Update to Life Sciences Databases

{
  "name": "civic-skill",
  "description": "Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC summaries",
  "included_files": [
    {
      "relative_path": "scripts/civic_graphql.py",
      "size_in_bytes": 6203
    }
  ],
  "skill_md_contents": "---\nname: civic-skill\ndescription: Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC 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 `civic-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/civic_graphql.py` for all CIViC GraphQL work.\n- Keep selection sets narrow and start with targeted, evidence-bearing entity queries; reserve schema introspection for resolving a concrete query failure.\n- Use `query_path` for longer GraphQL documents instead of pasting large inline queries.\n- Re-run requests in long conversations instead of relying on older tool output.\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 evidence queries over schema-only checks and broad graph dumps.\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 CIViC patterns:\n  - `{\"query\":\"query { search(query:\\\"BRAF\\\") { id name matchingText resultType } }\",\"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 { search(query:\\\"BRAF\\\") { id name matchingText resultType } }\",\"max_items\":5}' | python scripts/civic_graphql.py\n```\n"
}