| """ |
| Clinical Acronym and Abbreviation Expansion Engine. |
| |
| Provides high-coverage clinical abbreviation normalization, context-sensitive |
| disambiguation, and query augmentation across SNOMED CT, LOINC, and RxNorm domains. |
| """ |
|
|
| import re |
| from typing import Dict, List, Optional, Tuple |
|
|
|
|
| |
| CLINICAL_ACRONYMS: Dict[str, str] = { |
| |
| "HTN": "Hypertension", |
| "CAD": "Coronary artery disease", |
| "CABG": "Coronary artery bypass graft", |
| "CHF": "Congestive heart failure", |
| "HF": "Heart failure", |
| "HFpEF": "Heart failure with preserved ejection fraction", |
| "HFrEF": "Heart failure with reduced ejection fraction", |
| "AF": "Atrial fibrillation", |
| "AFIB": "Atrial fibrillation", |
| "A-FIB": "Atrial fibrillation", |
| "AFL": "Atrial flutter", |
| "STEMI": "ST elevation myocardial infarction", |
| "NSTEMI": "Non-ST elevation myocardial infarction", |
| "SVT": "Supraventricular tachycardia", |
| "VT": "Ventricular tachycardia", |
| "VF": "Ventricular fibrillation", |
| "DVT": "Deep vein thrombosis", |
| "PAD": "Peripheral artery disease", |
| "PVD": "Peripheral vascular disease", |
| "AAA": "Abdominal aortic aneurysm", |
| "AS": "Aortic valve stenosis", |
| "AR": "Aortic regurgitation", |
| "MR": "Mitral regurgitation", |
|
|
| |
| "COPD": "Chronic obstructive pulmonary disease", |
| "SOB": "Shortness of breath", |
| "DOE": "Dyspnea on exertion", |
| "URI": "Upper respiratory infection", |
| "OSA": "Obstructive sleep apnea", |
| "ARDS": "Acute respiratory distress syndrome", |
| "PNA": "Pneumonia", |
| "CAP": "Community acquired pneumonia", |
| "HAP": "Hospital acquired pneumonia", |
| "CF": "Cystic fibrosis", |
| "ILD": "Interstitial lung disease", |
| "IPF": "Idiopathic pulmonary fibrosis", |
|
|
| |
| "DM": "Diabetes mellitus", |
| "DM1": "Type 1 diabetes mellitus", |
| "T1DM": "Type 1 diabetes mellitus", |
| "DM2": "Type 2 diabetes mellitus", |
| "T2DM": "Type 2 diabetes mellitus", |
| "DKA": "Diabetic ketoacidosis", |
| "HHS": "Hyperosmolar hyperglycemic state", |
| "HTG": "Hypertriglyceridemia", |
| "HLD": "Hyperlipidemia", |
| "PCOS": "Polycystic ovary syndrome", |
|
|
| |
| "AKI": "Acute kidney injury", |
| "CKD": "Chronic kidney disease", |
| "ESRD": "End stage renal disease", |
| "UTI": "Urinary tract infection", |
| "BPH": "Benign prostatic hyperplasia", |
| "ATN": "Acute tubular necrosis", |
| "GN": "Glomerulonephritis", |
|
|
| |
| "CVA": "Cerebrovascular accident", |
| "TIA": "Transient ischemic attack", |
| "ICH": "Intracerebral hemorrhage", |
| "SAH": "Subarachnoid hemorrhage", |
| "SDH": "Subdural hematoma", |
| "ALS": "Amyotrophic lateral sclerosis", |
| "PD": "Parkinson's disease", |
| "AD": "Alzheimer's disease", |
| "ICP": "Intracranial pressure", |
|
|
| |
| "GERD": "Gastroesophageal reflux disease", |
| "IBD": "Inflammatory bowel disease", |
| "IBS": "Irritable bowel syndrome", |
| "PUD": "Peptic ulcer disease", |
| "UGIB": "Upper gastrointestinal bleeding", |
| "LGIB": "Lower gastrointestinal bleeding", |
| "SBO": "Small bowel obstruction", |
| "LBO": "Large bowel obstruction", |
| "NASH": "Nonalcoholic steatohepatitis", |
