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.
npx skills add GPTomics/bioSkills --skill ncbi-datasets-cligit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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.
[](https://agentmods.dev/skills/gptomics/bioskills/ncbi-datasets-cli)<a href="https://agentmods.dev/skills/gptomics/bioskills/ncbi-datasets-cli"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/ncbi-datasets-cli/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.
<a href="https://agentmods.dev/skills/gptomics/bioskills/ncbi-datasets-cli"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/ncbi-datasets-cli.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00126 | $0.03683 |
| Opus 5 | $0.00063 | $0.01842 |
| Sonnet 5 | $0.00025 | $0.00737 |
| Haiku 4.5 | $0.00013 | $0.00368 |
Grade A, and why
bio-ncbi-datasets-cli scanned grade A with 2 findings 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 8d 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 -O https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
out = subprocess.run(cmd, capture_output=True, text=True, check=True) Copies of this mod
1 near-identical copy found in the catalogue:
- bio-ncbi-datasets-cli — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 311 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: NCBI Datasets CLI 16.0+ (2024), dataformat 16.0+
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
datasets --version,dataformat --version - Subcommand help:
datasets <subcommand> --help
If a subcommand or flag is unrecognized, run datasets --help and adapt. The CLI is under active development; major releases (v15 -> v16) added subcommands and renamed flags.
NCBI Datasets CLI
"Pull genome / gene / ortholog data from NCBI in 2026" -> The Datasets v2 CLI (launched 2023) is the official, supported bulk endpoint for genome and gene-centric data. It replaces the prior best-practice of scraping assembly_summary.txt + parallel FTP + manual checksum verification. For genome-scale data, it is strictly better than E-utilities (EFetch).
The CLI is not the right answer for everything. PubMed, SRA reads, and custom Entrez queries still belong to E-utilities. The defection rule: if the question is about genome assemblies, gene records, or pre-computed orthologs, use Datasets; otherwise stay with E-utilities.
- CLI:
datasets download genome accession GCF_... - CLI:
datasets summary gene symbol BRCA1 --taxon human - Python:
subprocesswrapper; Python clientncbi-datasets-pylib(experimental as of 2024)
Installation
# conda
conda install -c conda-forge ncbi-datasets-cli
# Or direct download (Linux, macOS, Windows binaries)
curl -O https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets
datasets --version # 16.0+ expected
dataformat --version # bundled companion tool
What's in scope (use Datasets) vs out of scope (use E-utilities or other tools)
| Question | Datasets | Use instead |
|---|---|---|
| Genome assembly download | yes | — |
| All reference genomes for a taxon | yes | — |
| Gene record metadata (multi-species) | yes | — |
| Ortholog data for a gene | yes (datasets summary gene ... --ortholog) |
OrthoDB / Compara for tree-aware orthology |
| Virus data (assemblies, metadata) | yes (datasets download virus) |
— |
| Annotation files (GFF3, GTF) for a genome | yes | — |
| Protein records (curated, with cross-refs) | partial | UniProt REST for richer annotation |
| PubMed | no | entrez-search / entrez-fetch |
| SRA reads | no | sra-data |
| BLAST | no | blast-searches / local-blast |
| Custom Entrez queries | no | entrez-search |
| Pre-computed alignments (Compara) | no | ensembl-rest |
What ships with it
4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 8d ago First seen · 311 lines · 126 tokens per session scan A 4871acf86594
bio-ncbi-datasets-cli is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 126 tokens to every session and 3,683 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 2 findings (makes network calls, runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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