PR for adding sdtm->snomed mapping codes

.gitignore

@@ -2,6 +2,9 @@
 *.csv
 *.xlsx
 
+# except those storing codes
+!fhir/codes/*.csv
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -143,11 +146,15 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+isaric-venv
 
 # Spyder project settings
 .spyderproject
 .spyproject
 
+# VScode project settings
+.vscode
+
 # Rope project settings
 .ropeproject
 

fhir/codes/LB_LBSPEC_snomed_codes.csv

@@ -0,0 +1,4 @@
+name,FHIR Resource,code_snomed,label_snomed
+Arterial blood,,4635002,
+Capillary blood,,31675002,
+Venous blood,,53130003,

fhir/codes/LB_LBTEST_snomed_codes.csv

@@ -0,0 +1,77 @@
+name,FHIR Resource,code_snomed,label_snomed,Comment
+Hemoglobin,,38082009,Hemoglobin (substance),
+Ery. Mean Corpuscular Hemoglobin,Observation,103205003,,Removed code
+Platelets,,16378004,,
+Erythrocytes,,41898006,,
+Leukocytes,,702962009,Population of all leukocytes in portion of fluid,
+Iron,,3829006,,
+Potassium,,88480006,,
+Lactate Dehydrogenase,,259319003,,
+Lymphocyte,,56972008,Population of all lymphocytes in portion of fluid,
+Monocytes,,55918008,Population of all monocytes in portion of fluid,
+Sodium,,39972003,,
+Neutrophils,,702967003,Population of all neutrophils in portion of fluid,
+Eosinophils,,702964005,Population of all eosinophils in portion of fluid,
+Eosinophils/Leukocytes,,702964005,Population of all eosinophils in portion of fluid,
+Basophils/Leukocytes,,702963004,Population of all basophils in portion of fluid,
+Lymphocytes/Leukocytes,,56972008,Population of all lymphocytes in portion of fluid,
+Monocytes/Leukocytes,,55918008,Population of all monocytes in portion of fluid,
+Neutrophils/Leukocytes,,702967003,Population of all neutrophils in portion of fluid,
+Hematocrit,,28317006,Hematocrit determination (procedure),
+Ery. Mean Corpuscular Volume,,104133003,Erythrocyte mean corpuscular volume determination,
+Ery. Mean Corpuscular HGB Concentration,,103206002,,Removed code
+C Reactive Protein,,61425002,,
+Erythrocyte Sedimentation Rate,,416838001,,
+Bilirubin,,79706000,,
+Glucose,,365812005,,
+Urea Nitrogen,,95971004,,
+Alanine Aminotransferase,,56935002,,
+Aspartate Aminotransferase,,26091008,,
+Creatinine,,15373003,,
+Creatine Kinase,,75828004,,
+Albumin,,52454007,,
+Amylase,,387031005,,
+Mean Platelet Volume,,75672003,,
+Platelet Hematocrit,,250314004,,
+Basophils,,702963004,Population of all basophils in portion of fluid,
+Hemoglobin A1C,,103232008,,Removed code
+Cholesterol,,84698008,,
+Urate,,365822004,Finding of urate level (finding),
+Prothrombin Time Actual/Control,,396451008,,
+Fibrinogen,,23295004,,
+Direct Bilirubin,,54462003,,
+Calcium,,5540006,,
+Gamma Glutamyl Transferase,,60153001,,
+Activated Partial Thromboplastin Time,,42525009,,
+D-Dimer,,25607008,,
+Ferritin,,32789000,,
+Thrombin Time,,55323000,,
+Magnesium,,72717003,,
+Base Excess,,129907001,,
+"Calcium, Ionized",,21616002,,
+"Calcium, Ionized pH Adjusted",,391551009,Serum ionised calcium (pH 7.4) level,
+Carboxyhemoglobin,,62576004,,
+Deoxyhemoglobin,,9865006,,
+Methemoglobin,,27840003,,
+Oxyhemoglobin,,80873004,,
+Carbon Dioxide,,31811003,,
+Lactic Acid,,77370004,,
+Bicarbonate,,68615006,,
+pH,Observation,81065003,pH - observation,
+Partial Pressure Carbon Dioxide,,250564007,,
+Partial Pressure Oxygen,,250546000,,
+Oxygen Saturation,,104847001,Oxygen saturation measurement (procedure),
+Troponin T,,102682001,,
+"Neutrophils, Segmented",,703496004,Population of all segmented neutrophils in portion of fluid (body structure),
+Troponin,,102680009,,
+Procalcitonin,,418752001,,
+Alkaline Phosphatase,,57056007,,
+"Glomerular Filtration Rate, Estimated",Observation,80274001,,
+Urea,,387092000,,
+Interleukin 6,,30965005,,
+Cortisol,,259344006,Free cortisol (substance),
+Troponin I Type 3,,102683006,Troponin I (substance),
+Prothrombin time,,396451008,,
+CD4,,24655002,,
+Troponin I,,102683006,,
+Activated PTT/Standard,,42525009,,

