gnomad-graphql-skill

Imported from openai/plugins (plugins/life-science-research/skills/gnomad-graphql-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill gnomad-graphql-skill. Copyright stays with the author.

Operating rules

• Use scripts/gnomad_graphql.py for all gnomAD GraphQL work.
• For nested GraphQL results, start with max_items=3 to 5.
• Keep selection sets narrow and page or filter at the query level instead of asking for broad dumps.
• Use query_path for long GraphQL documents instead of pasting large inline queries.
• Re-run requests in long conversations instead of relying on earlier tool output.
• Treat displayed ... in tool previews as UI truncation, not part of the real query.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return raw JSON only if the user explicitly asks for machine-readable output.
• Prefer targeted queries for variant frequency, gene constraint, or transcript consequence context.
• If the user needs the full payload, set save_raw=true and report the saved file path.

Input

• Read one JSON object from stdin.
• Required field: query or query_path
• Optional fields: variables, max_items, max_depth, timeout_sec, save_raw, raw_output_path
• Common gnomAD patterns:
  • {"query":"query { meta { clinvar_release_date } }"}
  • {"query":"query Variant($variantId: String!, $dataset: DatasetId!) { variant(variantId: $variantId, dataset: $dataset) { variantId genome { ac an af } } }","variables":{"variantId":"1-55516888-G-GA","dataset":"gnomad_r4"},"max_items":3}

Output

• Success returns ok, source, top_keys, a compact summary, and raw_output_path when save_raw=true.
• Failure returns ok=false with error.code such as invalid_json, invalid_input, network_error, invalid_response, or graphql_error.

Execution

echo '{"query":"query { meta { clinvar_release_date } }"}' | python scripts/gnomad_graphql.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/gnomad_graphql.py.