cBioPortal/publicDatabase

cBioPortal Public Database

A weekly Parquet snapshot of the public cBioPortal ClickHouse database. Each database table is exposed as a separate dataset configuration so it can be browsed independently in the Hugging Face Dataset Viewer.

Current snapshot

• Database schema version: 3.1.0
• ClickHouse version: 26.6.1.2439
• Tables: 58

Only the latest successfully published snapshot is present on main. Source files and past snapshots are available from the cBioPortal Public Database Dumps.

Usage

Choose a table name as the dataset configuration:

from datasets import load_dataset

dataset = load_dataset("cBioPortal/publicDatabase", "cancer_study", split="latest")

The repository also contains:

• manifest.json with source row counts and version metadata
• schema.sql with the portable ClickHouse schema
• publication.json with source identity and file integrity metadata

Contact

For help, contact cbioportal@googlegroups.com.