fhir/codes/RP_PO_mappings.csv

@@ -0,0 +1,9 @@
+name,code_snomed,nname_snomed,code_icd10,name_icd10,code_loinc,name_loinc
+Estimated gestational age,57036006,Fetal gestational age (observable entity),,,,
+Pregnancy outcome,3950001,Birth (finding),,,,
+Live birth,281050002,Livebirth (finding),,,,
+Still birth,237364002,Stillbirth (finding),,,,
+Pregnancy status,,,,,82810-3,Pregnancy status
+Pregnant,77386006,Pregnant (finding),,,LA15173-0,Pregnant
+Not pregnant,60001007,Not pregnant (finding),,,LA26683-5,Not pregnant
+Pregnancy status unknown,261665006,Unknown (qualifier value),,,LA4489-6,Unknown

fhir/codes/SA_complications_SS_codes.csv

@@ -0,0 +1,208 @@
+name,code_snomed,note_snomed,code_icd10,note_icd10
+ABDOMINAL PAIN,21522001,Abdominal pain,,
+ACUTE CARDIAC INJURY,,,,
+ACUTE GASTROENTERITIS,69776003,,,
+ACUTE KIDNEY INJURY,14669001,,,
+ALOPECIA,56317004,,,
+ALTERED CONSCIOUSNESS/CONFUSION,443371007, Decreased level of consciousness,,
+ANAEMIA,271737000,,,
+ANOREXIA,56882008,Anorexia nervosa (disorder),,
+APNOEA,1023001,,,
+ARDS,67782005,,,
+ASTHMA,195967001,Asthma,,
+ASYMPTOMATIC,,,,
+ATOPIC SYMPTOMS,,,,
+ATRIAL FIBRILLATION,49436004,,,
+AUTOIMMUNE DISEASE,85828009,,,
+BACTERAEMIA,5758002,Bacteremia,,
+BACTERIAL PNEUMONIA,53084003,Bacterial pneumonia,,
+BENIGN NEOPLASM,3898006,,,
+BLEEDING,131148009,Bleeding,,
+BRONCHIECTASIS,12295008,,,
+BRONCHIOLITIS,4120002,Bronchiolitis,,
+CARDIAC ARREST,410429000,Cardiac arrest,,
+CARDIAC ARRHYTHMIA,698247007,,,
+CARDIAC ISCHAEMIA,414545008,Ischemic heart disease,,
+CARDIOGENIC SHOCK,89138009,,,
+CARDIOMYOPATHY,85898001,Cardiomyopathy,,
+CHANGES IN MENSTRUATION,,,,
+CHEST PAIN,29857009,Chest pain,,
+CHRONIC CARDIAC DISEASE (NOT HYPERTENSION),128292002,Chronic disease of cardiovascular system (disorder),,
+CHRONIC GASTROINTESTINAL DISEASE,8493009,chronic gastritis,,
+CHRONIC HAEMATOLOGICAL DISEASE,398983000,Chronic disease of hematopoietic system,,
+CHRONIC KIDNEY DISEASE,709044004,Chronic kidney disease,,
+CHRONIC NEUROLOGICAL DISORDER,128283000,Chronic nervous system disorder,,
+CHRONIC PULMONARY DISEASE (NOT ASTHMA),17097001,Chronic disease of respiratory system,,
+CLINICALLY-DIAGNOSED COVID-19,840533007,Severe acute respiratory syndrome coronavirus 2,,
+CO- OR SECONDARY INFECTION,,,,
+COAGULATION DISORDER,64779008,Blood coagulation disorder,,
+COGNITIVE IMPAIRMENT,386806002,,,
+CONGENITAL HEART DISEASE,13213009,,,
+CONGESTIVE HEART FAILURE,42343007,Congestive heart failure,,
+CONJUNCTIVITIS,9826008,conjunctavitis,,
+CONSTIPATION,14760008,,,
+COUGH,49727002,Cough,,
+COUGH - NON-PRODUCTIVE,11833005,,,
+COUGH - PRODUCTIVE,28743005,,,
+COUGH - WITH HAEMOPTYSIS,66857006,,,
+COVID TOES,,,,
+COVID-19,840533007,Severe acute respiratory syndrome coronavirus 2,,
+COVID-19 SYMPTOMS,840533007,Severe acute respiratory syndrome coronavirus 2,,
+CRYPTOGENIC ORGANIZING PNEUMONIA (COP),719218000,Cryptogenic organizing pneumonia,,
+CYANOSIS,3415004,,,
