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English
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Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
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File size: 10,249 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 | -- NegBioDB Clinical Trial Failure Domain — Initial Schema
-- Migration 001: Core tables for clinical trial failure tracking
--
-- Reuses Common Layer patterns from DTI domain:
-- - schema_migrations for version tracking
-- - dataset_versions for provenance
-- - Confidence tiers (gold/silver/bronze/copper)
-- - WAL journal mode + FK enforcement (set by ct_db.py)
-- ============================================================
-- Common Layer tables (same as DTI)
-- ============================================================
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: Clinical Trial Failure
-- ============================================================
-- Interventions (drugs, biologics, devices, etc.)
CREATE TABLE interventions (
intervention_id INTEGER PRIMARY KEY AUTOINCREMENT,
intervention_type TEXT NOT NULL CHECK (intervention_type IN (
'drug', 'biologic', 'device', 'procedure', 'behavioral',
'dietary', 'genetic', 'radiation', 'combination', 'other')),
intervention_name TEXT NOT NULL,
canonical_name TEXT,
drugbank_id TEXT,
pubchem_cid INTEGER,
chembl_id TEXT,
mesh_id TEXT,
atc_code TEXT,
mechanism_of_action TEXT,
canonical_smiles TEXT,
canonical_sequence 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'))
);
-- Conditions (diseases/indications)
CREATE TABLE conditions (
condition_id INTEGER PRIMARY KEY AUTOINCREMENT,
condition_name TEXT NOT NULL,
canonical_name TEXT,
mesh_id TEXT,
icd10_code TEXT,
icd11_code TEXT,
do_id TEXT,
therapeutic_area TEXT,
condition_class 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'))
);
-- Molecular targets (bridge to DTI domain)
CREATE TABLE intervention_targets (
intervention_id INTEGER NOT NULL REFERENCES interventions(intervention_id),
uniprot_accession TEXT NOT NULL,
gene_symbol TEXT,
target_role TEXT CHECK (target_role IN (
'primary', 'secondary', 'off_target')),
action_type TEXT,
source TEXT NOT NULL,
PRIMARY KEY (intervention_id, uniprot_accession)
);
-- Clinical trials
CREATE TABLE clinical_trials (
trial_id INTEGER PRIMARY KEY AUTOINCREMENT,
source_db TEXT NOT NULL CHECK (source_db IN (
'clinicaltrials_gov', 'eu_ctr', 'who_ictrp', 'literature')),
source_trial_id TEXT NOT NULL,
overall_status TEXT NOT NULL,
trial_phase TEXT CHECK (trial_phase IN (
'early_phase_1', 'phase_1', 'phase_1_2', 'phase_2',
'phase_2_3', 'phase_3', 'phase_4', 'not_applicable')),
study_type TEXT,
study_design TEXT,
blinding TEXT,
randomized INTEGER DEFAULT 0,
enrollment_target INTEGER,
enrollment_actual INTEGER,
primary_endpoint TEXT,
primary_endpoint_type TEXT,
control_type TEXT,
sponsor_type TEXT CHECK (sponsor_type IN (
'industry', 'academic', 'government', 'other')),
sponsor_name TEXT,
start_date TEXT,
primary_completion_date TEXT,
completion_date TEXT,
results_posted_date TEXT,
why_stopped TEXT,
has_results INTEGER DEFAULT 0,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
UNIQUE(source_db, source_trial_id)
);
-- Junction: trials <-> interventions (many-to-many)
CREATE TABLE trial_interventions (
trial_id INTEGER NOT NULL REFERENCES clinical_trials(trial_id),
intervention_id INTEGER NOT NULL REFERENCES interventions(intervention_id),
arm_group TEXT,
arm_role TEXT CHECK (arm_role IN (
'experimental', 'active_comparator', 'placebo_comparator', 'no_intervention')),
dose_regimen TEXT,
PRIMARY KEY (trial_id, intervention_id)
);
-- Junction: trials <-> conditions (many-to-many)
CREATE TABLE trial_conditions (
trial_id INTEGER NOT NULL REFERENCES clinical_trials(trial_id),
condition_id INTEGER NOT NULL REFERENCES conditions(condition_id),
PRIMARY KEY (trial_id, condition_id)
);
-- Junction: trials <-> publications
CREATE TABLE trial_publications (
trial_id INTEGER NOT NULL REFERENCES clinical_trials(trial_id),
pubmed_id INTEGER NOT NULL,
pub_type TEXT,
PRIMARY KEY (trial_id, pubmed_id)
);
-- Combination therapy decomposition
CREATE TABLE combination_components (
combination_id INTEGER NOT NULL REFERENCES interventions(intervention_id),
