What is ncbi-datasets-api?

An API for retrieving genome assemblies, gene records, sequences, and taxonomy data from NCBI, a major public biology database. It covers organisms and reference data from sources such as RefSeq and GenBank.

Use it to find genomes by organism, retrieve genes by symbol or identifier, download genome files, and explore taxonomy.

It provides programmatic access to genomic records and downloads, so research scripts do not need to rely on manual database searches.

ncbi-datasets-api — Skill for Claude Code and Codex by wentorai

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add wentorai/research-plugins --skill ncbi-datasets-api

Clone the repo

git clone --depth 1 https://github.com/wentorai/research-plugins

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/wentorai/research-plugins/ncbi-datasets-api/github.svg)](https://agentmods.dev/skills/wentorai/research-plugins/ncbi-datasets-api)

Your own site

<a href="https://agentmods.dev/skills/wentorai/research-plugins/ncbi-datasets-api"><img src="https://agentmods.dev/badge/skills/wentorai/research-plugins/ncbi-datasets-api/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/wentorai/research-plugins/ncbi-datasets-api"><img src="https://agentmods.dev/badge/skills/wentorai/research-plugins/ncbi-datasets-api.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 23 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,774 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector warn 7 Sept 2026

SkillSpector: 12 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

medium Data Exfiltration · line 24
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 31
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 34
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 38
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 46
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 49
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 52
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 56
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 63
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 66
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 69
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
medium Data Exfiltration · line 122
Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.

Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00023	$0.01774
Opus 5	$0.00012	$0.00887
Sonnet 5	$0.00005	$0.00355
Haiku 4.5	$0.00002	$0.00177

Measured 6d ago against content hash fcb65908ea40, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

ncbi-datasets-api scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/9606?page_size=5"

skills/domains/biomedical/ncbi-datasets-api/SKILL.md · 221 lines

How it starts

The opening of the file, as written. The whole thing — 221 lines — stays where its author put it; the contents beside it link to each section on GitHub.

NCBI Datasets v2 API

Overview

NCBI Datasets is the modern API for accessing NCBI's genomic, gene, and taxonomic data — replacing older E-utilities for sequence data retrieval. It provides clean REST endpoints for genome assemblies, gene records, taxonomy trees, and sequence downloads. Covers all organisms in NCBI's databases including RefSeq and GenBank. Free, no authentication required.

API Endpoints

Base URL

https://api.ncbi.nlm.nih.gov/datasets/v2

Genome Data

# Search genome assemblies by organism
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/9606?page_size=5"

# Get assembly by accession
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40"

# Download genome package
curl -o genome.zip \
  "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40/download?\
include_annotation_type=GENOME_FASTA,GENOME_GFF"

Gene Data

# Search genes by symbol
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/TP53/taxon/human"

# Get gene by NCBI Gene ID
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157"

# Search genes by keyword
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/search?query=BRCA&taxon=9606&page_size=20"

# Download gene data package
curl -o gene.zip \
  "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157/download?include_annotation_type=FASTA_GENE"

Taxonomy

# Get taxonomy info
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9606"

# Search taxonomy by name
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/name_report?taxon_query=Homo+sapiens"

# Get taxonomy tree (subtree)
curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9443/subtree"

Query Parameters

Parameter	Description	Example
`page_size`	Results per page	`page_size=20`
`page_token`	Pagination token	From previous response
`include_annotation_type`	Download content	`GENOME_FASTA`, `GENOME_GFF`, `PROT_FASTA`
`filters.assembly_level`	Assembly quality	`complete_genome`, `chromosome`
`filters.refseq_only`	RefSeq assemblies	`true`

Read the full file on GitHub · 221 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

6d ago First seen · 221 lines · 23 tokens per session scan A fcb65908ea40

Subscribe to this mod's changes

ncbi-datasets-api is a skill published in the GitHub repository wentorai/research-plugins (291 stars, last pushed 2mo ago), licensed MIT. It adds 23 tokens to every session and 1,774 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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ncbi-datasets-api