Update to Life Sciences Databases

{
  "name": "gnomad-graphql-skill",
  "description": "Submit compact gnomAD GraphQL requests for frequency, gene constraint, and variant context queries. Use when a user wants concise gnomAD summaries",
  "included_files": [
    {
      "relative_path": "scripts/gnomad_graphql.py",
      "size_in_bytes": 6223
    }
  ],
  "skill_md_contents": "---\nname: gnomad-graphql-skill\ndescription: Submit compact gnomAD GraphQL requests for frequency, gene constraint, and variant context queries. Use when a user wants concise gnomAD summaries\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 `gnomad-graphql-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/gnomad_graphql.py` for all gnomAD GraphQL work.\n- For nested GraphQL results, start with `max_items=3` to `5`.\n- Keep selection sets narrow and page or filter at the query level instead of asking for broad dumps.\n- Use `query_path` for long GraphQL documents instead of pasting large inline queries.\n- Re-run requests in long conversations instead of relying on earlier tool output.\n- Treat displayed `...` in tool previews as UI truncation, not part of the real query.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Return raw JSON only if the user explicitly asks for machine-readable output.\n- Prefer targeted queries for variant frequency, gene constraint, or transcript consequence context.\n- If the user needs the full payload, set `save_raw=true` and report the saved file path.\n\n## Input\n- Read one JSON object from stdin.\n- Required field: `query` or `query_path`\n- Optional fields: `variables`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common gnomAD patterns:\n  - `{\"query\":\"query Variant($variantId: String!, $dataset: DatasetId!) { variant(variantId: $variantId, dataset: $dataset) { variantId genome { ac an af } } }\",\"variables\":{\"variantId\":\"10-112998590-C-T\",\"dataset\":\"gnomad_r4\"},\"max_items\":5}`\n\n## Output\n- Success returns `ok`, `source`, `top_keys`, a compact `summary`, and `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` such as `invalid_json`, `invalid_input`, `network_error`, `invalid_response`, or `graphql_error`.\n\n## Execution\n```bash\necho '{\"query\":\"query Variant($variantId: String!, $dataset: DatasetId!) { variant(variantId: $variantId, dataset: $dataset) { variantId genome { ac an af } } }\",\"variables\":{\"variantId\":\"10-112998590-C-T\",\"dataset\":\"gnomad_r4\"},\"max_items\":5}' | python scripts/gnomad_graphql.py\n```\n"
}