Publish latest public database snapshot

README.md

@@ -3,5 +3,287 @@ 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_definition"
+  data_files:
+  - split: latest
+    path: "data/resource_definition.parquet"
+- config_name: "resource_patient"
+  data_files:
+  - split: latest
+    path: "data/resource_patient.parquet"
+- config_name: "resource_sample"
+  data_files:
+  - split: latest
+    path: "data/resource_sample.parquet"
+- config_name: "resource_study"
+  data_files:
+  - split: latest
+    path: "data/resource_study.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 (Coming soon...)
+
+# 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
+
+- Source dump: [dump_2026_08_31_v3_0_0](https://sc-203403084713-pp-jbeobuumvm3r4-bucket-rbgakorqrcyx.s3.us-east-1.amazonaws.com/clickhouse/dump_2026_08_31_v3_0_0/)
+- Database schema version: `3.0.0`
+- ClickHouse version: `26.4.1.2212`
+- Tables: 60
+
+Only the latest successfully published snapshot is present on `main`.
+The source dump remains available from the cBioPortal public database
+dump site.
+
+## 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
+
+## Data scope
+
+This publication follows the same scope as the public S3 dump. The
+exporter excludes authentication, user, token, session, password,
+credential, and secret-related tables before creating the snapshot.
+
+For help, contact cbioportal@googlegroups.com.

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