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Skill v1.0.0
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PublishedApril 26, 2026 at 05:57 AM
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version: "1.0.0" 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/assembly_descriptors","params":{"taxons":"9606"}}{"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
bash
echo '{"path":"genome/taxon/assembly_descriptors","params":{"taxons":"9606"}}' | 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.