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parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 9,156 Bytes
6d1bbc7 | 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 | -- NegBioDB Gene Essentiality (GE) Domain — Initial Schema
-- Migration 001: Core tables for DepMap CRISPR/RNAi gene essentiality negatives
--
-- Design decisions:
-- - Asymmetric pairs: gene + cell_line (not symmetric like PPI)
-- - Separate genes/cell_lines tables (separate DB from DTI/CT/PPI)
-- - Confidence tiers: gold/silver/bronze (same framework as DTI/CT/PPI)
-- - PRISM bridge tables: cross-domain link to DTI via InChIKey/ChEMBL
-- - Dedup: UNIQUE on (gene_id, cell_line_id, screen_id, source_db)
-- - Reference flags on genes table for common essential / nonessential sets
-- ============================================================
-- Common Layer tables (same as DTI/CT/PPI)
-- ============================================================
CREATE TABLE IF NOT EXISTS schema_migrations (
version TEXT PRIMARY KEY,
applied_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE TABLE IF NOT EXISTS dataset_versions (
dataset_id INTEGER PRIMARY KEY AUTOINCREMENT,
name TEXT NOT NULL,
version TEXT NOT NULL,
source_url TEXT,
download_date TEXT,
file_hash TEXT,
row_count INTEGER,
notes TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
-- ============================================================
-- Domain-specific tables: Gene Essentiality
-- ============================================================
-- Genes table
CREATE TABLE genes (
gene_id INTEGER PRIMARY KEY AUTOINCREMENT,
entrez_id INTEGER UNIQUE,
gene_symbol TEXT NOT NULL,
ensembl_id TEXT,
description TEXT,
is_common_essential INTEGER DEFAULT 0,
is_reference_nonessential INTEGER DEFAULT 0,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
updated_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE INDEX idx_genes_symbol ON genes(gene_symbol);
CREATE INDEX idx_genes_entrez ON genes(entrez_id) WHERE entrez_id IS NOT NULL;
-- Cell lines table
CREATE TABLE cell_lines (
cell_line_id INTEGER PRIMARY KEY AUTOINCREMENT,
model_id TEXT NOT NULL UNIQUE,
ccle_name TEXT,
stripped_name TEXT,
lineage TEXT,
primary_disease TEXT,
subtype TEXT,
sex TEXT,
primary_or_metastasis TEXT,
sample_collection_site TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
updated_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE INDEX idx_cell_lines_ccle ON cell_lines(ccle_name) WHERE ccle_name IS NOT NULL;
CREATE INDEX idx_cell_lines_stripped ON cell_lines(stripped_name) WHERE stripped_name IS NOT NULL;
CREATE INDEX idx_cell_lines_lineage ON cell_lines(lineage) WHERE lineage IS NOT NULL;
-- Screen configurations
CREATE TABLE ge_screens (
screen_id INTEGER PRIMARY KEY AUTOINCREMENT,
source_db TEXT NOT NULL CHECK (source_db IN (
'depmap', 'project_score', 'demeter2')),
depmap_release TEXT NOT NULL,
screen_type TEXT NOT NULL CHECK (screen_type IN ('crispr', 'rnai')),
library TEXT,
algorithm TEXT,
notes TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE UNIQUE INDEX idx_ge_screens_source
ON ge_screens(source_db, depmap_release, screen_type);
-- Core fact table: GE negative results (non-essential gene-cell_line pairs)
CREATE TABLE ge_negative_results (
result_id INTEGER PRIMARY KEY AUTOINCREMENT,
gene_id INTEGER NOT NULL REFERENCES genes(gene_id),
cell_line_id INTEGER NOT NULL REFERENCES cell_lines(cell_line_id),
screen_id INTEGER REFERENCES ge_screens(screen_id),
gene_effect_score REAL,
dependency_probability REAL,
evidence_type TEXT NOT NULL CHECK (evidence_type IN (
'crispr_nonessential',
'rnai_nonessential',
'multi_screen_concordant',
'reference_nonessential',
'context_nonessential')),
confidence_tier TEXT NOT NULL CHECK (confidence_tier IN (
'gold', 'silver', 'bronze')),
source_db TEXT NOT NULL,
