Datasets:
File size: 7,558 Bytes
db6acdb 05c141d 70837a4 0f53479 70837a4 58be468 70837a4 58be468 70837a4 58be468 70837a4 14b0ca1 70837a4 58be468 0f53479 70837a4 d78a411 70837a4 d78a411 70837a4 d78a411 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 | ---
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).
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