| "NAFLD": "Nonalcoholic fatty liver disease", |
|
|
| |
| "RA": "Rheumatoid arthritis", |
| "OA": "Osteoarthritis", |
| "SLE": "Systemic lupus erythematosus", |
| "HIV": "Human immunodeficiency virus infection", |
| "AIDS": "Acquired immunodeficiency syndrome", |
| "TB": "Tuberculosis", |
| "MRSA": "Methicillin resistant Staphylococcus aureus", |
| "MSSA": "Methicillin susceptible Staphylococcus aureus", |
| "C. DIFF": "Clostridioides difficile infection", |
| "CDIFF": "Clostridioides difficile infection", |
|
|
| |
| "CBC": "Complete blood count", |
| "BMP": "Basic metabolic panel", |
| "CMP": "Comprehensive metabolic panel", |
| "LFT": "Liver function tests", |
| "HGB": "Hemoglobin", |
| "HB": "Hemoglobin", |
| "HCT": "Hematocrit", |
| "WBC": "White blood cell count", |
| "RBC": "Red blood cell count", |
| "PLT": "Platelet count", |
| "INR": "International normalized ratio", |
| "PT": "Prothrombin time", |
| "PTT": "Partial thromboplastin time", |
| "CR": "Creatinine", |
| "BUN": "Blood urea nitrogen", |
| "HBA1C": "Hemoglobin A1c", |
| "A1C": "Hemoglobin A1c", |
| "TSH": "Thyroid stimulating hormone", |
| "ESR": "Erythrocyte sedimentation rate", |
| "CRP": "C-reactive protein", |
| "BNP": "B-type natriuretic peptide", |
| "UA": "Urinalysis", |
|
|
| |
| "EGD": "Esophagogastroduodenoscopy", |
| "CXR": "Chest X-ray", |
| "CT": "Computed tomography", |
| "CTA": "Computed tomography angiography", |
| "MRI": "Magnetic resonance imaging", |
| "MRA": "Magnetic resonance angiography", |
| "ECHO": "Echocardiogram", |
| "EKG": "Electrocardiogram", |
| "ECG": "Electrocardiogram", |
| "US": "Ultrasound", |
| "LP": "Lumbar puncture", |
| } |
|
|
| |
| |
| CONTEXT_DISAMBIGUATION_RULES: Dict[str, List[Tuple[List[str], str]]] = { |
| "MS": [ |
| (["valve", "mitral", "murmur", "stenosis", "rheumatic", "cardiac", "heart"], "Mitral valve stenosis"), |
| (["sclerosis", "demyelinating", "relapse", "flare", "neurologic", "mri", "brain", "spine", "optic"], "Multiple sclerosis"), |
| (["mental", "status", "alert", "oriented", "confused"], "Mental status"), |
| ], |
| "MI": [ |
| (["chest", "pain", "troponin", "stemi", "nstemi", "cardiac", "coronary", "ecg", "ekg"], "Myocardial infarction"), |
| (["mitral", "insufficiency", "valve", "regurgitation", "murmur"], "Mitral valve insufficiency"), |
| ], |
| "PE": [ |
| (["chest", "pain", "shortness", "breath", "d-dimer", "cta", "thrombus", "embolism", "clot", "dvt", "lung"], "Pulmonary embolism"), |
| (["exam", "physical", "vital", "abdomen", "extremities", "heent", "neuro", "pupils", "clear"], "Physical examination"), |
| (["effusion", "pleural", "thoracentesis", "fluid"], "Pleural effusion"), |
| ], |
| "MR": [ |
| (["valve", "mitral", "regurgitation", "systolic", "murmur", "cardiac"], "Mitral regurgitation"), |
| (["retardation", "mental", "intellectual"], "Mental retardation"), |
| (["resonance", "magnetic", "scan", "imaging"], "Magnetic resonance"), |
| ], |
| "AS": [ |
| (["valve", "aortic", "stenosis", "systolic", "murmur", "cardiac", "tavr", "echo"], "Aortic valve stenosis"), |
| (["ankylosing", "spondylitis", "hla-b27", "back", "sacroiliac"], "Ankylosing spondylitis"), |
