Update to Life Sciences Databases

{
  "name": "clinvar-variation-skill",
  "description": "Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping",
  "included_files": [
    {
      "relative_path": "scripts/clinvar_variation.py",
      "size_in_bytes": 9749
    }
  ],
  "skill_md_contents": "---\nname: clinvar-variation-skill\ndescription: Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping\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 `clinvar-variation-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/clinvar_variation.py` for all ClinVar and NCBI Variation work.\n- The script accepts `max_items`; for `action=search`, start around `max_items=10`.\n- For `vcv`, `rcv`, `scv`, and `refsnp`, omit `max_items` unless you need to trim nested arrays in the summary.\n- Re-run requests in long conversations instead of relying on prior tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n- If the user asks for full JSON, set `save_raw=true` and report the saved file path instead of pasting large payloads into chat.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Return the JSON verbatim only if the user explicitly asks for machine-readable output.\n- Use `action=search` for the Clinical Tables endpoint.\n- Use `action=vcv|rcv|scv|refsnp` for NCBI Variation beta objects.\n\n## Input\n- Read one JSON object from stdin.\n- Required field: `action`\n- Action-specific required fields:\n  - `search`: `terms`\n  - `vcv`: `vcv`\n  - `rcv`: `rcv`\n  - `scv`: `scv`\n  - `refsnp`: `refsnp`\n- Optional fields: `params`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n\n## Output\n- `search` returns `total`, `identifiers`, `display_rows`, `extra_fields`, and truncation metadata.\n- `vcv|rcv|scv|refsnp` return a compact `summary` and optional `top_keys`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failures return `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"action\":\"search\",\"terms\":\"VCV000013080\",\"max_items\":10}' | python scripts/clinvar_variation.py\n```\n"
}