| --- |
| 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](https://public-db-dump.assets.cbioportal.org/). |
|
|
| ## Usage |
|
|
| Choose a table name as the dataset configuration: |
|
|
| ```python |
| 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](mailto:cbioportal@googlegroups.com). |
|
|
