cbioportal-skill

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

Operating rules

• Use scripts/rest_request.py for all cBioPortal API calls.
• Use base_url=https://www.cbioportal.org/api.
• Collection endpoints are better with pageSize=10 and max_items=10; single study or profile lookups usually do not need max_items.
• Use method=POST plus json_body for fetch-style endpoints such as mutation fetches.
• Send Accept: application/json in headers.
• Re-run requests in long conversations instead of relying on older tool output.
• Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Prefer these paths: studies, studies/<studyId>/molecular-profiles, molecular-profiles/<profileId>/mutations/fetch, and study-level clinical or sample endpoints.
• 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 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 cBioPortal patterns:
  • {"base_url":"https://www.cbioportal.org/api","path":"studies","params":{"keyword":"breast","projection":"SUMMARY","pageSize":10},"headers":{"Accept":"application/json"},"max_items":10}
  • {"base_url":"https://www.cbioportal.org/api","path":"molecular-profiles/brca_tcga_mutations/mutations/fetch","method":"POST","json_body":{"sampleListId":"brca_tcga_all","entrezGeneIds":[7157]},"headers":{"Accept":"application/json"},"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.cbioportal.org/api","path":"studies","params":{"keyword":"breast","projection":"SUMMARY","pageSize":10},"headers":{"Accept":"application/json"},"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.