ncbi-datasets-skill

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/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 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/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.