Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 10,326 Bytes
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-- NegBioDB Schema v1.0
-- Migration: 001_initial_schema
-- Database: SQLite 3.35+
-- ============================================================
PRAGMA journal_mode = WAL;
PRAGMA foreign_keys = ON;
PRAGMA encoding = 'UTF-8';
-- ============================================================
-- COMMON LAYER
-- ============================================================
CREATE TABLE compounds (
compound_id INTEGER PRIMARY KEY AUTOINCREMENT,
canonical_smiles TEXT NOT NULL,
inchikey TEXT NOT NULL,
inchikey_connectivity TEXT NOT NULL,
inchi TEXT,
pubchem_cid INTEGER,
chembl_id TEXT,
bindingdb_id INTEGER,
molecular_weight REAL,
logp REAL,
hbd INTEGER,
hba INTEGER,
tpsa REAL,
rotatable_bonds INTEGER,
num_heavy_atoms INTEGER,
qed REAL,
pains_alert INTEGER DEFAULT 0,
aggregator_alert INTEGER DEFAULT 0,
lipinski_violations 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 UNIQUE INDEX idx_compounds_inchikey ON compounds(inchikey);
CREATE INDEX idx_compounds_connectivity ON compounds(inchikey_connectivity);
CREATE INDEX idx_compounds_pubchem ON compounds(pubchem_cid) WHERE pubchem_cid IS NOT NULL;
CREATE INDEX idx_compounds_chembl ON compounds(chembl_id) WHERE chembl_id IS NOT NULL;
CREATE INDEX idx_compounds_smiles ON compounds(canonical_smiles);
CREATE TABLE targets (
target_id INTEGER PRIMARY KEY AUTOINCREMENT,
uniprot_accession TEXT NOT NULL,
uniprot_entry_name TEXT,
amino_acid_sequence TEXT,
sequence_length INTEGER,
chembl_target_id TEXT,
gene_symbol TEXT,
ncbi_gene_id INTEGER,
target_family TEXT,
target_subfamily TEXT,
dto_class TEXT,
development_level TEXT CHECK (development_level IN ('Tclin', 'Tchem', 'Tbio', 'Tdark')),
organism TEXT DEFAULT 'Homo sapiens',
taxonomy_id INTEGER DEFAULT 9606,
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 UNIQUE INDEX idx_targets_uniprot ON targets(uniprot_accession);
CREATE INDEX idx_targets_chembl ON targets(chembl_target_id) WHERE chembl_target_id IS NOT NULL;
CREATE INDEX idx_targets_gene ON targets(gene_symbol) WHERE gene_symbol IS NOT NULL;
CREATE INDEX idx_targets_family ON targets(target_family);
CREATE INDEX idx_targets_dev_level ON targets(development_level);
CREATE TABLE assays (
assay_id INTEGER PRIMARY KEY AUTOINCREMENT,
source_db TEXT NOT NULL CHECK (source_db IN (
'pubchem', 'chembl', 'bindingdb', 'literature', 'community')),
source_assay_id TEXT NOT NULL,
assay_type TEXT,
assay_format TEXT CHECK (assay_format IN (
'biochemical', 'cell-based', 'in_vivo', 'unknown')),
assay_technology TEXT,
detection_method TEXT,
screen_type TEXT CHECK (screen_type IN (
'primary_single_point', 'confirmatory_dose_response',
'counter_screen', 'orthogonal_assay',
'literature_assay', 'unknown')),
z_factor REAL,
ssmd REAL,
cell_line TEXT,
description TEXT,
pubmed_id INTEGER,
doi TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
CREATE UNIQUE INDEX idx_assays_source ON assays(source_db, source_assay_id);
CREATE INDEX idx_assays_format ON assays(assay_format);
CREATE INDEX idx_assays_screen ON assays(screen_type);
-- ============================================================
-- DTI DOMAIN LAYER
-- ============================================================
CREATE TABLE negative_results (
result_id INTEGER PRIMARY KEY AUTOINCREMENT,
compound_id INTEGER NOT NULL REFERENCES compounds(compound_id),
target_id INTEGER NOT NULL REFERENCES targets(target_id),
assay_id INTEGER REFERENCES assays(assay_id),
result_type TEXT NOT NULL CHECK (result_type IN (
'hard_negative', 'conditional_negative',
'methodological_negative', 'dose_time_negative',
'hypothesis_negative')),
confidence_tier TEXT NOT NULL CHECK (confidence_tier IN (
'gold', 'silver', 'bronze', 'copper')),
activity_type TEXT,
activity_value REAL,
activity_unit TEXT,
activity_relation TEXT DEFAULT '=',
pchembl_value REAL,
inactivity_threshold REAL,
inactivity_threshold_unit TEXT DEFAULT 'nM',
max_concentration_tested REAL,
num_replicates INTEGER,
species_tested TEXT DEFAULT 'Homo sapiens',
source_db TEXT NOT NULL,
source_record_id TEXT NOT NULL,
extraction_method TEXT NOT NULL CHECK (extraction_method IN (
'database_direct', 'text_mining',
'llm_extracted', 'community_submitted')),
curator_validated INTEGER DEFAULT 0,
publication_year INTEGER,
deposition_date 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_results_compound ON negative_results(compound_id);
CREATE INDEX idx_results_target ON negative_results(target_id);
CREATE INDEX idx_results_pair ON negative_results(compound_id, target_id);
CREATE INDEX idx_results_tier ON negative_results(confidence_tier);
CREATE INDEX idx_results_source ON negative_results(source_db);
CREATE INDEX idx_results_year ON negative_results(publication_year);
CREATE INDEX idx_results_type ON negative_results(result_type);
-- COALESCE handles NULL assay_id: SQLite treats NULL as distinct in UNIQUE indexes,
-- which would allow duplicate rows when assay_id is missing.
