diff --git a/.gitignore b/.gitignore index 9b9a9ac..d4e1c4b 100644 --- a/.gitignore +++ b/.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 diff --git a/fhir/codes/LB_LBSPEC_snomed_codes.csv b/fhir/codes/LB_LBSPEC_snomed_codes.csv new file mode 100644 index 0000000..eb1c73d --- /dev/null +++ b/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, \ No newline at end of file diff --git a/fhir/codes/LB_LBTEST_snomed_codes.csv b/fhir/codes/LB_LBTEST_snomed_codes.csv new file mode 100644 index 0000000..9071738 --- /dev/null +++ b/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,, \ No newline at end of file diff --git a/fhir/codes/RP_PO_mappings.csv b/fhir/codes/RP_PO_mappings.csv new file mode 100644 index 0000000..16cbb7c --- /dev/null +++ b/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 diff --git a/fhir/codes/SA_complications_SS_codes.csv b/fhir/codes/SA_complications_SS_codes.csv new file mode 100644 index 0000000..df58ac0 --- /dev/null +++ b/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,, diff --git a/fhir/codes/SA_history_codes.csv b/fhir/codes/SA_history_codes.csv new file mode 100644 index 0000000..fca0bb9 --- /dev/null +++ b/fhir/codes/SA_history_codes.csv @@ -0,0 +1,175 @@ +name,code_snomed,note_snomed,code_icd10,note_icd10 +ABDOMINAL PAIN,21522001,Abdominal pain (finding),, +ACUTE GASTROENTERITIS,69776003,Acute gastroenteritis (disorder),, +ACUTE KIDNEY INJURY,14669001,Acute kidney injury (disorder),, +ALOPECIA,56317004,Alopecia (disorder),, +ALTERED CONSCIOUSNESS/CONFUSION,40917007,clouded consciousness,, +ANAEMIA,275538002,History of anemia,, +ANOREXIA,56882008,Anorexia nervosa (disorder),, +APNOEA,1023001,Apnea (finding),, +ARDS,67782005,Acute respiratory distress syndrome (disorder),, +ASPLENIA,707147002,Asplenia (disorder),, +ASTHMA,195967001,Asthma (disorder),, +ASYMPTOMATIC,,,, +ATOPIC SYMPTOMS,,,, +ATRIAL FIBRILLATION,312442005,H/O: atrial fibrillation,, +AUTOIMMUNE DISEASE,85828009,Autoimmune disease (disorder),, +BACTERAEMIA,5758002,Bacteremia (finding),, +BACTERIAL PNEUMONIA,53084003,,, +BENIGN NEOPLASM,3898006,"Neoplasm, benign (morphologic abnormality)",, +BLEEDING,,,, +BRONCHIECTASIS,12295008,Bronchiectasis (disorder),, +BRONCHIOLITIS,4120002,Bronchiolitis (disorder),, +CARDIAC ARREST,429007001,History of cardiac arrest,, +CARDIAC ARRHYTHMIA,131471000119104,History of cardiac arrhythmia,, +CARDIAC ISCHAEMIA,414795007,,, +CARDIOGENIC SHOCK,89138009,,, +CARDIOMYOPATHY,85898001,,, +CHEST PAIN,16089411000119109,History of chest pain,, +CHRONIC CARDIAC DISEASE (NOT HYPERTENSION),128238001,Chronic heart disease (disorder),, +CHRONIC GASTROINTESTINAL DISEASE,8493009,chronic gastritis,, +CHRONIC HAEMATOLOGICAL DISEASE,,,, +CHRONIC HEMATOLOGICAL DISEASE,,,, +CHRONIC INFECTION,,,, +CHRONIC INFLAMMATORY CONDITION (UNSPECIFIED),128294001,Chronic inflammatory disorder (disorder),, +CHRONIC KIDNEY DISEASE,709044004,Chronic kidney disease (disorder),, +CHRONIC METABOLIC/ENDOCRINE DISEASE,,,, +CHRONIC NEUROLOGICAL DISORDER,128283000,chronic nervous system disorder,, +CHRONIC PULMONARY DISEASE,17097001,Chronic disease of respiratory system (disorder),, +CHRONIC PULMONARY DISEASE (NOT ASTHMA),17097001,Chronic disease of respiratory system (disorder),, +CHRONIC VIRAL HEPATITIS,10295004,Chronic viral hepatitis (disorder),, +COAGULATION DISORDER,64779008,Blood coagulation disorder (disorder),, +COGNITIVE IMPAIRMENT,386806002,Impaired cognition (finding),, +CONGENITAL HEART DISEASE,13213009,Congenital heart disease (disorder),, +CONGESTIVE HEART FAILURE,42343007,Congestive heart failure (disorder),, +CONJUNCTIVITIS,9826008,Conjunctivitis (disorder),, +CONNECTIVE TISSUE DISEASE,105969002,Disorder of connective tissue (disorder),, +CONSTIPATION,14760008,Constipation (finding),, +COUGH,49727002,Cough (finding),, +COUGH - NON-PRODUCTIVE,11833005,Dry cough (finding),, +COUGH - PRODUCTIVE,28743005,Productive cough (finding),, +COUGH - WITH HAEMOPTYSIS,66857006,Hemoptysis (finding),, +COVID-19,,,, +CRYPTOGENIC ORGANIZING PNEUMONIA (COP),719218000,Cryptogenic organizing pneumonia (disorder),, +DEEP VEIN THROMBOSIS,128053003,Deep venous thrombosis (disorder),, +DEHYDRATION,34095006,Dehydration (disorder),, +DEMENTIA,52448006,Dementia (disorder),, +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,Ketoacidosis due to diabetes mellitus (disorder),, +DIARRHOEA,62315008,Diarrhea (finding),, +DIZZINESS,404640003,Dizziness (finding),, +DRY SKIN,52475004,Xeroderma (disorder),, +EAR PAIN,301354004,Pain of ear (finding),, +ELEVATED TROPONIN,444931001,High troponin I level,, +EMPYEMA,66696003,Empyema (morphologic abnormality),, +ENCEPHALOPATHY,81308009,Disorder of brain (disorder),, +ENDOCARDITIS,428287001,History of endocarditis,, +ERECTILE DYSFUNCTION,860914002,Erectile dysfunction (disorder),, +FAINTING/BLACKOUTS,271594007,Syncope (finding),, +FATIGUE/MALAISE,271795006,Malaise and fatigue (finding),, +FEVER/HISTORY OF FEVER,386661006,fever,, +GASTRO-OESOPHAGEAL REFLUX DISEASE,235595009,Gastroesophageal reflux disease (disorder),, +GASTROINTESTINAL BLEEDING,74474003,Gastrointestinal hemorrhage (disorder),, +HEADACHE,25064002,Headache (finding),, +HEART FAILURE,161505003,H/O: heart failure,, +HEMATO MALIGNANCIES,,,, +HEMATO OTHER,,,, +HEMATURIA,34436003,Blood in urine (finding),, +HEPATOMEGALY,80515008,Large liver (disorder),, +HIV,86406008,Human immunodeficiency virus infection (disorder),, +HIV/ACQUIRED IMMUNOSUPPRESSION,38013005,Immunosuppression (finding),, +HYPERGLYCAEMIA,80394007,Hyperglycemia (disorder),, +HYPERTENSION,38341003,"Hypertensive disorder, systemic arterial (disorder)",, +HYPERTHYROIDISM,34486009,Hyperthyroidism (disorder),, +HYPOGLYCAEMIA,302866003,Hypoglycemia (disorder),, +HYPOTENSION,,,, +HYPOTHYROIDISM,40930008,Hypothyroidism (disorder),, +IMMUNOSUPPRESSION,234532001,Immunodeficiency disorder (disorder),, +INABILITY