OpenSafety 🩺

OpenSafety is an open-source Pharmacovigilance (PV) AI toolkit that combines fine-tuned Small Language Models (SLMs) with deterministic MedDRA v28.0 ontology verification for:

1. Adverse Drug Reaction (ADR) Extraction from clinical narratives.
2. MedDRA Coding (LLT, Preferred Term, and Primary System Organ Class).
3. Regulatory Listedness Assessment against Reference Safety Information (RSI / Product Labels).

Installation

pip install opensafety

Quick Start

1. Instant MedDRA v28.0 Search & Coding

from opensafety import MedDRADatabase, HybridMedDRAMatcher

# 1. Connect to the indexed MedDRA database
db = MedDRADatabase("meddra.db")

# 2. Look up exact regulatory terms
res = db.search_term("Dry cough")
print(res[0]["pt_name"])  # "Cough"
print(res[0]["soc_name"]) # "Respiratory, thoracic and mediastinal disorders"

# 3. Fuzzy & colloquial matching from patient verbatims
matcher = HybridMedDRAMatcher("meddra.db")
matches = matcher.search("stomach ache", top_k=1)
print(matches[0]["pt_name"])  # "Abdominal pain upper"

2. End-to-End AI Pharmacovigilance Pipeline

from opensafety import OpenSafetyEngine

# Initialize the engine with your trained LoRA adapter and MedDRA database
engine = OpenSafetyEngine(
    adapter_path="opensafety_qwen_adapter",
    meddra_db_path="meddra.db"
)

# Analyze a raw clinical narrative
report = engine.analyze(
    drug="Atorvastatin",
    narrative="A 62-year-old female taking Atorvastatin 40mg daily developed acute muscle weakness and soreness in her calves.",
    rsi="Section 4.8 Undesirable Effects: Common: myalgia, arthralgia, pain in extremity, muscle spasms."
)

# Inspect verified regulatory output
for event in report.adverse_events:
    print(f"Verbatim: {event.verbatim}")
    print(f"MedDRA PT: {event.meddra_pt} (Code: {event.meddra_pt_code})")
    print(f"Primary SOC: {event.meddra_soc}")
    print(f"Listedness: {event.listedness.status}")
    print(f"Rationale: {event.listedness.rationale}")

Architecture: Hybrid Safety Engine

[ Clinical Narrative / Case Report ] + [ Reference Safety Info (RSI) ]
                                  │
                                  ▼
      Fine-Tuned Qwen 2.5 (1.5B) Pharmacovigilance SLM
                                  │
                                  ▼
                     Extracted Structured JSON
                                  │
                                  ▼
         Deterministic MedDRA v28.0 SQLite Verification
            (Zero hallucination, verified 8-digit codes)
                                  │
                                  ▼
              Validated ICH E2B(R3) Structured Report

License

Apache License 2.0. MedDRA is copyrighted by the International Council for Harmonisation (ICH) and maintained by MSSO.