cBioPortal Cancer Genomics Scraper

Extract cancer genomics data from cBioPortal — the open-access platform hosting 300+ curated cancer study cohorts from TCGA, MSK-IMPACT, Broad, ICGC and more. Pull the study catalog, gene lookups, the cancer-type taxonomy, and per-study somatic mutations as clean, structured JSON. No API key required.

Runs on the free public cBioPortal REST API (https://www.cbioportal.org/api).

Estimated cost: ~$0.50 per 1,000 records on the Apify platform.

Modes

Mode	What you get
studies (default)	The full catalog of cancer study cohorts with sample counts, reference genome, PubMed id, citation and cancer type — filterable by cancer type and free-text search.
genes	HUGO / Entrez gene records. Look up a specific list (geneSymbols) or walk the gene catalog.
cancertypes	The cancer-type OncoTree taxonomy (id, name, short name, parent, color).
mutations	Per-study somatic mutations for an explicit gene list. Requires studyId + geneSymbols.

Input

Field	Type	Description
mode	select	studies, genes, cancertypes, or mutations. Default studies.
cancerTypeFilter	string	Studies mode. Substring match on cancer-type id/name, e.g. brca.
searchQuery	string	Studies mode. Substring match on study name/id, e.g. tcga.
geneSymbols	array	HUGO symbols, e.g. ["TP53","KRAS"]. Used by genes and required by mutations.
studyId	string	Mutations mode. A study id such as brca_tcga_pub.
maxItems	integer	Max records (1–5000). Default 300.

Example — breast-cancer studies

{ "mode": "studies", "cancerTypeFilter": "brca", "maxItems": 100 }

Example — TP53 mutations in a TCGA breast cohort

{ "mode": "mutations", "studyId": "brca_tcga_pub", "geneSymbols": ["TP53"] }

Output samples

Study

{
  "type": "study",
  "study_id": "brca_tcga_pub",
  "name": "Breast Invasive Carcinoma (TCGA, Nature 2012)",
  "cancer_type": "Breast Invasive Ductal Carcinoma",
  "cancer_type_id": "idc",
  "sample_count": 825,
  "sequenced_sample_count": 507,
  "reference_genome": "hg19",
  "pmid": "23000897",
  "url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pub",
  "source": "cbioportal"
}

Mutation

{
  "type": "mutation",
  "study_id": "brca_tcga_pub",
  "sample_id": "TCGA-A1-A0SK-01",
  "entrez_gene_id": 7157,
  "hugo_symbol": "TP53",
  "protein_change": "M133K",
  "mutation_type": "Missense_Mutation",
  "chromosome": "17",
  "start_position": 7578532
}

Use cases

• Cancer research — assemble cohort metadata across hundreds of published studies.
• Biomarker discovery — pull somatic mutation frequencies for candidate genes.
• Cohort selection — filter studies by cancer type, sample count and reference genome.
• Precision oncology — map gene variants observed across tumor datasets.

Data source, licensing & terms

Data comes from cBioPortal's public REST API. cBioPortal is an open-source project; much of the study data derives from TCGA and other consortia. Individual studies carry their own data-use terms — most curated public cBioPortal data is available under the Open Database License (ODbL), but you are responsible for checking the license/attribution of each specific study before redistribution or publication. This actor only reads publicly exposed API endpoints and does not bypass any access control. Please cite cBioPortal (Cerami et al. 2012; Gao et al. 2013) and the original study publications where required.

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