| ], |
| "RA": [ |
| (["arthritis", "rheumatoid", "joint", "swelling", "rf", "anti-ccp", "methotrexate"], "Rheumatoid arthritis"), |
| (["atrium", "right", "atrial", "cardiac", "enlargement"], "Right atrium"), |
| ], |
| "PT": [ |
| (["inr", "prothrombin", "coagulation", "warfarin", "bleeding"], "Prothrombin time"), |
| (["physical", "therapy", "rehab", "ambulation", "gait", "exercises"], "Physical therapy"), |
| (["patient"], "Patient"), |
| ], |
| } |
|
|
|
|
| class ClinicalAcronymExpander: |
| """ |
| Normalizes clinical shorthand and expands domain acronyms |
| into fully qualified medical terminology. |
| """ |
|
|
| def __init__(self, custom_dict: Optional[Dict[str, str]] = None): |
| self.lexicon = dict(CLINICAL_ACRONYMS) |
| if custom_dict: |
| self.lexicon.update(custom_dict) |
| self.context_rules = dict(CONTEXT_DISAMBIGUATION_RULES) |
|
|
| def disambiguate(self, acronym: str, context: Optional[str] = None) -> Optional[str]: |
| """ |
| Disambiguates an acronym using contextual note keywords if ambiguous. |
| """ |
| acr_upper = acronym.strip().upper() |
| if acr_upper in self.context_rules: |
| if context: |
| context_lower = context.lower() |
| best_expansion = None |
| max_matches = 0 |
| for keywords, expansion in self.context_rules[acr_upper]: |
| matches = sum(1 for kw in keywords if re.search(rf"\b{re.escape(kw)}\b", context_lower)) |
| if matches > max_matches: |
| max_matches = matches |
| best_expansion = expansion |
| if best_expansion and max_matches > 0: |
| return best_expansion |
| |
| return self.context_rules[acr_upper][0][1] |
|
|
| return self.lexicon.get(acr_upper, None) |
|
|
| def expand_mention(self, mention: str, context: Optional[str] = None) -> str: |
| """ |
| Expands a standalone clinical mention string if it is an acronym, |
| or returns the original mention if not recognized. |
| """ |
| cleaned = mention.strip() |
| cleaned_upper = cleaned.upper() |
|
|
| expansion = self.disambiguate(cleaned_upper, context) |
| if expansion: |
| return expansion |
| return cleaned |
|
|
| def get_search_queries(self, mention: str, context: Optional[str] = None) -> List[str]: |
| """ |
| Generates enriched search query representations for retrieval: |
| e.g. ['HTN', 'Hypertension', 'HTN (Hypertension)'] |
| """ |
| cleaned = mention.strip() |
| expansion = self.disambiguate(cleaned, context) |
|
|
| queries = [cleaned] |
| if expansion and expansion.lower() != cleaned.lower(): |
| queries.append(expansion) |
| queries.append(f"{cleaned} ({expansion})") |
| return list(dict.fromkeys(queries)) |
|
|
| def normalize_text_acronyms(self, text: str) -> str: |
| """ |
| Scans a clinical narrative for known unambiguous uppercase acronyms |
| and attaches their expansions inline: e.g. 'c/o SOB' -> 'c/o SOB (Shortness of breath)' |
| """ |
| def replace_fn(match): |
| word = match.group(0) |
| word_upper = word.upper() |
| if word_upper in self.lexicon and word_upper not in self.context_rules: |
| exp = self.lexicon[word_upper] |
| return f"{word} ({exp})" |
| return word |
|
|
| |
| pattern = r"\b[A-Z0-9\-\.]{2,6}\b" |
| return re.sub(pattern, replace_fn, text) |
|
|
