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Skill v1.0.0
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PublishedApril 26, 2026 at 05:57 AM
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version: "1.0.0" name: cbioportal-skill description: Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries
Operating rules
- Use
scripts/rest_request.pyfor all cBioPortal API calls. - Use
base_url=https://www.cbioportal.org/api. - Collection endpoints are better with
pageSize=10andmax_items=10; single study or profile lookups usually do not needmax_items. - Use
method=POSTplusjson_bodyfor fetch-style endpoints such as mutation fetches. - Send
Accept: application/jsoninheaders. - 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=trueand 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 compactrecordsor a compactsummary. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.message.
Execution
bash
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.