Publish latest public database snapshot

README.md

@@ -21,10 +21,6 @@ configs:
   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
@@ -193,22 +189,14 @@ configs:
   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"
+- config_name: "resource"
   data_files:
   - split: latest
-    path: "data/resource_sample.parquet"
-- config_name: "resource_study"
+    path: "data/resource.parquet"
+- config_name: "resource_definition"
   data_files:
   - split: latest
-    path: "data/resource_study.parquet"
+    path: "data/resource_definition.parquet"
 - config_name: "sample"
   data_files:
   - split: latest
@@ -255,9 +243,9 @@ it can be browsed independently in the Hugging Face Dataset Viewer.
 
 ## Current snapshot
 
-- Database schema version: `3.0.0`
+- Database schema version: `3.1.0`
 - ClickHouse version: `26.6.1.2326`
-- Tables: 60
+- Tables: 57
 
 Only the latest successfully published snapshot is present on `main`.
 Source files and past snapshots are available from the

data/allele_specific_copy_number.parquet

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data/geneset_gene.parquet

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data/{cbioportal_sequence_state.parquet → resource.parquet}

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data/resource_study.parquet

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data/type_of_cancer.parquet

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manifest.json

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 {
-  "timestamp": "2026-10-11T22:25:12Z",
+  "timestamp": "2026-10-18T22:29:29Z",
   "clickhouse_version": "26.6.1.2326",
-  "schema_version": "3.0.0",
+  "schema_version": "3.1.0",
   "tables": [
     {
       "name": "allele_specific_copy_number",
@@ -16,27 +16,22 @@
     {
       "name": "cancer_study",
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-      "row_count": 550
+      "row_count": 551
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       "name": "gistic",
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+  "manifest_sha256": "00d2a1b3399c464f8a78567958c0ca84f4011cd070a9c2d3b03d260231893614",
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+  "schema_version": "3.1.0",
+  "source_url": "https://sc-203403084713-pp-jbeobuumvm3r4-bucket-rbgakorqrcyx.s3.us-east-1.amazonaws.com/clickhouse/dump_2026_10_18_v3_1_0"
 }

schema.sql

@@ -58,15 +58,6 @@ ENGINE = MergeTree
 ORDER BY cancer_study_id
 SETTINGS index_granularity = 8192;
 
-CREATE TABLE cbioportal_sequence_state
-(
-    `sequence_name` String,
-    `last_value` UInt64
-)
-ENGINE = ReplacingMergeTree
-ORDER BY sequence_name
-SETTINGS index_granularity = 8192;
-
 CREATE TABLE clinical_attribute_meta
 (
     `attr_id` String,
@@ -648,6 +639,22 @@ ENGINE = MergeTree
 ORDER BY (entrez_gene_id, reference_genome_id)
 SETTINGS index_granularity = 8192;
 
+CREATE TABLE resource
+(
+    `internal_id` Int64,
+    `resource_id` String,
+    `cancer_study_id` Int64,
+    `resource_scope` String,
+    `patient_id` Nullable(String),
+    `sample_id` Nullable(String),
+    `url` String,
+    `display_name` Nullable(String),
+    `metadata` Nullable(String)
+)
+ENGINE = MergeTree
+ORDER BY (cancer_study_id, resource_id, patient_id, sample_id, internal_id)
+SETTINGS allow_nullable_key = 1, index_granularity = 8192;
+
 CREATE TABLE resource_definition
 (
     `resource_id` String,
@@ -663,36 +670,6 @@ 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,