diff --git a/README.md b/README.md index 87be4474fd1a77806968e5b821243b1110209d4b..d75ee442afe22ded085bf7c44eade01ebd571baa 100644 --- a/README.md +++ b/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...) \ No newline at end of file + +# 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. diff --git a/data/allele_specific_copy_number.parquet b/data/allele_specific_copy_number.parquet new file mode 100644 index 0000000000000000000000000000000000000000..7db38189bd22d4f58e1fe0c0adce76dda236de4b --- /dev/null +++ b/data/allele_specific_copy_number.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0443a22b684e781579de08bc63e70ea9c2275823f8ce4a2098017d5d9d7391c5 +size 8897110 diff --git a/data/alteration_driver_annotation.parquet b/data/alteration_driver_annotation.parquet new file mode 100644 index 0000000000000000000000000000000000000000..20d697d9142a9b278dc6403bcbe14e298afa6eb8 --- /dev/null +++ b/data/alteration_driver_annotation.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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`key` String, + `value` String, + `start_date` Int32, + `stop_date` Int32 DEFAULT 0, + `event_type` LowCardinality(String), + `cancer_study_identifier` LowCardinality(String) +) +ENGINE = MergeTree +ORDER BY (cancer_study_identifier, event_type, patient_unique_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE clinical_event_derived +( + `clinical_event_id` Int64, + `patient_id` Nullable(Int64), + `patient_stable_id` String, + `start_date` Nullable(Int64), + `stop_date` Nullable(Int64), + `event_type` LowCardinality(String), + `cancer_study_identifier` LowCardinality(String) +) +ENGINE = MergeTree +PRIMARY KEY (cancer_study_identifier, event_type, clinical_event_id) +ORDER BY (cancer_study_identifier, event_type, clinical_event_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE clinical_patient +( + `internal_id` Int64, + `attr_id` String, + `attr_value` String +) +ENGINE = ReplacingMergeTree +ORDER BY (internal_id, attr_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE clinical_sample +( + `internal_id` Int64, + `attr_id` String, + `attr_value` String +) +ENGINE = ReplacingMergeTree +ORDER BY (internal_id, attr_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE cna_event +( + `cna_event_id` Int64, + `entrez_gene_id` Int64, + `alteration` Int32 +) +ENGINE = MergeTree +ORDER BY cna_event_id +SETTINGS index_granularity = 8192; + +CREATE TABLE copy_number_seg +( + `seg_id` Int64, + `cancer_study_id` Int64, + `sample_id` Int64, + `chr` String, + `start` Int64, + `end` Int64, + `num_probes` Int64, + `segment_mean` Float64 +) +ENGINE = MergeTree +ORDER BY seg_id +SETTINGS index_granularity = 8192; + +CREATE TABLE copy_number_seg_file +( + `seg_file_id` Int64, + `cancer_study_id` Int64, + `reference_genome_id` String, + `description` String, + `filename` String +) +ENGINE = MergeTree +ORDER BY seg_file_id +SETTINGS index_granularity = 8192; + +CREATE TABLE gene +( + `entrez_gene_id` Int64, + `hugo_gene_symbol` String, + `genetic_entity_id` Int64, + `type` Nullable(String) +) +ENGINE = MergeTree +ORDER BY entrez_gene_id +SETTINGS index_granularity = 8192; + +CREATE TABLE gene_alias +( + `entrez_gene_id` Int64, + `gene_alias` String +) +ENGINE = MergeTree +ORDER BY (entrez_gene_id, gene_alias) +SETTINGS index_granularity = 8192; + +CREATE TABLE gene_panel +( + `internal_id` Int64, + `stable_id` String, + `description` Nullable(String) +) +ENGINE = MergeTree +ORDER BY internal_id +SETTINGS index_granularity = 8192; + +CREATE TABLE gene_panel_list +( + `internal_id` Int64, + `gene_id` Int64 +) +ENGINE = MergeTree +ORDER BY (internal_id, gene_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE gene_panel_to_gene_derived +( + `gene_panel_id` LowCardinality(String), + `gene` String +) +ENGINE = MergeTree +ORDER BY gene_panel_id +SETTINGS index_granularity = 8192; + +CREATE TABLE generic_assay_data_derived +( + `sample_unique_id` String, + `patient_unique_id` String, + `genetic_entity_id` String, + `value` String, + `generic_assay_type` String, + `profile_stable_id` String, + `entity_stable_id` String, + `datatype` String, + `patient_level` Decimal(10, 0), + `profile_type` String +) +ENGINE = MergeTree +ORDER BY (profile_type, entity_stable_id, patient_unique_id, sample_unique_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE generic_assay_meta_derived +( + `entity_stable_id` String, + `entity_type` LowCardinality(String), + `properties` Map(String, String) +) +ENGINE = MergeTree +ORDER BY entity_stable_id +SETTINGS index_granularity = 8192; + +CREATE TABLE generic_assay_profile_entity_derived +( + `profile_stable_id` LowCardinality(String), + `entity_stable_id` String +) +ENGINE = MergeTree +ORDER BY (profile_stable_id, entity_stable_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE generic_entity_properties +( + `id` Int64, + `genetic_entity_id` Int64, + `name` String, + `value` String +) +ENGINE = MergeTree +ORDER BY id +SETTINGS index_granularity = 8192; + +CREATE TABLE geneset +( + `id` Int64, + `genetic_entity_id` Int64, + `external_id` String, + `name` String, + `description` String, + `ref_link` Nullable(String) +) +ENGINE = MergeTree +ORDER BY id +SETTINGS index_granularity = 8192; + +CREATE TABLE geneset_gene +( + `geneset_id` Int64, + `entrez_gene_id` Int64 +) +ENGINE = MergeTree +ORDER BY (geneset_id, entrez_gene_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE geneset_hierarchy_leaf +( + `node_id` Int64, + `geneset_id` Int64 +) +ENGINE = MergeTree +ORDER BY (node_id, geneset_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE geneset_hierarchy_node +( + `node_id` Int64, + `node_name` String, + `parent_id` Nullable(Int64) +) +ENGINE = MergeTree +ORDER BY node_id +SETTINGS index_granularity = 8192; + +CREATE TABLE genetic_alteration +( + `genetic_profile_id` Int64, + `genetic_entity_id` Int64, + `values` String +) +ENGINE = ReplacingMergeTree +ORDER BY (genetic_profile_id, genetic_entity_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE genetic_alteration_derived +( + `sample_unique_id` String, + `cancer_study_identifier` LowCardinality(String), + `hugo_gene_symbol` String, + `profile_type` LowCardinality(String), + `alteration_value` Nullable(String) +) +ENGINE = MergeTree +ORDER BY (cancer_study_identifier, hugo_gene_symbol, profile_type, sample_unique_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE genetic_entity +( + `id` Int64, + `entity_type` String, + `stable_id` Nullable(String) +) +ENGINE = MergeTree +ORDER BY id +SETTINGS index_granularity = 8192; + +CREATE TABLE genetic_profile +( + `genetic_profile_id` Int64, + `stable_id` String, + `cancer_study_id` Int64, + `genetic_alteration_type` String, + `generic_assay_type` Nullable(String), + `datatype` String, + `name` String, + `description` Nullable(String), + `show_profile_in_analysis_tab` Int32, + `pivot_threshold` Nullable(Float64), + `sort_order` Nullable(String), + `patient_level` Nullable(Int32) +) +ENGINE = MergeTree +ORDER BY genetic_profile_id +SETTINGS index_granularity = 8192; + +CREATE TABLE genetic_profile_link +( + `referring_genetic_profile_id` Int64, + `referred_genetic_profile_id` Int64, + `reference_type` Nullable(String) +) +ENGINE = MergeTree +ORDER BY (referring_genetic_profile_id, referred_genetic_profile_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE genetic_profile_samples +( + `genetic_profile_id` Int64, + `ordered_sample_list` String +) +ENGINE = ReplacingMergeTree +ORDER BY genetic_profile_id +SETTINGS index_granularity = 8192; + +CREATE TABLE genomic_event_derived +( + `sample_unique_id` String, + `hugo_gene_symbol` String, + `entrez_gene_id` Int32, + `gene_panel_stable_id` LowCardinality(String), + `cancer_study_identifier` LowCardinality(String), + `genetic_profile_stable_id` LowCardinality(String), + `variant_type` LowCardinality(String), + `mutation_variant` String, + `mutation_type` LowCardinality(String), + `mutation_status` LowCardinality(String), + `driver_filter` LowCardinality(String), + `driver_filter_annotation` String, + `driver_tiers_filter` LowCardinality(String), + `driver_tiers_filter_annotation` String, + `cna_alteration` Nullable(Int8), + `cna_cytoband` String, + `sv_event_info` String, + `patient_unique_id` String, + `off_panel` Bool DEFAULT false +) +ENGINE = MergeTree +ORDER BY (genetic_profile_stable_id, cancer_study_identifier, variant_type, entrez_gene_id, hugo_gene_symbol, sample_unique_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE gistic +( + `gistic_roi_id` Int64, + `cancer_study_id` Int64, + `chromosome` Int64, + `cytoband` String, + `wide_peak_start` Int64, + `wide_peak_end` Int64, + `q_value` Float64, + `amp` Int32 +) +ENGINE = MergeTree +ORDER BY gistic_roi_id +SETTINGS index_granularity = 8192; + +CREATE TABLE gistic_to_gene +( + `gistic_roi_id` Int64, + `entrez_gene_id` Int64 +) +ENGINE = MergeTree +ORDER BY (gistic_roi_id, entrez_gene_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE info +( + `db_schema_version` Nullable(String), + `geneset_version` Nullable(String), + `gene_table_version` Nullable(String) +) +ENGINE = MergeTree +ORDER BY tuple() +SETTINGS index_granularity = 8192; + +CREATE TABLE mut_sig +( + `cancer_study_id` Int64, + `entrez_gene_id` Int64, + `rank` Int64, + `NumBasesCovered` Int64, + `NumMutations` Int64, + `p_value` Float64, + `q_value` Float64 +) +ENGINE = MergeTree +ORDER BY (cancer_study_id, entrez_gene_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE mutation +( + `mutation_event_id` Int64 COMMENT 'References mutation_event.mutation_event_id.', + `genetic_profile_id` Int64 COMMENT 'References genetic_profile.genetic_profile_id.', + `sample_id` Int64 COMMENT 'References sample.internal_id.', + `entrez_gene_id` Int64 COMMENT 'References gene.entrez_gene_id.', + `center` Nullable(String) COMMENT 'Center where sequencing was performed.', + `sequencer` Nullable(String) COMMENT 'Sequencing platform used.', + `mutation_status` Nullable(String) COMMENT 'Mutation status: Germline,\n Somatic,\n or LOH.', + `validation_status` Nullable(String) COMMENT 'Validation status.', + `tumor_seq_allele1` Nullable(String) COMMENT 'Tumor allele 1 sequence.', + `tumor_seq_allele2` Nullable(String) COMMENT 'Tumor allele 2 sequence.', + `matched_norm_sample_barcode` Nullable(String) COMMENT 'Matched normal sample barcode.', + `match_norm_seq_allele1` Nullable(String) COMMENT 'Matched normal allele 1 sequence.', + `match_norm_seq_allele2` Nullable(String) COMMENT 'Matched normal allele 2 sequence.', + `tumor_validation_allele1` Nullable(String) COMMENT 'Tumor validation allele 1 sequence.', + `tumor_validation_allele2` Nullable(String) COMMENT 'Tumor validation allele 2 sequence.', + `match_norm_validation_allele1` Nullable(String) COMMENT 'Matched normal validation allele 1.', + `match_norm_validation_allele2` Nullable(String) COMMENT 'Matched normal validation allele 2.', + `verification_status` Nullable(String) COMMENT 'Verification status.', + `sequencing_phase` Nullable(String) COMMENT 'Sequencing phase.', + `sequence_source` String COMMENT 'Source of sequencing data.', + `validation_method` Nullable(String) COMMENT 'Validation method used.', + `score` Nullable(String) COMMENT 