cbioportal-database

Fetch genomic alteration data for a gene from the cBioPortal REST API.

1|Updated Mar 11, 2026

Search Tags:#bioinformatics #genomics #mutations #clinical #survival #cbioportal #cna

Ready to run

npx skills add https://github.com/SciMate-AI/scicli --skill cbioportal-database-scimate-ai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cbioportal-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/cbioportal-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill cbioportal-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Researchers need programmatic access to cancer genomics data from cBioPortal to perform large-scale analyses, integrate mutation/CNA/expression and clinical data, and validate targets across studies.

Core Features & Use Cases

Retrieve mutations and CNAs across studies via REST API for gene-centric analyses.
Access clinical attributes and survival data to correlate genotypes with outcomes.
Conduct pan-cancer comparisons and study-specific queries (e.g., brca_tcga, msk_impact_2017, genie_14_1_public) to validate biomarkers.

Quick Start

Run a quick mutation and CNA profile for a gene in a chosen study.

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 mutations and CNA data from cBioPortal for a specific gene?▼

Query cancer genomics mutations and CNA data by fetching gene alterations through the cBioPortal REST API. It retrieves molecular profiles and sample lists across studies like brca_tcga to enable precise, reproducible gene-centric analyses.

Can I correlate mutation data with clinical survival outcomes across different cancer studies?▼

You can correlate mutation data with clinical survival outcomes by retrieving clinical attributes and survival data via the cBioPortal REST API. It supports pan-cancer comparisons across studies like genie_14_1_public to validate biomarkers.

What's the best way to access clinical attributes and expression data for pan-cancer analyses?▼

Access clinical attributes and expression data for pan-cancer analyses by using cBioPortal REST endpoints to retrieve study metadata and molecular profiles. This enables genotype-phenotype correlations across multiple cancer studies.

Do I need to perform a gene lookup before fetching genomic alteration data from cBioPortal?▼

Yes, you need to perform a gene lookup using the /genes/fetch endpoint before retrieving genomic alteration data. This ensures precise targeting when querying mutations, copy-number alterations, and expression profiles across cBioPortal studies.

Does the cBioPortal API support querying copy-number alterations alongside mutation profiles?▼

The cBioPortal API supports querying copy-number alterations alongside mutation profiles through its REST endpoints. It retrieves comprehensive genomic alteration data, integrating CNA and mutation data for targeted gene analyses across studies.

What are the limitations when retrieving study metadata and molecular profiles for large-scale analyses?▼

Limitations include dependency on cBioPortal REST API rate limits and study-specific data availability when retrieving study metadata and molecular profiles. Queries require precise gene lookups and study identifiers to return reproducible genomic alteration results.