Agent Skills
› openai/plugins
› ncbi-datasets-skill
ncbi-datasets-skill
GitHub封装NCBI Datasets v2 API调用，支持基因组、分类学等元数据查询。默认返回精简Markdown摘要，按需保存原始JSON，通过stdin传递请求参数并执行Python脚本。
Trigger Scenarios
用户需要查询NCBI生物数据集信息
获取特定物种或基因组的元数据报告
Install
npx skills add openai/plugins --skill ncbi-datasets-skill -g -y
SKILL.md
Frontmatter
{
"name": "ncbi-datasets-skill",
"description": "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."
}
Operating rules
- Use
scripts/ncbi_datasets.pyfor all Datasets v2 calls in this package. - Use explicit REST
pathvalues relative tohttps://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=trueand 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 compactrecords, a compactsummary, ortext_head. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.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.
Version History
- 11c74d6 Current 2026-07-19 09:39
