drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/cbioportal.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
cBioPortal API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/cbioportal.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

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

1. Find studies: GET /studies — browse available cancer studies, get studyId values
2. Get molecular profiles: GET /studies/{studyId}/molecular-profiles — find profile IDs (e.g. brca_tcga_mutations, brca_tcga_gistic)
3. Get sample lists: GET /studies/{studyId}/sample-lists — find sample list IDs (e.g. brca_tcga_all, brca_tcga_sequenced)
4. 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