cbioportal-skill — Codex skill: what it does, how to install
Sends compact queries to the cBioPortal REST API for cancer studies and mutations. It outputs concise markdown summaries directly into the agent session.
npx skills add openai/plugins --skill cbioportal-skill -a codexWhat cbioportal-skill does
The skill routes queries to https://www.cbioportal.org/api through a local helper script named scripts/rest_request.py. The agent pipes a JSON payload into standard input. This script handles cancer studies and mutation lookups.
Batch endpoints restrict outputs with pageSize=10 and max_items=10 to avoid filling the context window. Setting save_raw=true dumps the raw JSON response to a chosen file path. Long chat threads re-execute network calls. Reusing truncated previews from earlier messages causes errors. Only Python and the provided helper script are required.
What it helps with
- search cBioPortal cancer studies by keyword
- fetch molecular profiles for a specific study ID
- retrieve mutation records using POST requests with gene lists
- save uncompressed API JSON payloads to disk
Example prompts for the agent
- Search cBioPortal for breast cancer studies and list the first ten entries
- Fetch TP53 mutations for profile brca_tcga_mutations and write the raw payload to disk
- Show molecular profiles available for the brca_tcga study
How to install cbioportal-skill
1Skills CLI (Vercel)
npx skills add openai/plugins --skill cbioportal-skill -a codex2Manually: put the files in place
.agents/skills/cbioportal-skill/SKILL.mdFor all projects use ~/.agents/skills/
1Skills CLI (Vercel)
npx skills add openai/plugins --skill cbioportal-skill -a claude-code2Manually: put the files in place
~/.claude/skills/cbioportal-skill/SKILL.mdCopy the whole skill folder; for one project use .claude/skills/cbioportal-skill/
Manually: put the files in place
.cursor/skills/cbioportal-skill/SKILL.mdCursor also reads .agents/skills/ and .claude/skills/
1GitHub CLI
gh skill install openai/plugins cbioportal-skill2Manually: put the files in place
.github/skills/cbioportal-skill/SKILL.mdPlatform CLI
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/cbioportal-skillManually: put the files in place
.devin/skills/cbioportal-skill/SKILL.mdThe legacy .windsurf/skills/ path still works
Claude.ai
Zip the folder and upload it in Settings → Capabilities → Skills
Step by step, with commands for each platform: Codex skills: how to install, where they live, how to call them
Questions about cbioportal-skill
How to install cbioportal-skill in Codex?
Run npx skills add openai/plugins --skill cbioportal-skill in your terminal. You can also target the platform explicitly with npx skills add openai/plugins --skill cbioportal-skill -a codex.
What does cbioportal-skill do?
It queries cancer genomics data from the cBioPortal REST API and returns concise summaries of studies and gene mutations.
Are extra runtime packages required?
No external dependencies are needed. The execution relies solely on Python and the bundled scripts/rest_request.py file.
