cBioPortal web Public API [Alpha]

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

★ Only Publicly Available OpenAPI DocumentHealthcareClinical Datanone156 EndpointsREST

For Agents

Install Jentic One Beta

Connect the cBioPortal web Public API [Alpha] to your agent

Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the cBioPortal web Public API [Alpha], or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.

Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.

Step 1: Jentic One Host machine

# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh

Step 2: Agent machine

# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register       # connects your agent to your Jentic One instance

Jentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.

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

GET STARTED

Start building with cBioPortal web Public API [Alpha] API

Explore with Jentic

View OpenAPI Document

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 Jentic?

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

Credential isolation

cBioPortal's public API needs no credential, so there is nothing to store, and no key ever enters the agent's prompt, logs, or context.

Intent-based discovery

Agents search Jentic by intent such as 'fetch cancer mutations across a sample list' or 'get survival data for a study', and Jentic returns the matching cBioPortal operation with its input schema so the agent calls the right endpoint without browsing the reference docs.

Time to first call

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 with Jentic One, the self-hosted execution layer.

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.

Can I limit what my agent is allowed to do with the cBioPortal API?

Yes. Because you run Jentic One self-hosted, your own rules decide which cBioPortal operations the agent may call, so you can allow only the read-only fetch endpoints it needs, such as /api/mutations/fetch or /api/survival-data/fetch, and withhold the rest. Since cBioPortal puts the study id in the URL path for calls like /api/studies/{studyId}/clinical-data/fetch, you can pin the agent to a single study for its clinical-data reads. The public API is read-only over curated cohort data and needs no credential, so the agent cannot write to it or reach anything you have not scoped in.

cBioPortal web Public API [Alpha]

Connect the cBioPortal web Public API [Alpha] to your agent

Capabilities

Start building with cBioPortal web Public API [Alpha] API

Use Cases

Key Endpoints

Why Jentic?

Related APIs

FAQs