| 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.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.