'Score or quality metric.', + `bam_file` Nullable(String) COMMENT 'Associated BAM file.', + `tumor_alt_count` Nullable(Int64) COMMENT 'Tumor alternate allele count.', + `tumor_ref_count` Nullable(Int64) COMMENT 'Tumor reference allele count.', + `normal_alt_count` Nullable(Int64) COMMENT 'Normal alternate allele count.', + `normal_ref_count` Nullable(Int64) COMMENT 'Normal reference allele count.', + `amino_acid_change` Nullable(String) COMMENT 'Amino acid change from mutation.', + `annotation_json` Nullable(String) COMMENT 'JSON-formatted annotations.' +) +ENGINE = MergeTree +ORDER BY (genetic_profile_id, entrez_gene_id) +SETTINGS index_granularity = 8192 +COMMENT 'Mutation observations in specific samples and profiles. References mutation_event, gene, genetic_profile, and sample.'; + +CREATE TABLE mutation_count_by_keyword +( + `genetic_profile_id` Int64, + `keyword` Nullable(String), + `entrez_gene_id` Int64, + `keyword_count` Int64, + `gene_count` Int64 +) +ENGINE = MergeTree +ORDER BY (genetic_profile_id, entrez_gene_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE mutation_derived +( + `molecularProfileId` String COMMENT 'Stable ID of the genetic profile', + `sampleId` String COMMENT 'Stable ID of the sample', + `sampleInternalId` Int64, + `patientId` String COMMENT 'Stable ID of the patient', + `entrezGeneId` Int64 COMMENT 'Entrez Gene ID from mutation table (NOT NULL)', + `studyId` String COMMENT 'Cancer study identifier', + `center` Nullable(String) COMMENT 'Sequencing center', + `mutationStatus` Nullable(String) COMMENT 'Mutation status (e.g., Somatic, Germline)', + `validationStatus` Nullable(String) COMMENT 'Validation status', + `tumorAltCount` Nullable(Int64) COMMENT 'Tumor alternate allele count', + `tumorRefCount` Nullable(Int64) COMMENT 'Tumor reference allele count', + `normalAltCount` Nullable(Int64) COMMENT 'Normal alternate allele count', + `normalRefCount` Nullable(Int64) COMMENT 'Normal reference allele count', + `aminoAcidChange` Nullable(String) COMMENT 'Amino acid change', + `chr` Nullable(String) COMMENT 'Chromosome', + `startPosition` Nullable(Int64) COMMENT 'Start position', + `endPosition` Nullable(Int64) COMMENT 'End position', + `referenceAllele` Nullable(String) COMMENT 'Reference allele', + `tumorSeqAllele` Nullable(String) COMMENT 'Tumor sequence allele', + `proteinChange` Nullable(String) COMMENT 'Protein change', + `mutationType` Nullable(String) COMMENT 'Type of mutation', + `ncbiBuild` Nullable(String) COMMENT 'NCBI build version', + `variantType` Nullable(String) COMMENT 'Variant type', + `refseqMrnaId` Nullable(String) COMMENT 'RefSeq mRNA ID', + `proteinPosStart` Nullable(Int64) COMMENT 'Protein position start', + `proteinPosEnd` Nullable(Int64) COMMENT 'Protein position end', + `keyword` Nullable(String) COMMENT 'Keyword', + `annotationJSON` Nullable(String) COMMENT 'Annotation JSON', + `driverFilter` Nullable(String) COMMENT 'Driver filter', + `driverFilterAnnotation` Nullable(String) COMMENT 'Driver filter annotation', + `driverTiersFilter` Nullable(String) COMMENT 'Driver tiers filter', + `driverTiersFilterAnnotation` Nullable(String) COMMENT 'Driver tiers filter annotation', + `GENE.entrezGeneId` Nullable(Int64) COMMENT 'Gene entrez ID', + `GENE.hugoGeneSymbol` Nullable(String) COMMENT 'HUGO gene symbol', + `GENE.type` Nullable(String) COMMENT 'Gene type', + `alleleSpecificCopyNumber.ascnIntegerCopyNumber` Nullable(Int64) COMMENT 'ASCN integer copy number', + `alleleSpecificCopyNumber.ascnMethod` Nullable(String) COMMENT 'ASCN method', + `alleleSpecificCopyNumber.ccfExpectedCopiesUpper` Nullable(Float64) COMMENT 'CCF expected copies upper bound', + `alleleSpecificCopyNumber.ccfExpectedCopies` Nullable(Float64) COMMENT 'CCF