CREATE UNIQUE INDEX idx_results_unique_source ON negative_results(
compound_id, target_id, COALESCE(assay_id, -1), source_db, source_record_id);
CREATE TABLE dti_context (
result_id INTEGER PRIMARY KEY REFERENCES negative_results(result_id),
binding_site TEXT CHECK (binding_site IN (
'orthosteric', 'allosteric', 'unknown')),
selectivity_panel INTEGER DEFAULT 0,
counterpart_active INTEGER DEFAULT 0,
cell_permeability_issue INTEGER DEFAULT 0,
compound_solubility REAL,
compound_stability TEXT
);
-- ============================================================
-- AGGREGATION LAYER (for ML export)
-- ============================================================
CREATE TABLE compound_target_pairs (
pair_id INTEGER PRIMARY KEY AUTOINCREMENT,
compound_id INTEGER NOT NULL REFERENCES compounds(compound_id),
target_id INTEGER NOT NULL REFERENCES targets(target_id),
num_assays INTEGER NOT NULL,
num_sources INTEGER NOT NULL,
best_confidence TEXT NOT NULL,
best_result_type TEXT,
earliest_year INTEGER,
median_pchembl REAL,
min_activity_value REAL,
max_activity_value REAL,
has_conflicting_results INTEGER DEFAULT 0,
compound_degree INTEGER,
target_degree INTEGER,
UNIQUE(compound_id, target_id)
);
CREATE INDEX idx_pairs_compound ON compound_target_pairs(compound_id);
CREATE INDEX idx_pairs_target ON compound_target_pairs(target_id);
CREATE INDEX idx_pairs_confidence ON compound_target_pairs(best_confidence);
-- ============================================================
-- BENCHMARK / ML LAYER
-- ============================================================
CREATE TABLE split_definitions (
split_id INTEGER PRIMARY KEY AUTOINCREMENT,
split_name TEXT NOT NULL,
split_strategy TEXT NOT NULL CHECK (split_strategy IN (
'random', 'cold_compound', 'cold_target', 'cold_both',
'temporal', 'scaffold', '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 split_assignments (
pair_id INTEGER NOT NULL REFERENCES compound_target_pairs(pair_id),
split_id INTEGER NOT NULL REFERENCES split_definitions(split_id),
fold TEXT NOT NULL CHECK (fold IN ('train', 'val', 'test')),
PRIMARY KEY (pair_id, split_id)
);
CREATE INDEX idx_splits_fold ON split_assignments(split_id, fold);
-- ============================================================
-- METADATA LAYER
-- ============================================================
CREATE TABLE dataset_versions (
version_id INTEGER PRIMARY KEY AUTOINCREMENT,
version_tag TEXT NOT NULL UNIQUE,
description TEXT,
num_compounds INTEGER,
num_targets INTEGER,
num_pairs INTEGER,
num_results INTEGER,
schema_version TEXT,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
checksum_sha256 TEXT
);
CREATE TABLE schema_migrations (
migration_id INTEGER PRIMARY KEY AUTOINCREMENT,
version TEXT NOT NULL,
description TEXT,
applied_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
sql_up TEXT,
sql_down TEXT
);
-- Record this migration
INSERT INTO schema_migrations (version, description, sql_up)
VALUES ('001', 'Initial NegBioDB schema', 'Full DDL');
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