cBioPortal web Public API [Alpha]

Name: cBioPortal web Public API [Alpha] API
Brand: cBioPortal web Public API
Availability: InStock

★ Only Publicly Available SpecHealthcareClinical Datanone156 EndpointsREST

For Agents

Query cBioPortal cancer genomics data — pull mutations, copy number alterations, structural variants, and clinical data across public oncology studies for analysis or report generation.

Quickstart

Get started with cBioPortal web Public API [Alpha] in minutes using your preferred integration method.

# Add to your MCP client config (Claude Desktop, Cursor, Windsurf)
{
  "jentic": {
    "url": "https://api.jentic.com/mcp",
    "auth": "oauth"
  }
}

# Then ask your agent:
"fetch cancer mutations from cBioPortal"

# → Jentic returns the GET /events tool with parameter schema, agent executes.

Capabilities

What an agent can do with cBioPortal web Public API [Alpha] API.

Browse curated public cancer studies with their cohort metadata

Fetch mutations across gene and sample lists for cohort analysis

Pull copy number alterations and structural variants for selected samples

Retrieve clinical attributes and clinical events for patient cohorts

GET STARTED

Start building with cBioPortal web Public API [Alpha] API

Explore with Jentic

View OpenAPI Spec

Use for: I need to list all cancer studies available in cBioPortal, Get all mutations in TP53 across a list of breast cancer studies, Retrieve clinical data for a specific patient cohort, Find structural variants in a sample list

Not supported: Does not handle clinical EHR records, patient scheduling, or genomic sequencing pipelines — use for querying curated cancer cohort data on the cBioPortal platform only.

Jentic publishes the only available OpenAPI specification for cBioPortal web Public API [Alpha], keeping it validated and agent-ready.

Jentic publishes the only available OpenAPI specification for cBioPortal web Public API, keeping it validated and agent-ready. cBioPortal is the cancer genomics portal that hosts curated mutation, copy number, structural variant, and clinical data across hundreds of public studies. The API exposes endpoints for browsing studies, fetching sample and patient cohorts, retrieving mutation and copy number alterations, and pulling clinical attributes for downstream analysis. Most data fetch operations use POST bodies that take lists of study, sample, or gene identifiers, with matched GET endpoints for browsing.

Use Cases

Patterns agents use cBioPortal web Public API [Alpha] API for, with concrete tasks.

★ Cohort Mutation Analysis

Researchers and computational biology agents pull mutations across a list of samples and genes to identify driver alterations in a cancer cohort. The API's mutations fetch endpoint accepts a sample list id and a gene panel and returns all variants with annotations. This replaces ad-hoc downloads from the cBioPortal web UI when running large analyses.

POST to /api/mutations/fetch with a sample list id and entrez gene ids for TP53, PIK3CA, and EGFR, and summarise the variants by sample

Clinical Data Pull for Survival Analysis

An agent retrieves clinical attributes and survival endpoints for a specific cancer study so a downstream notebook can run Kaplan-Meier analysis on overall survival by mutation status. The clinical-data and survival-data fetch endpoints return structured records keyed by patient or sample identifier, suitable for direct ingestion into pandas.

POST to /api/survival-data/fetch and /api/studies/{studyId}/clinical-data/fetch for the BRCA TCGA study, then return a merged dataframe

Cross-Study Structural Variant Discovery

Agents scan structural variant data across multiple studies to identify recurrent fusions or rearrangements in a gene of interest. The structural-variant fetch endpoint accepts study ids and entrez gene ids, returning the matching events with breakpoints and supporting metadata. This is useful for translational research teams looking for candidate therapeutic targets.

POST to /api/structural-variant/fetch with study ids for lung cancer cohorts and the EML4 and ALK gene ids to surface fusion candidates

AI Agent Integration via Jentic

A research assistant agent uses Jentic to discover the cBioPortal endpoints relevant to a question (mutations, copy number, clinical), load their schemas, and execute calls without holding cBioPortal data access tokens. This lets a single research agent combine cBioPortal evidence with literature search and other oncology APIs.

