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metadata 
license: agpl-3.0
language:
  - en
pretty_name: cBioPortal Public Database
configs:
  - config_name: allele_specific_copy_number
    data_files:
      - split: latest
        path: data/allele_specific_copy_number.parquet
  - config_name: alteration_driver_annotation
    data_files:
      - split: latest
        path: data/alteration_driver_annotation.parquet
  - config_name: cancer_study
    default: true
    data_files:
      - split: latest
        path: data/cancer_study.parquet
  - config_name: cancer_study_tags
    data_files:
      - split: latest
        path: data/cancer_study_tags.parquet
  - config_name: cbioportal_sequence_state
    data_files:
      - split: latest
        path: data/cbioportal_sequence_state.parquet
  - config_name: clinical_attribute_meta
    data_files:
      - split: latest
        path: data/clinical_attribute_meta.parquet
  - config_name: clinical_data_derived
    data_files:
      - split: latest
        path: data/clinical_data_derived.parquet
  - config_name: clinical_event
    data_files:
      - split: latest
        path: data/clinical_event.parquet
  - config_name: clinical_event_data
    data_files:
      - split: latest
        path: data/clinical_event_data.parquet
  - config_name: clinical_event_data_derived
    data_files:
      - split: latest
        path: data/clinical_event_data_derived.parquet
  - config_name: clinical_event_derived
    data_files:
      - split: latest
        path: data/clinical_event_derived.parquet
  - config_name: clinical_patient
    data_files:
      - split: latest
        path: data/clinical_patient.parquet
  - config_name: clinical_sample
    data_files:
      - split: latest
        path: data/clinical_sample.parquet
  - config_name: cna_event
    data_files:
      - split: latest
        path: data/cna_event.parquet
  - config_name: copy_number_seg
    data_files:
      - split: latest
        path: data/copy_number_seg.parquet
  - config_name: copy_number_seg_file
    data_files:
      - split: latest
        path: data/copy_number_seg_file.parquet
  - config_name: gene
    data_files:
      - split: latest
        path: data/gene.parquet
  - config_name: gene_alias
    data_files:
      - split: latest
        path: data/gene_alias.parquet
  - config_name: gene_panel
    data_files:
      - split: latest
        path: data/gene_panel.parquet
  - config_name: gene_panel_list
    data_files:
      - split: latest
        path: data/gene_panel_list.parquet
  - config_name: gene_panel_to_gene_derived
    data_files:
      - split: latest
        path: data/gene_panel_to_gene_derived.parquet
  - config_name: generic_assay_data_derived
    data_files:
      - split: latest
        path: data/generic_assay_data_derived.parquet
  - config_name: generic_assay_meta_derived
    data_files:
      - split: latest
        path: data/generic_assay_meta_derived.parquet
  - config_name: generic_assay_profile_entity_derived
    data_files:
      - split: latest
        path: data/generic_assay_profile_entity_derived.parquet
  - config_name: generic_entity_properties
    data_files:
      - split: latest
        path: data/generic_entity_properties.parquet
  - config_name: geneset
    data_files:
      - split: latest
        path: data/geneset.parquet
  - config_name: geneset_gene
    data_files:
      - split: latest
        path: data/geneset_gene.parquet
  - config_name: geneset_hierarchy_leaf
    data_files:
      - split: latest
        path: data/geneset_hierarchy_leaf.parquet
  - config_name: geneset_hierarchy_node
    data_files:
      - split: latest
        path: data/geneset_hierarchy_node.parquet
  - config_name: genetic_alteration
    data_files:
      - split: latest
        path: data/genetic_alteration.parquet
  - config_name: genetic_alteration_derived
    data_files:
      - split: latest
        path: data/genetic_alteration_derived.parquet
  - config_name: genetic_entity
    data_files:
      - split: latest
        path: data/genetic_entity.parquet
  - config_name: genetic_profile
    data_files:
      - split: latest
        path: data/genetic_profile.parquet
  - config_name: genetic_profile_link
    data_files:
      - split: latest
        path: data/genetic_profile_link.parquet
  - config_name: genetic_profile_samples
    data_files:
      - split: latest
        path: data/genetic_profile_samples.parquet
  - config_name: genomic_event_derived
    data_files:
      - split: latest
        path: data/genomic_event_derived.parquet
  - config_name: gistic
    data_files:
      - split: latest
        path: data/gistic.parquet
  - config_name: gistic_to_gene
    data_files:
      - split: latest
        path: data/gistic_to_gene.parquet
  - config_name: info
    data_files:
      - split: latest
        path: data/info.parquet
  - config_name: mut_sig
    data_files:
      - split: latest
        path: data/mut_sig.parquet
  - config_name: mutation
    data_files:
      - split: latest
        path: data/mutation.parquet
  - config_name: mutation_count_by_keyword
    data_files:
      - split: latest
        path: data/mutation_count_by_keyword.parquet
  - config_name: mutation_derived
    data_files:
      - split: latest
        path: data/mutation_derived.parquet
  - config_name: mutation_event
    data_files:
      - split: latest
        path: data/mutation_event.parquet
  - config_name: patient
    data_files:
      - split: latest
        path: data/patient.parquet
  - config_name: reference_genome
    data_files:
      - split: latest
        path: data/reference_genome.parquet
  - config_name: reference_genome_gene
    data_files:
      - split: latest
        path: data/reference_genome_gene.parquet
  - config_name: resource
    data_files:
      - split: latest
        path: data/resource.parquet
  - config_name: resource_definition
    data_files:
      - split: latest
        path: data/resource_definition.parquet
  - config_name: sample
    data_files:
      - split: latest
        path: data/sample.parquet
  - config_name: sample_cna_event
    data_files:
      - split: latest
        path: data/sample_cna_event.parquet
  - config_name: sample_derived
    data_files:
      - split: latest
        path: data/sample_derived.parquet
  - config_name: sample_list
    data_files:
      - split: latest
        path: data/sample_list.parquet
  - config_name: sample_list_list
    data_files:
      - split: latest
        path: data/sample_list_list.parquet
  - config_name: sample_profile
    data_files:
      - split: latest
        path: data/sample_profile.parquet
  - config_name: sample_to_gene_panel_derived
    data_files:
      - split: latest
        path: data/sample_to_gene_panel_derived.parquet
  - config_name: structural_variant
    data_files:
      - split: latest
        path: data/structural_variant.parquet
  - config_name: type_of_cancer
    data_files:
      - split: latest
        path: data/type_of_cancer.parquet

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.