component_id INTEGER NOT NULL REFERENCES interventions(intervention_id),
role TEXT CHECK (role IN ('experimental', 'backbone', 'comparator')),
PRIMARY KEY (combination_id, component_id)
);
-- Trial failure results (core fact table)
CREATE TABLE trial_failure_results (
result_id INTEGER PRIMARY KEY AUTOINCREMENT,
intervention_id INTEGER NOT NULL REFERENCES interventions(intervention_id),
condition_id INTEGER NOT NULL REFERENCES conditions(condition_id),
trial_id INTEGER REFERENCES clinical_trials(trial_id),
-- Hierarchical failure classification
failure_category TEXT NOT NULL CHECK (failure_category IN (
'efficacy', 'safety', 'pharmacokinetic', 'enrollment',
'strategic', 'regulatory', 'design', 'other')),
failure_subcategory TEXT,
failure_detail TEXT,
-- Confidence tier (reused from DTI)
confidence_tier TEXT NOT NULL CHECK (confidence_tier IN (
'gold', 'silver', 'bronze', 'copper')),
-- Arm-level context (multi-arm trials)
arm_description TEXT,
arm_type TEXT CHECK (arm_type IN (
'experimental', 'active_comparator', 'placebo_comparator', 'overall')),
-- Quantitative outcome data
primary_endpoint_met INTEGER,
p_value_primary REAL,
effect_size REAL,
effect_size_type TEXT,
ci_lower REAL,
ci_upper REAL,
sample_size_treatment INTEGER,
sample_size_control INTEGER,
-- Safety signals
serious_adverse_events INTEGER,
deaths_treatment INTEGER,
deaths_control INTEGER,
dsmb_stopped INTEGER DEFAULT 0,
-- Phase context
highest_phase_reached TEXT,
prior_phase_succeeded INTEGER DEFAULT 0,
-- Provenance
source_db TEXT NOT NULL,
source_record_id TEXT NOT NULL,
extraction_method TEXT NOT NULL CHECK (extraction_method IN (
'database_direct', 'nlp_classified', 'text_mining',
'llm_extracted', 'community_submitted')),
curator_validated INTEGER DEFAULT 0,
publication_year INTEGER,
created_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now')),
updated_at TEXT DEFAULT (strftime('%Y-%m-%dT%H:%M:%SZ', 'now'))
);
-- Aggregation table
CREATE TABLE intervention_condition_pairs (
pair_id INTEGER PRIMARY KEY AUTOINCREMENT,
intervention_id INTEGER NOT NULL REFERENCES interventions(intervention_id),
condition_id INTEGER NOT NULL REFERENCES conditions(condition_id),
num_trials INTEGER NOT NULL,
num_sources INTEGER NOT NULL,
best_confidence TEXT NOT NULL,
primary_failure_category TEXT,
earliest_year INTEGER,
highest_phase_reached TEXT,
has_any_approval INTEGER DEFAULT 0,
intervention_degree INTEGER,
condition_degree INTEGER,
UNIQUE(intervention_id, condition_id)
);
-- Trial failure context (extended metadata)
CREATE TABLE trial_failure_context (
result_id INTEGER PRIMARY KEY REFERENCES trial_failure_results(result_id),
patient_population TEXT,
biomarker_stratified INTEGER DEFAULT 0,
companion_diagnostic TEXT,
prior_treatment_lines INTEGER,
comparator_drug TEXT,
geographic_regions TEXT,
regulatory_pathway TEXT,
genetic_evidence INTEGER DEFAULT 0,
class_effect_known INTEGER DEFAULT 0,
has_negbiodb_dti_data INTEGER DEFAULT 0
);
-- ============================================================
-- Indices for performance
-- ============================================================
CREATE INDEX idx_tfr_failure_category ON trial_failure_results(failure_category);
CREATE INDEX idx_tfr_confidence ON trial_failure_results(confidence_tier);
CREATE INDEX idx_tfr_intervention ON trial_failure_results(intervention_id);
CREATE INDEX idx_tfr_condition ON trial_failure_results(condition_id);
CREATE INDEX idx_tfr_trial ON trial_failure_results(trial_id);
CREATE INDEX idx_ct_status ON clinical_trials(overall_status);
CREATE INDEX idx_ct_phase ON clinical_trials(trial_phase);
CREATE INDEX idx_ct_completion ON clinical_trials(primary_completion_date);
CREATE INDEX idx_ct_source ON clinical_trials(source_db);
CREATE INDEX idx_interv_chembl ON interventions(chembl_id);
CREATE INDEX idx_interv_drugbank ON interventions(drugbank_id);
CREATE INDEX idx_interv_name ON interventions(intervention_name);
CREATE INDEX idx_cond_mesh ON conditions(mesh_id);
CREATE INDEX idx_cond_icd10 ON conditions(icd10_code);
CREATE INDEX idx_icp_intervention ON intervention_condition_pairs(intervention_id);
CREATE INDEX idx_icp_condition ON intervention_condition_pairs(condition_id);
-- Record migration
INSERT INTO schema_migrations (version) VALUES ('001');
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