Update to Life Sciences Databases

{
  "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.",
  "included_files": [
    {
      "relative_path": "scripts/ncbi_datasets.py",
      "size_in_bytes": 9461
    }
  ],
  "skill_md_contents": "---\nname: ncbi-datasets-skill\ndescription: 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.\n---\n\n## Source presentation\n<!-- source-presentation-contract:v2 -->\n- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.\n- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.\n- Use the `ncbi-datasets-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/ncbi_datasets.py` for all Datasets v2 calls in this package.\n- Use explicit REST `path` values relative to `https://api.ncbi.nlm.nih.gov/datasets/v2`.\n- Prefer targeted metadata paths instead of broad unfiltered pulls.\n- Re-run requests in long conversations instead of relying on older tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n\n## Execution behavior\n- Return concise markdown summaries from the script output by default.\n- Return raw JSON or text only if the user explicitly asks for machine-readable output.\n- Prefer targeted endpoint calls instead of broad unfiltered dumps.\n- If the user needs the full raw response, set `save_raw=true` and report the saved file path.\n\n## Input\n- Read one JSON object from stdin.\n- Required field: `path`\n- Optional fields: `params`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common Datasets patterns:\n  - `{\"path\":\"genome/taxon/assembly_descriptors\",\"params\":{\"taxons\":\"9606\"}}`\n  - `{\"path\":\"genome/accession/GCF_000001405.40/dataset_report\"}`\n  - `{\"path\":\"taxonomy/taxon/9606\"}`\n\n## Output\n- Success returns `ok`, `source`, path metadata, and either compact `records`, a compact `summary`, or `text_head`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"path\":\"genome/taxon/assembly_descriptors\",\"params\":{\"taxons\":\"9606\"}}' | python scripts/ncbi_datasets.py\n```\n"
}