VAERS de-junking

README.md

Regexes to de-junk VAERS, removing nominal test results, maintenance and other non-symptomatic entities.

regexes.py

import re

p_normals = r".*negative$|.*\snormal$|.*(scopy|graphy|gram|metry|opsy)$|.*(count|percentage|level|test|assay|culture|X-ray|imaging|gradient|band(s)?|index|surface area|gas|scale|antibod(y|ies)|urine absent|Carotid pulse|partial pressure|time|P(C)?O2)$|Oxygen saturation$|End-tidal.*"
p_tests = r".*(ase|ose|ine|enzyme|in|ine|ines|ium|ol|ole|ate|lytes|ogen|gases|oids|ide|one|an|copper|iron)$|.*(level therapeutic)$|.*(globulin)\s.{1,2}$|Barium (swallow|enema)"
p_procedures = r".*(plasty|insertion|tomy|ery|puncture|therapy|treatment|tripsy|operation|repair|procedure|bypass|insertion|removal|graft|closure|implant|lavage|support|transplant|match|bridement|application|ablation)$|Incisional drainage$|.* stimulation$|Immunisation$"
p_normal_procedures = r"(Biopsy|pH|.* examination|X-ray|.* pulse|Blood|Electro(.*)gram|.* test(s)?|Echo(.*)gram|.*(scopy)|Cardiac (imaging|monitoring|ventriculogram)|Chromosomal|Carbohydrate antigen|Cell marker|.* examination|Computerised tomogram|Culture|.* evoked potential(s)?|Cytology|Doppler)(?!.*(abnormal|increased|decreased|depression|elevation|present|absent))"
p_managements = r"(Catheter|Device\).*|.* care$|.* user$|Cardiac pacemaker .*"
p_other_irrelevants = r"Blood group.*|Blood don(or|ation)$|Drug (abuse(r)?|dependence|screen).*|Elderly|Non-tobacco user|No adverse event"
p_covid_related = r".*COVID-19(prophylaxis|immunisation|screening)|Asymptomatic COVID-19"

p = re.compile("|".join([p_normals, p_tests, p_procedures, p_normal_procedures, p_other_irrelevants, p_covid_related]))