Use Jentic to search 'fetch cBioPortal mutations across a sample list', load the schema for /api/mutations/fetch, and execute against TP53 in the MSK-IMPACT cohort

Key Endpoints

156 endpoints — jentic publishes the only available openapi specification for cbioportal web public api, keeping it validated and agent-ready.

METHOD

PATH

DESCRIPTION

GET

/api/studies

List all cancer studies

POST

/api/mutations/fetch

Fetch mutations across samples and genes

POST

/api/structural-variant/fetch

Fetch structural variants

POST

/api/studies/{studyId}/clinical-data/fetch

Fetch clinical data for a study

POST

/api/survival-data/fetch

Fetch survival data for cohorts

GET

/api/molecular-profiles

List molecular profiles

POST

/api/samples/fetch

Fetch sample records by identifier

POST

/api/patients/fetch

Fetch patient records by identifier

GET

/api/studies

List all cancer studies

POST

/api/mutations/fetch

Fetch mutations across samples and genes

POST

/api/structural-variant/fetch

Fetch structural variants

POST

/api/studies/{studyId}/clinical-data/fetch

Fetch clinical data for a study

POST

/api/survival-data/fetch

Fetch survival data for cohorts

Why though Jentic?

Three things that make agents converge on Jentic-routed access.

Credential isolation

The public cBioPortal API requires no key, so Jentic still routes calls through a single authenticated execution path that records usage and applies fair-use throttling, keeping the agent's request pattern observable.

Intent-based discovery

Agents search Jentic by intent (e.g., 'fetch cancer mutations across a sample list') and Jentic returns the matching cBioPortal fetch endpoints with their input schemas, so the agent doesn't have to navigate 156 paths manually.

Time to first call

Direct cBioPortal integration: 1-3 days mapping the fetch payload shapes for mutations, CNAs, and clinical data. Through Jentic: under 1 hour — search, load schema, execute.

Related APIs

Alternatives and complements available in the Jentic catalogue.

Complementary

CDC Open Data API

Public health and epidemiology datasets that complement molecular cohort studies

Pair with cBioPortal when an agent needs population-level cancer incidence or surveillance data alongside molecular evidence

Complementary

US Census API

Population and demographic data for normalising cohort outcomes

Use Census data to contextualise cBioPortal cohort findings against the underlying population

Alternative

CBP Public API

Different domain — included only as a corpus-verified neighbour

Not a clinical data substitute — choose cBioPortal for any oncology genomics work

FAQs

Specific to using cBioPortal web Public API [Alpha] API through Jentic.

Why is there no official OpenAPI spec for cBioPortal web Public API?

cBioPortal hosts a Swagger UI but the curated, validated OpenAPI 3 spec used here is maintained by Jentic. Jentic generates and maintains this spec so that AI agents and developers can call cBioPortal API via structured tooling. It is validated against the live API and kept up to date. Get started at https://app.jentic.com/sign-up.

What authentication does the cBioPortal API use?

The public cBioPortal instance at www.cbioportal.org does not require authentication for its read-only endpoints. The spec exposes a /api/data-access-tokens endpoint for private deployments that have user accounts enabled, but the public study data is open.

Can I run cohort analysis with the cBioPortal API?

Yes. The fetch endpoints — /api/mutations/fetch, /api/structural-variant/fetch, /api/studies/{studyId}/clinical-data/fetch, and /api/survival-data/fetch — accept sample lists and gene panels, returning the data needed for cohort-level mutation, structural variant, and survival analysis.

What are the rate limits for the cBioPortal API?

cBioPortal does not publish hard rate limits for the public service, but it asks heavy users to install the portal locally for large bulk pulls. Treat the API as a fair-use research resource and avoid hammering /fetch endpoints with thousands of parallel requests.

How do I fetch mutations for a sample list through Jentic?

Search Jentic for 'fetch cBioPortal mutations', load the schema for POST /api/mutations/fetch, and execute with a sample list identifier and entrez gene ids. The agent receives structured JSON ready for downstream analysis.

Is the cBioPortal API free?

Yes. The public cBioPortal instance is open and free, supported by the cancer research community. Private institutional deployments may apply their own access rules.