+DEEP VEIN THROMBOSIS,128053003,,,
+DEHYDRATION,34095006,,,
+DEMENTIA,52448006,Dementia,,
+DIABETES MELLITUS - GESTATIONAL,11687002,Gestational diabetes mellitus (disorder),,
+DIABETES MELLITUS - TYPE 1,46635009,Diabetes mellitus type 1 (disorder),,
+DIABETES MELLITUS - TYPE 2,44054006,Diabetes mellitus type 2 (disorder),,
+DIABETES MELLITUS - TYPE NOT SPECIFIED,73211009,Diabetes mellitus (disorder),,
+DIABETIC KETOACIDOSIS,420422005,,,
+DIARRHOEA,62315008,Diarrhea,,
+DIFFICULTY EATING OR DRINKING,,,,
+DISSEMINATED INTRAVASCULAR COAGULATION,,,,
+DISTURBANCE IN ATTENTION,,,,
+DIZZINESS,404640003,,,
+DRY SKIN,52475004,,,
+EAR PAIN,301354004,,,
+ELEVATED BNP,681121000124101,,,
+ELEVATED TROPONIN,444931001,High troponin I level,,
+EMPYEMA,66696003,,,
+ENCEPHALOPATHY,81308009,,,
+ENDOCARDITIS,56819008,Endocarditis,,
+ENDOCARDITIS/MYOCARDITIS/PERICARDITIS,128998007,Inflammatory disorder of the cardiovascular system,,
+ERECTILE DYSFUNCTION,860914002,,,
+FAECAL INCONTINENCE,72042002,,,
+FAINTING/BLACKOUTS,271594007,,,
+FATIGUE/MALAISE,13791008,Asthenia,,
+FEVER/HISTORY OF FEVER,386661006,,,
+GASTRO-OESOPHAGEAL REFLUX DISEASE,235595009,,,
+GASTROINTESTINAL BLEEDING,74474003,,,
+GRUNTING,62085005,,,
+HAEMODYNAMIC DECOMPENSATION,,,,
+HAEMOGLOBINURIA,68600005,Hemoglobinuria (finding),,
+HEADACHE,25064002,Headache,,
+HEART FAILURE,84114007,,,
+HEMATO MALIGNANCIES,,,,
+HEMATO OTHER,,,,
+HEMATURIA,34436003,,,
+HEPATOMEGALY,80515008,,,
+HIV,86406008,Human immunodeficiency virus infection (disorder),,
+HIV/ACQUIRED IMMUNOSUPPRESSION,86406008,Human immunodeficiency virus infection (disorder),,
+HYPERGLYCAEMIA,80394007,,,
+HYPERTENSION,38341003,Hypertensive disorder,,
+HYPERTENSIVE CRISIS,706882009,,,
+HYPERTHYROIDISM,34486009,,,
+HYPOGLYCAEMIA,302866003,,,
+HYPOTENSION,45007003,,,
+HYPOTHYROIDISM,40930008,,,
+IMMUNOSUPPRESSION,234532001,,,
+INABILITY TO WALK,282145008,Unable to walk,,
+INCREASED THIRST,,,,
+IRRITABILITY,55929007,Feeling irritable (finding),,
+ISCHAEMIC HEART DISEASE,,,,
+ITCHY AND/OR RED EYES,,,,
+JAUNDICE,267030001,,,
+KIDNEY DISEASE,709044004,Chronic kidney disease,,
+LEUKOCYTURIA,,,,
+LIPID DISORDER,,,,
+LIVER DISEASE (SEVERITY NOT SPECIFIED),235856003,Disorder of liver,,
+LIVER DYSFUNCTION,235856003,Disorder of liver,,
+LOSS OF SENSATION,,,,
+LOST/ALTERED SENSE OF SMELL,44169009,Loss of sense of smell,,
+LOST/ALTERED SENSE OF TASTE,36955009,Loss of taste,,
+LUNG ABSCESSES,,,,
+LYMPHADENOPATHY,30746006,Lymphadenopathy,,
+MALARIA,61462000,,,
+MALIGNANT NEOPLASM,363346000,Malignant neoplastic disease,,
+MALIGNANT NEOPLASM NLP,363346000,Malignant neoplastic disease,,
+MALNUTRITION,2492009,Nutritional disorder (disorder),,
+MENINGITIS/ENCEPHALITIS,,,,
+MENTAL DISORDER,,,,
+MIGRAINE,37796009,Migraine,,
+MILD LIVER DISEASE,235856003,Disorder of liver,,
+MODERATE OR SEVERE LIVER DISEASE,197270009,Acute hepatic failure,,
+MOTOR OR SENSORY DEFICIT,,,,
+MOUTH ULCERS,26284000,,,
