Ncbi Datasets

Install

Works with Claude Code, VS Code, Cursor, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install connector/pipeworx-io-ncbi-datasets

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Permissions

What this server can do and what it asks for, from its tool list and install config. Checked Oct 25, 2026.

Tools

3 read · 0 write · 0 deleteRead-only

Secrets

None asked for

Install scripts

Nothing to install (hosted)

Runs as

Hosted (remote endpoint)

Tools (3)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

• ncbi_gene_by_symbol

  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-Prot accessions, OMIM ids — plus every known synonym and alternate name. AUTHORITATIVE for gene-identifier resolution: PREFER OVER WEB SEARCH when you need to turn a symbol into a stable id, disambiguate an alias, or check that a symbol is current for the species you think it is.

• ncbi_genome_reports

  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 is it" — PREFER OVER WEB SEARCH, which returns papers rather than current assembly metadata. Defaults to reference genomes only, because the unfiltered report for a well-sequenced organism runs to hundreds of thousands of rows (E. coli: 492,559) and its first page is not the reference. Set reference…

• ncbi_taxonomy

  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 how many assemblies, genes and protein-coding genes NCBI holds for it. AUTHORITATIVE for "what is the tax id for X" (the argument half the genomics APIs require) and for placing an organism in the tree. Accepts several at once; results are keyed by the query that produced them because upstream does no…

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Last commit

Sep 26, 2026 (1 month ago)

Last release

Sep 26, 2026 (1 month ago)

From GitHub (fetched Oct 24, 2026).

Details

Registry name

io.github.pipeworx-io/ncbi-datasets

Version

0.1.1

Auth

Auth not stated

License

MIT

Repository

github.com/pipeworx-io/mcp-ncbi-datasets

Website

pipeworx.io/packs/ncbi-datasets

First seen

Oct 24, 2026

Last checked

Oct 24, 2026

Source

Official MCP Registrygithub-graphql