alterlab-cbioportal

cBioPortal Database

Overview

cBioPortal for Cancer Genomics (https://www.cbioportal.org/) is an open-access resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. It hosts data from The Cancer Genome Atlas (TCGA), AACR Project GENIE, MSK-IMPACT, and hundreds of other cancer studies — covering mutations, copy number alterations (CNA), structural variants, mRNA/protein expression, methylation, and clinical data for thousands of cancer samples.

Key resources:

• cBioPortal website: https://www.cbioportal.org/
• REST API: https://www.cbioportal.org/api/swagger-ui/index.html
• API docs (Swagger): https://www.cbioportal.org/api/swagger-ui/index.html
• Python client: bravado or requests
• GitHub: https://github.com/cBioPortal/cbioportal

When to Use This Skill

Use cBioPortal when:

• Mutation landscape: What fraction of a cancer type has mutations in a specific gene?
• Oncogene/TSG validation: Is a gene frequently mutated, amplified, or deleted in cancer?
• Co-mutation patterns: Are mutations in gene A and gene B mutually exclusive or co-occurring?
• Survival analysis: Do mutations in a gene associate with better or worse patient outcomes?
• Alteration profiles: What types of alterations (missense, truncating, amplification, deletion) affect a gene?
• Pan-cancer analysis: Compare alteration frequencies across cancer types
• Clinical associations: Link genomic alterations to clinical variables (stage, grade, treatment response)
• TCGA/GENIE exploration: Systematic access to TCGA and clinical sequencing datasets

Core Capabilities

1. cBioPortal REST API

Base URL: https://www.cbioportal.org/api

The API is RESTful, returns JSON, and requires no API key for public data.

import requests

BASE_URL = "https://www.cbioportal.org/api"
HEADERS = {"Accept": "application/json", "Content-Type": "application/json"}

def cbioportal_get(endpoint, params=None):
    url = f"{BASE_URL}/{endpoint}"
    response = requests.get(url, params=params, headers=HEADERS)
    response.raise_for_status()
    return response.json()

def cbioportal_post(endpoint, body):
    url = f"{BASE_URL}/{endpoint}"
    response = requests.post(url, json=body, headers=HEADERS)
    response.raise_for_status()
    return response.json()