Ncbi Datasets Skill for Codex

Submit compact NCBI Datasets v2 requests for assembly, genome, taxonomy, and related metadata endpoints. Use when a user wants concise NCBI Datasets summaries; save raw JSON or text only on request.

3k tokens

context cost

the whole folder, loaded on every use

files

ships runnable scripts

copies elsewhere

how many repositories repackaged it

4915

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/openai/plugins --skill ncbi-datasets-skill

What comes with it

8 481 bytes besides the instruction

agents/openai.yaml

scripts/ncbi_datasets.py

The instruction itself

6 sections, as written by the author

Operating rules

Use scripts/ncbi_datasets.py for all Datasets v2 calls in this package.
Use explicit REST path values relative to https://api.ncbi.nlm.nih.gov/datasets/v2.
Prefer targeted metadata paths instead of broad unfiltered pulls.
Re-run requests in long conversations instead of relying on older tool output.
Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

Return concise markdown summaries from the script output by default.
Return raw JSON or text only if the user explicitly asks for machine-readable output.
Prefer targeted endpoint calls instead of broad unfiltered dumps.
If the user needs the full raw response, set save_raw=true and report the saved file path.

Input

Read one JSON object from stdin.
Required field: path
Optional fields: params, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
Common Datasets patterns:
{"path":"genome/taxon/9606/dataset_report","params":{"page_size":10},"record_path":"reports","max_items":10}
{"path":"genome/accession/GCF_000001405.40/dataset_report"}
{"path":"taxonomy/taxon/9606"}

Output

Success returns ok, source, path metadata, and either compact records, a compact summary, or text_head.
Use raw_output_path when save_raw=true.
Failure returns ok=false with error.code and error.message.

Execution

echo '{"path":"genome/taxon/9606/dataset_report","params":{"page_size":10},"record_path":"reports","max_items":10}' | python scripts/ncbi_datasets.py

References

No additional runtime references are required; keep the import package limited to this file and scripts/ncbi_datasets.py.

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How to use it

Copy the folder

Take openai/ncbi-datasets-skill from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.