expected copies', + `alleleSpecificCopyNumber.clonal` Nullable(String) COMMENT 'Clonality annotation', + `alleleSpecificCopyNumber.minorCopyNumber` Nullable(Int64) COMMENT 'Minor copy number', + `alleleSpecificCopyNumber.expectedAltCopies` Nullable(Int64) COMMENT 'Expected alternate copies', + `alleleSpecificCopyNumber.totalCopyNumber` Nullable(Int64) COMMENT 'Total copy number' +) +ENGINE = MergeTree +ORDER BY (molecularProfileId, sampleId, entrezGeneId) +SETTINGS index_granularity = 8192 +COMMENT 'Mutation query results with detailed annotations including driver status and allele-specific copy numbers'; + +CREATE TABLE mutation_event +( + `mutation_event_id` Int64, + `entrez_gene_id` Int64, + `chr` Nullable(String), + `start_position` Nullable(Int64), + `end_position` Nullable(Int64), + `reference_allele` Nullable(String), + `tumor_seq_allele` Nullable(String), + `protein_change` Nullable(String), + `mutation_type` Nullable(String), + `ncbi_build` Nullable(String), + `strand` Nullable(String), + `variant_type` Nullable(String), + `db_snp_rs` Nullable(String), + `db_snp_val_status` Nullable(String), + `refseq_mrna_id` Nullable(String), + `codon_change` Nullable(String), + `uniprot_accession` Nullable(String), + `protein_pos_start` Nullable(Int64), + `protein_pos_end` Nullable(Int64), + `canonical_transcript` Nullable(Int32), + `keyword` Nullable(String) +) +ENGINE = MergeTree +ORDER BY mutation_event_id +SETTINGS index_granularity = 8192; + +CREATE TABLE patient +( + `internal_id` Int64, + `stable_id` String, + `cancer_study_id` Int64 +) +ENGINE = MergeTree +ORDER BY internal_id +SETTINGS index_granularity = 8192; + +CREATE TABLE reference_genome +( + `reference_genome_id` Int64, + `species` String, + `name` String, + `build_name` String, + `genome_size` Nullable(Int64), + `url` String, + `release_date` Nullable(DateTime64(6)) +) +ENGINE = MergeTree +ORDER BY reference_genome_id +SETTINGS index_granularity = 8192; + +CREATE TABLE reference_genome_gene +( + `entrez_gene_id` Int64, + `reference_genome_id` Int64, + `chr` Nullable(String), + `cytoband` Nullable(String), + `start` Nullable(Int64), + `end` Nullable(Int64) +) +ENGINE = MergeTree +ORDER BY (entrez_gene_id, reference_genome_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE resource_definition +( + `resource_id` String, + `display_name` String, + `description` Nullable(String), + `resource_type` String, + `open_by_default` Nullable(Int32), + `priority` Int64, + `cancer_study_id` Int64, + `custom_metadata` Nullable(String) +) +ENGINE = MergeTree +ORDER BY (resource_id, cancer_study_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE resource_patient +( + `internal_id` Int64, + `resource_id` String, + `url` String +) +ENGINE = MergeTree +ORDER BY (internal_id, resource_id, url) +SETTINGS index_granularity = 8192; + +CREATE TABLE resource_sample +( + `internal_id` Int64, + `resource_id` String, + `url` String +) +ENGINE = MergeTree +ORDER BY (internal_id, resource_id, url) +SETTINGS index_granularity = 8192; + +CREATE TABLE resource_study +( + `internal_id` Int64, + `resource_id` String, + `url` String +) +ENGINE = MergeTree +ORDER BY (internal_id, resource_id, url) +SETTINGS index_granularity = 8192; + +CREATE TABLE sample +( + `internal_id` Int64, + `stable_id` String, + `sample_type` String, + `patient_id` Int64 +) +ENGINE = MergeTree +ORDER BY internal_id +SETTINGS index_granularity = 8192; + +CREATE TABLE sample_cna_event +( + `cna_event_id` Int64 COMMENT 'References cna_event.cna_event_id.', + `sample_id` Int64 COMMENT 'References sample.internal_id.', + `genetic_profile_id` Int64 COMMENT 'References genetic_profile.genetic_profile_id.', + `annotation_json` Nullable(String) COMMENT 'JSON-formatted annotation