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mgnify-skill

✓ Official★ 4,000

by openai · part of openai/plugins

Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries

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🧩 One of 7 skills in the openai/plugins package — works on its own, and pairs well with its siblings.

This is the playbook your agent receives when the skill activates — you don't need to read it to use the skill, but it's here to audit before installing.

name: mgnify-skill description: Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries

Operating rules

  • Use scripts/rest_request.py for all MGnify calls.
  • Use base_url=https://www.ebi.ac.uk/metagenomics/api/v1.
  • MGnify uses JSON:API-style responses. Prefer record_path=data for collection endpoints.
  • Keep requests narrow by study accession, sample accession, or biome whenever possible.
  • 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 these paths: studies, samples, and biomes.

Input

  • Read one JSON object from stdin.
  • Required fields: base_url, path
  • Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common MGnify patterns:
    • {"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"studies","params":{"page_size":10},"record_path":"data","max_items":10}
    • {"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"biomes","params":{"page_size":10},"record_path":"data","max_items":10}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://www.ebi.ac.uk/metagenomics/api/v1","path":"studies","params":{"page_size":10},"record_path":"data","max_items":10}' | python scripts/rest_request.py

References

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