skills.rest
LeonChaoX
LeonChaoXCOMMUNITY
Explore all skills by this author →
GitHub

cbioportal-database

Query cBioPortal REST API for cancer genomics mutation and survival data.

783|65|Updated Feb 27, 2026
Search Tags:#rest api#clinical data#cancer genomics#survival analysis#cbioportal#copy number alteration#mutation frequency
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill cbioportal-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cbioportal-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/07-%E4%B8%B4%E5%BA%8A%E5%8C%BB%E5%AD%A6%E4%B8%8E%E7%B2%BE%E5%87%86%E5%8C%BB%E7%96%97/cbioportal-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill cbioportal-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

It eliminates the manual effort of finding and downloading cancer genomics results by providing programmatic access to mutation, copy-number, expression, and survival data for many studies.

Core Features & Use Cases

  • cBioPortal REST API access: Use public API endpoints to query studies, molecular profiles, genes, and clinical attributes.
  • Multi-omics retrieval: Fetch somatic mutations and discrete/continuous copy-number alteration data, then combine with clinical variables for analysis.
  • Analysis-ready workflows: Support tasks like alteration frequency calculation, gene-centric alteration summaries, and survival split by mutation status across tumor cohorts.
  • Use Case: For a chosen cancer type, retrieve TP53 mutation counts, CNA amplification/deletion counts, and relate them to OS/DFS clinical outcomes.

Quick Start

Ask an agent to query cBioPortal for the mutation frequency and survival association of TP53 in brca_tcga using the public REST API endpoints.

Frequently Asked Questions about cbioportal-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query cancer genomics data from cBioPortal using a REST API?▼

Query cancer genomics data from cBioPortal by using public REST API endpoints to retrieve mutations, copy number alterations, and clinical survival attributes for specified genes and cohort studies in JSON format.

Can I perform survival analysis stratified by mutation status across TCGA cohorts?▼

Yes, survival analysis stratified by mutation status is supported. You can retrieve somatic mutations and overall survival clinical attributes, then split patient cohorts based on mutation presence across TCGA and other studies.

What is the best way to calculate pan-cancer mutation frequency for a specific gene?▼

Calculate pan-cancer mutation frequency by retrieving mutation counts for a specified gene across multiple molecular profiles and sample lists, then comparing alteration frequencies between different cancer studies.

Do I need an API key to access cBioPortal public endpoints for clinical data?▼

No, you do not need an API key to access cBioPortal public endpoints. The queries handle public REST API endpoints directly to fetch clinical data, copy number alterations, and mutation profiles without authentication.

How do I map gene symbols to Entrez IDs when fetching copy number alterations?▼

Map gene symbols to Entrez IDs by querying the cBioPortal REST API for gene identifiers, then use the correct molecular profile and sample list identifiers to fetch discrete or continuous copy number alteration data.

Why does my cBioPortal query fail when fetching alterations for a specific study?▼

cBioPortal queries often fail when using incorrect molecular profile identifiers or mismatched sample list IDs. Ensure you select the correct study-specific molecular profile and sample list identifiers for your target cancer cohort.

Related Skills

Explore More Education & Research Skills→
Hung-3008Hung-3008
1

cbioportal-database

Query the cBioPortal REST API for cancer genomics mutations, CNAs, and expression data.

Community
Intermediate
jaechang-hitsjaechang-hits
298

cbioportal-database

Retrieve cancer genomics data from the cBioPortal REST API.

Community
Intermediate
monarch-initiativemonarch-initiative
50

cancer-curator

Curate cancer entries with genetic drivers, pathophysiology, and ontology bindings.

Official
Advanced
qinyan-aiqinyan-ai
48

cbioportal-database

Access cancer genomics data via the cBioPortal REST API.

Community
Advanced