source_record_id TEXT NOT NULL,
extraction_method TEXT NOT NULL CHECK (extraction_method IN (
'score_threshold', 'reference_set', 'multi_source_concordance')),
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
updated_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE INDEX idx_ge_nr_gene ON ge_negative_results(gene_id);
CREATE INDEX idx_ge_nr_cell_line ON ge_negative_results(cell_line_id);
CREATE INDEX idx_ge_nr_pair ON ge_negative_results(gene_id, cell_line_id);
CREATE INDEX idx_ge_nr_tier ON ge_negative_results(confidence_tier);
CREATE INDEX idx_ge_nr_source ON ge_negative_results(source_db);
CREATE UNIQUE INDEX idx_ge_nr_unique_source ON ge_negative_results(
gene_id, cell_line_id,
COALESCE(screen_id, -1),
source_db);
-- ============================================================
-- Aggregation table
-- ============================================================
CREATE TABLE gene_cell_pairs (
pair_id INTEGER PRIMARY KEY AUTOINCREMENT,
gene_id INTEGER NOT NULL REFERENCES genes(gene_id),
cell_line_id INTEGER NOT NULL REFERENCES cell_lines(cell_line_id),
num_screens INTEGER NOT NULL,
num_sources INTEGER NOT NULL,
best_confidence TEXT NOT NULL,
best_evidence_type TEXT,
min_gene_effect REAL,
max_gene_effect REAL,
mean_gene_effect REAL,
gene_degree INTEGER,
cell_line_degree INTEGER,
UNIQUE(gene_id, cell_line_id)
);
CREATE INDEX idx_gcp_gene ON gene_cell_pairs(gene_id);
CREATE INDEX idx_gcp_cell_line ON gene_cell_pairs(cell_line_id);
CREATE INDEX idx_gcp_confidence ON gene_cell_pairs(best_confidence);
-- ============================================================
-- Benchmark split tables
-- ============================================================
CREATE TABLE ge_split_definitions (
split_id INTEGER PRIMARY KEY AUTOINCREMENT,
split_name TEXT NOT NULL,
split_strategy TEXT NOT NULL CHECK (split_strategy IN (
'random', 'cold_gene', 'cold_cell_line',
'cold_both', 'degree_balanced')),
description TEXT,
random_seed INTEGER,
train_ratio REAL DEFAULT 0.7,
val_ratio REAL DEFAULT 0.1,
test_ratio REAL DEFAULT 0.2,
date_created TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
version TEXT DEFAULT '1.0',
UNIQUE(split_name, version)
);
CREATE TABLE ge_split_assignments (
pair_id INTEGER NOT NULL REFERENCES gene_cell_pairs(pair_id),
split_id INTEGER NOT NULL REFERENCES ge_split_definitions(split_id),
fold TEXT NOT NULL CHECK (fold IN ('train', 'val', 'test')),
PRIMARY KEY (pair_id, split_id)
);
CREATE INDEX idx_ge_splits_fold ON ge_split_assignments(split_id, fold);
-- ============================================================
-- PRISM drug sensitivity bridge tables
-- ============================================================
CREATE TABLE prism_compounds (
compound_id INTEGER PRIMARY KEY AUTOINCREMENT,
broad_id TEXT UNIQUE,
name TEXT,
smiles TEXT,
inchikey TEXT,
chembl_id TEXT,
pubchem_cid INTEGER,
mechanism_of_action TEXT,
target_name TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE INDEX idx_prism_inchikey ON prism_compounds(inchikey)
WHERE inchikey IS NOT NULL;
CREATE INDEX idx_prism_chembl ON prism_compounds(chembl_id)
WHERE chembl_id IS NOT NULL;
CREATE TABLE prism_sensitivity (
sensitivity_id INTEGER PRIMARY KEY AUTOINCREMENT,
compound_id INTEGER NOT NULL REFERENCES prism_compounds(compound_id),
cell_line_id INTEGER NOT NULL REFERENCES cell_lines(cell_line_id),
screen_type TEXT CHECK (screen_type IN ('primary', 'secondary')),
log_fold_change REAL,
auc REAL,
ic50 REAL,
ec50 REAL,
depmap_release TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE INDEX idx_prism_sens_compound ON prism_sensitivity(compound_id);
CREATE INDEX idx_prism_sens_cell_line ON prism_sensitivity(cell_line_id);
-- Record migration
INSERT INTO schema_migrations (version) VALUES ('001');
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