
Uniprot
Protein research over UniProtKB: search by function, fetch curated records, map IDs, proteomes.
Uniprot
UniProt MCP — protein sequence + function database.
Gnomad
gnomAD MCP — Broad Institute Genome Aggregation Database (GraphQL).
Jean — Molecular Biology & Genomics
Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics

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