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Data Science & AIopenai

cbioportal-skill

Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--cbioportal-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/cbioportal-skill/SKILL.md -o .claude/skills/cbioportal-skill.md

Drops the SKILL.md into .claude/skills/cbioportal-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

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.