details.' +) +ENGINE = MergeTree +PRIMARY KEY (genetic_profile_id, cna_event_id, sample_id) +ORDER BY (genetic_profile_id, cna_event_id, sample_id) +SETTINGS index_granularity = 8192 +COMMENT 'Observed CNA events per sample and profile. References cna_event, sample, and genetic_profile.'; + +CREATE TABLE sample_derived +( + `sample_unique_id` String, + `sample_unique_id_base64` String, + `sample_stable_id` String, + `patient_unique_id` String, + `patient_unique_id_base64` String, + `patient_stable_id` String, + `cancer_study_identifier` LowCardinality(String), + `internal_id` Int32, + `patient_internal_id` Int32, + `sample_type` String, + `sequenced` Int32, + `copy_number_segment_present` Int32 +) +ENGINE = MergeTree +ORDER BY (cancer_study_identifier, sample_unique_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE sample_list +( + `list_id` Int64, + `stable_id` String, + `category` String, + `cancer_study_id` Int64, + `name` String, + `description` Nullable(String) +) +ENGINE = MergeTree +ORDER BY list_id +SETTINGS index_granularity = 8192; + +CREATE TABLE sample_list_list +( + `list_id` Int64, + `sample_id` Int64 +) +ENGINE = MergeTree +ORDER BY (list_id, sample_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE sample_profile +( + `sample_id` Int64, + `genetic_profile_id` Int64, + `panel_id` Nullable(Int64) +) +ENGINE = ReplacingMergeTree +ORDER BY (sample_id, genetic_profile_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE sample_to_gene_panel_derived +( + `sample_unique_id` String, + `alteration_type` LowCardinality(String), + `gene_panel_id` LowCardinality(String), + `cancer_study_identifier` LowCardinality(String), + `genetic_profile_id` LowCardinality(String) +) +ENGINE = MergeTree +ORDER BY (gene_panel_id, alteration_type, genetic_profile_id, sample_unique_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE structural_variant +( + `internal_id` Int64, + `genetic_profile_id` Int64, + `sample_id` Int64, + `site1_entrez_gene_id` Nullable(Int64), + `site1_ensembl_transcript_id` Nullable(String), + `site1_chromosome` Nullable(String), + `site1_region` Nullable(String), + `site1_region_number` Nullable(Int64), + `site1_contig` Nullable(String), + `site1_position` Nullable(Int64), + `site1_description` Nullable(String), + `site2_entrez_gene_id` Nullable(Int64), + `site2_ensembl_transcript_id` Nullable(String), + `site2_chromosome` Nullable(String), + `site2_region` Nullable(String), + `site2_region_number` Nullable(Int64), + `site2_contig` Nullable(String), + `site2_position` Nullable(Int64), + `site2_description` Nullable(String), + `site2_effect_on_frame` Nullable(String), + `ncbi_build` Nullable(String), + `dna_support` Nullable(String), + `rna_support` Nullable(String), + `normal_read_count` Nullable(Int64), + `tumor_read_count` Nullable(Int64), + `normal_variant_count` Nullable(Int64), + `tumor_variant_count` Nullable(Int64), + `normal_paired_end_read_count` Nullable(Int64), + `tumor_paired_end_read_count` Nullable(Int64), + `normal_split_read_count` Nullable(Int64), + `tumor_split_read_count` Nullable(Int64), + `annotation` Nullable(String), + `breakpoint_type` Nullable(String), + `connection_type` Nullable(String), + `event_info` Nullable(String), + `class` Nullable(String), + `length` Nullable(Int64), + `comments` Nullable(String), + `sv_status` String, + `annotation_json` Nullable(String) +) +ENGINE = MergeTree +ORDER BY (sample_id, genetic_profile_id) +SETTINGS index_granularity = 8192; + +CREATE TABLE type_of_cancer +( + `type_of_cancer_id` String, + `name` String, + `dedicated_color` String, + `short_name` Nullable(String), + `parent` Nullable(String) +) +ENGINE = MergeTree +ORDER BY type_of_cancer_id +SETTINGS index_granularity = 8192; +