cbioportal

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• SKILL.md
• study_exploration.md · references/

SKILL.md (first lines)

# 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.

```python
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()
```

### 2. Browse Studies

```python
def get_all_studies():
    """List all available cancer studies."""
    return cbioportal_get("studies", {"pageSize": 500})

# Each study has:
# studyId: unique identifier (e.g., "brca_tcga")
# name: human-readable name
# description: dataset description
# cancerTypeId: cancer type abbreviation
# referenceGenome: GRCh37 or GRCh38
# pmid: associated publication

studies = get_all_studies()
print(f"Total studies: {len(studies)}")

# Common TCGA study IDs:
# brca_tcga, luad_tcga, coadread_tcga, gbm_tcga, prad_tcga,
# skcm_tcga, blca_tcga, hnsc_tcga, lihc_tcga, stad_tcga

# Filter for TCGA studies
tcga_studies = [s for s in studies if "tcga" in s["studyId"]]
print([s["studyId"] for s in tcga_studies[:10]])
```

### 3. Molecular Profiles

Each study has multiple molecular profiles (mutation, CNA, expression, etc.):

```python
def get_molecular_profiles(study_id):
    """Get all molecular profiles for a study."""
    return cbioportal_get(f"studies/{study_id}/molecular-profiles")

profiles = get_molecular_profiles("brca_tcga")
for p in profiles:
    print(f"  {p['molecularProfileId']}: {p['name']} ({p['molecularAlterationType']})")

# Alteration types:
# MUTATION_EXTENDED — somatic mutations
# COPY_NUMBER_ALTERATION — CNA (GISTIC)
# MRNA_EXPRESSION — mRNA expression
# PROTEIN_LEVEL — RPPA protein expression
# STRUCTURAL_VARIANT — fusions/rearrangements
```

### 4. Mutation Data

```python
def get_mutations(molecular_profile_id, entrez_gene_ids, sample_list_id=None):
    """Get mutations for specified genes in a molecular profile."""
    body = {
        "entrezGeneIds": entrez_gene_ids,
        "sampleListId": sample_list_id or molecular_profile_id.replace("_mutations", "_all")
    }
    return cbioportal_post(
        f"molecular-profiles/{molecular_profile_id}/mutations/fetch",
        body
    )

# BRCA1 Entrez ID is 672, TP53 is 7157, PTEN is 5728
mutations = get_mutations("brca_tcga_mutations", entrez_gene_ids=[7157])  # TP53

# Each mutation record contains:

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