+MULTISYSTEM INFLAMMATORY SYNDROME,,,,
+MUSCLE ACHES/JOINT PAIN,,,,
+MUSCLE WEAKNESS,,,,
+MYOCARDIAL INFARCTION,22298006,Myocardial infarction,,
+MYOCARDITIS,50920009,Myocarditis,,
+MYOCARDITIS/PERICARDITIS,128998007,Inflammatory disorder of the cardiovascular system,,
+NASAL FLARING,248568003,,,
+NEOPLASM (UNSPECIFIED),108369006,Neoplasm (morphologic abnormality),,
+NEUROLOGICAL COMPLICATION,,,,
+NOSOCOMIAL SEPSIS,,,,
+OBESITY,414916001,Obesity (disorder),,
+OTHER,,,,
+OTHER ACUTE RESPIRATORY INFECTION,,,,
+PAIN (SITE NOT SPECIFIED),,,,
+PALLOR,1209208002,Pale face,,
+PALPITATIONS,80313002,,,
+PANCREATITIS,75694006,,,
+PARAESTHESIA,91019004,,,
+PEPTIC ULCER DISEASE,13200003,,,
+PERICARDITIS,3238004,,,
+PERIPHERAL VASCULAR DISEASE,,,,
+PHOTOPHOBIA,409668002,,,
+PLEURAL EFFUSION,60046008,Pleural effusion,,
+PLEURISY,196075003,,,
+PNEUMONIA,233604007,,,
+PNEUMOTHORAX,36118008,Pneumothorax,,
+POSSIBLE NEOPLASM (AMBIGUOUS) NLP,,,,
+POST SURGICAL COMPLICATIONS,385486001,postoperative complication,,
+PRESSURE ULCERS,19429009,Chronic ulcer of skin,,
+PROBLEMS PASSING URINE,,,,
+PROBLEMS SEEING,,,,
+PROBLEMS SLEEPING,,,,
+PROBLEMS SPEAKING OR COMMUNICATING,,,,
+PROBLEMS SWALLOWING OR CHEWING,288939007,Difficulty swallowing,,
+PROBLEMS WITH BALANCE,387603000,impairment of balance,,
+PROTEINURIA,29738008,,,
+PULMONARY EMBOLISM,59282003,Pulmonary embolism,,
+PULMONARY EMBOLISM OR DVT,128053003,Deep venous thrombosis,,
+QTC PROLONGATION,,,,
+RALES,48409008,,,
+RAPID HEART BEAT/PULSE,,,,
+RESPIRATORY SYMPTOMS NOT SPECIFIED,,,,
+RHABDOMYOLYSIS,240131006,,,
+RHEUMATOLOGICAL DISORDER,69896004,Rheumatoid arthritis disorder,,
+RUNNY NOSE,64531003,Nasal discharge,,
+SEIZURES,230433003,Isolated seizures (disorder),,
+SEPSIS,91302008,Sepsis,,
+SEPTIC SHOCK,76571007,,,
+SHOCK,27942005,Shock,,
+SHORTNESS OF BREATH,267036007,Dyspnea,,
+SINUS PAIN,4969004,sinus headache,,
+SKIN RASH,271807003,Eruption of skin,,
+SMOKING,77176002,Smoker,,
+SNEEZING,76067001,,,
+SOLID TUMOR,369757002,,,
+SORE THROAT,162397003,Pain in throat,,
+SPLENECTOMY,234319005,,,
+SPLENOMEGALY,16294009,,,
+SPONTANEOUS BRUISING,161887000,,,
+ST ELEVATION,76388001,,,
+STROKE,25133001,,,
+STROKE/TRANSIENT ISCHAEMIC ATTACK,,,,
+SUPRAVENTRICULAR ARRHYTHMIA,72654001,,,
+SUSPECTED NEOPLASM,,,,
+SWELLING,65124004,,,
+THROMBOEMBOLSIM (NOT PE OR DVT),371039008,Thromboembolic disorder,,
+THROMBOSIS,439127006,,,
+TINNITUS,60862001,,,
+TRANSIENT ISCHAEMIC ATTACK,266257000,,,
+TRANSPLANTATION,,,,
+TREMOR,26079004,,,
+TUBERCULOSIS,56717001,Tuberculosis,,
+UPPER RESPIRATORY TRACT SYMPTOMS (NOT SPECIFIED),,,,
+URINARY INCONTINENCE,165232002,,,
+URINARY TRACT INFECTION,68566005,,,
+USE OF ACCESSORY RESPIRATORY MUSCLES,,,,
+VENTILATOR-ASSOCIATED PNEUMONIA,429271009,,,
+VENTRICULAR ARRHYTHMIA,44103008,,,
+VIRAL PNEUMONIA,75570004,Viral pneumonia,,
+VOMITING/NAUSEA,16932000,Nausea and vomiting,,
+WEIGHT LOSS,816160009,,,
+WHEEZING,56018004,Wheezing,,