Skillintermediate

cBioPortal API

Most list endpoints support these:

Claude Code Knowledge Pack7/10/2026

Overview

cBioPortal API

Base URL

https://www.cbioportal.org/api

Auth

No authentication for the public instance. Private/institutional instances (e.g. genie.cbioportal.org) require a data access token via Authorization: Bearer <token> header.

Common Headers

Accept: application/json
Content-Type: application/json

Common Query Parameters

Most list endpoints support these:

Parameter	Type	Description	Default
`projection`	string	Detail level: `ID`, `SUMMARY`, `DETAILED`, `META`	`SUMMARY`
`pageNumber`	int	Zero-based page index	`0`
`pageSize`	int	Results per page	`10000000`
`sortBy`	string	Property to sort by	varies
`direction`	string	`ASC` or `DESC`	`ASC`

Key Endpoints

Studies

Method	Endpoint	Description
GET	`/studies`	List all cancer studies
GET	`/studies/{studyId}`	Get a single study
POST	`/studies/fetch`	Fetch multiple studies by ID

Example:

GET https://www.cbioportal.org/api/studies?projection=SUMMARY&pageSize=10
GET https://www.cbioportal.org/api/studies/brca_tcga

Response fields: studyId, name, description, cancerTypeId, pmid, citation, allSampleCount, referenceGenome, publicStudy, importDate

Cancer Types

Method	Endpoint	Description
GET	`/cancer-types`	List all cancer types
GET	`/cancer-types/{cancerTypeId}`	Get one cancer type

Response fields: cancerTypeId, name, shortName, dedicatedColor, parent

Genes

Method	Endpoint	Description
GET	`/genes`	List all genes (paginated)
GET	`/genes/{geneId}`	Gene by Hugo symbol or Entrez ID
GET	`/genes/{geneId}/aliases`	Gene aliases
POST	`/genes/fetch`	Fetch multiple genes

Example:

GET https://www.cbioportal.org/api/genes/TP53

Response: {"entrezGeneId": 7157, "hugoGeneSymbol": "TP53", "type": "protein-coding"}

Molecular Profiles

Method	Endpoint	Description
GET	`/molecular-profiles`	All profiles across all studies
GET	`/studies/{studyId}/molecular-profiles`	Profiles in a study
GET	`/molecular-profiles/{molecularProfileId}`	Single profile

Profile types (molecularAlterationType): MUTATION_EXTENDED, COPY_NUMBER_ALTERATION, MRNA_EXPRESSION, PROTEIN_LEVEL, METHYLATION

Example:

GET https://www.cbioportal.org/api/studies/brca_tcga/molecular-profiles

Mutations

Method	Endpoint	Description
GET	`/molecular-profiles/{profileId}/mutations`	Mutations in a profile
POST	`/molecular-profiles/{profileId}/mutations/fetch`	Filtered mutation query
POST	`/mutations/fetch`	Multi-profile mutation fetch

Parameters for GET:

Parameter	Type	Description
`sampleListId`	string	Sample list to query (e.g. `brca_tcga_all`)
`entrezGeneId`	int	Filter by gene
`projection`	string	`SUMMARY`, `DETAILED`, `ID`, `META`

Example — TP53 mutations in TCGA breast cancer:

GET https://www.cbioportal.org/api/molecular-profiles/brca_tcga_mutations/mutations?sampleListId=brca_tcga_all&entrezGeneId=7157&projection=DETAILED

POST body for multi-gene fetch:

{
  "sampleListId": "brca_tcga_all",
  "entrezGeneIds": [7157, 672]
}

Response fields: entrezGeneId, sampleId, patientId, proteinChange, mutationType, mutationStatus, chr, startPosition, endPosition, referenceAllele, variantAllele, variantType, ncbiBuild, tumorAltCount, tumorRefCount

Copy Number Alterations

Method	Endpoint	Description
GET	`/molecular-profiles/{profileId}/discrete-copy-number`	CNA data
POST	`/molecular-profiles/{profileId}/discrete-copy-number/fetch`	Filtered CNA query
POST	`/discrete-copy-number/fetch`	Multi-profile CNA fetch

Molecular Data (expression, methylation)

Method	Endpoint	Description
GET	`/molecular-profiles/{profileId}/molecular-data`	Expression/methylation data
POST	`/molecular-data/fetch`	Multi-profile molecular data fetch

Clinical Data

Method	Endpoint	Description
GET	`/studies/{studyId}/clinical-data`	Clinical data for a study
POST	`/clinical-data/fetch`	Multi-study clinical data
GET	`/studies/{studyId}/clinical-attributes`	Available clinical attributes

Parameters for GET:

Parameter	Type	Description
`clinicalDataType`	string	`PATIENT` or `SAMPLE`
`attributeId`	string	e.g. `OS_STATUS`, `OS_MONTHS`, `CANCER_TYPE`

Example:

GET https://www.cbioportal.org/api/studies/brca_tcga/clinical-data?clinicalDataType=PATIENT&attributeId=OS_STATUS&projection=SUMMARY

Patients & Samples

Method	Endpoint	Description
GET	`/studies/{studyId}/patients`	Patients in a study
GET	`/studies/{studyId}/samples`	Samples in a study
POST	`/patients/fetch`	Multi-study patient fetch
POST	`/samples/fetch`	Multi-study sample fetch

Sample Lists

Method	Endpoint	Description
GET	`/studies/{studyId}/sample-lists`	Predefined sample groups
GET	`/sample-lists/{sampleListId}`	Single sample list

Gene Panels

Method	Endpoint	Description
GET	`/gene-panels`	All gene panels
GET	`/gene-panels/{genePanelId}`	Panel details with gene list
POST	`/gene-panel-data/fetch`	Which panels cover which samples

Treatments

Method	Endpoint	Description
POST	`/treatments/patient`	Patient-level treatment data
POST	`/treatments/sample`	Sample-level treatment data

System

Method	Endpoint	Description
GET	`/health`	Server health check
GET	`/info`	Portal version, DB schema version

Typical Workflow

Find studies: GET /studies — browse available cancer studies, get studyId values
Get molecular profiles: GET /studies/{studyId}/molecular-profiles — find profile IDs (e.g. brca_tcga_mutations, brca_tcga_gistic)
Get sample lists: GET /studies/{studyId}/sample-lists — find sample list IDs (e.g. brca_tcga_all, brca_tcga_sequenced)
Query data: Use the profile ID and sample list ID to fetch mutations, CNA, expression, or clinical data

Rate Limits

No published rate limits. Be courteous — avoid hammering with many concurrent requests. For bulk data needs, cBioPortal offers downloadable datasets at https://docs.cbioportal.org/downloads/.

Tips

Study IDs follow a pattern: {cancer_type}_{source} (e.g. brca_tcga, luad_tcga, prad_mskcc_2017)
Molecular profile IDs extend the study ID: {studyId}_mutations, {studyId}_gistic, {studyId}_rna_seq_v2_mrna
Use projection=DETAILED to get the richest response including nested objects
POST /fetch endpoints are for batch queries across multiple studies, genes, or samples — they're the most flexible way to query
Gene lookup accepts both Hugo symbols (TP53) and Entrez IDs (7157)
The Swagger UI at https://www.cbioportal.org/api/swagger-ui/index.html documents every endpoint interactively