cBioPortal web Public API [Alpha]
★ Only Publicly Available OpenAPI DocumentHealthcareClinical 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.
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, 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.
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.
1
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 | sh2
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 instanceJentic 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
Retrieve clinical attributes and clinical events for patient cohorts
Compute mutated gene and structural variant counts across sample sets
Access survival data for study cohorts to power outcome analyses
List molecular profiles and sample lists for a study
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
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
Why 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.
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.
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