bio-ncbi-datasets-cli SKILL.md skillA
bio-ncbi-datasets-cli from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-ncbi-datasets-cli@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-ncbi-datasets-cli/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 14,514 bytes
- Repository stars
- 662
- License
- MIT
Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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_...` …
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How to install
mdr add pku-yuangroup/openai4s/bio-ncbi-datasets-cli@sha256:41a9c15534000625The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_ubsek4vwr2tnrmoh)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ubsek4vwr2tnrmoh GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-ncbi-datasets-cli GET https://markdownregistry.com/api/v1/blob/41a9c15534000625fe8445591b90e62bce45b717f1b1cdc8f16734e4f138db06
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.