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Skill

civic-skill

request cancer variant data from CIViC

Published by OpenAI Updated Apr 10
Covers Research Life Sciences Bioinformatics API Development

Description

Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC summaries

SKILL.md

Operating rules

  • Use scripts/civic_graphql.py for all CIViC GraphQL work.
  • Keep selection sets narrow and start with schema or targeted entity queries.
  • Use query_path for longer GraphQL documents instead of pasting large inline queries.
  • Re-run requests in long conversations instead of relying on older tool output.

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 sanity, schema, and targeted evidence queries over broad graph dumps.

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 CIViC patterns:
    • {"query":"query { __typename }"}
    • {"query":"query { __schema { queryType { fields { name } } } }","max_items":20}

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 { __typename }"}' | python scripts/civic_graphql.py

References

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

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