TO WALK,,,, +ISCHAEMIC HEART DISEASE,,,, +KIDNEY DISEASE,,,, +LIPID DISORDER,267431006,Disorder of lipid metabolism (disorder),, +LIVER DISEASE (SEVERITY NOT SPECIFIED),235856003,Disorder of liver (disorder),, +LIVER DYSFUNCTION,,,, +LOST/ALTERED SENSE OF SMELL,44169009,Loss of sense of smell (finding),, +LOST/ALTERED SENSE OF TASTE,36955009,Loss of taste (finding),, +LYMPHADENOPATHY,429125006,History of lymphadenopathy,, +MALARIA,161416007,History of malaria,, +MALIGNANT NEOPLASM,1240414004,Malignant neoplasm,, +MALIGNANT NEOPLASM NLP,,,, +MALNUTRITION,2492009,Nutritional disorder (disorder),, +MENINGITIS/ENCEPHALITIS,,,, +MENTAL DISORDER,,,, +MIGRAINE,161481007,H/O: migraine,, +MILD LIVER DISEASE,328383001,,, +MODERATE OR SEVERE LIVER DISEASE,328383001,chronic liver disease,, +MOUTH ULCERS,26284000,Ulcer of mouth (disorder),, +MUSCLE ACHES/JOINT PAIN,,,, +MUSCLE WEAKNESS,,,, +MYOCARDIAL INFARCTION,22298006,Myocardial infarction (disorder),, +MYOCARDITIS,50920009,Myocarditis (disorder),, +NEOPLASM (UNSPECIFIED),108369006,Neoplasm,, +NEUROLOGICAL COMPLICATION,,,, +OBESITY,414916001,Obesity (disorder),, +OTHER,,,, +OTHER ACUTE RESPIRATORY INFECTION,,,, +PALPITATIONS,80313002,Palpitations (finding),, +PANCREATITIS,75694006,Pancreatitis (disorder),, +PARAESTHESIA,91019004,Paresthesia (finding),, +PEPTIC ULCER DISEASE,13200003,Peptic ulcer (disorder),, +PERICARDITIS,3238004,Pericarditis (disorder),, +PERIPHERAL VASCULAR DISEASE,,,, +PLEURAL EFFUSION,60046008,Pleural effusion (disorder),, +PLEURISY,196075003,Pleurisy (disorder),, +PNEUMONIA,161525004,History of pneumonia (situation),, +PNEUMOTHORAX,36118008,Pneumothorax (disorder),, +POSSIBLE NEOPLASM (AMBIGUOUS),,,, +POSSIBLE NEOPLASM (AMBIGUOUS) NLP,,,, +PRESSURE ULCERS,,,, +PREVIOUS COVID-19 INFECTION,,,, +PREVIOUS COVID-19 INFECTION - CONFIRMED BY TESTING,,,, +PREVIOUS COVID-19 INFECTION - NOT CONFIRMED BY TESTING,,,, +PROBLEMS SEEING,63102001,visual disturbance,, +PROBLEMS SLEEPING,301345002,Difficulty sleeping (finding),, +PROBLEMS WITH BALANCE,387603000,impairment of balance,, +PROTEINURIA,29738008,Proteinuria (finding),, +PULMONARY EMBOLISM,59282003,Pulmonary embolism (disorder),, +PULMONARY EMBOLISM OR DVT,,,, +RARE DISEASES AND INBORN ERRORS OF METABOLISM,,,, +RHABDOMYOLYSIS,240131006,Rhabdomyolysis (disorder),, +RHEUMATOLOGICAL DISORDER,,,, +RUNNY NOSE,64531003,nasal discharge,, +SEIZURES,91175000,Seizure (finding),, +SEPSIS,91302008,Sepsis (disorder),, +SEPTIC SHOCK,76571007,Septic shock (disorder),, +SEVERE LIVER DISEASE,328383001,chronic liver disease,, +SHORTNESS OF BREATH,267036007,Dyspnea (finding),, +SKIN RASH,271807003,Eruption of skin (disorder),, +SMOKING,,,, +SOLID ORGAN TRANSPLANT,,,, +SOLID TUMOR,369757002,solid tumor configuration,, +SORE THROAT,162388002,Has a sore throat (situation),, +SPLENECTOMY,,,, +SPLENOMEGALY,16294009,Splenomegaly (disorder),, +ST ELEVATION,76388001,ST segment elevation,, +STROKE,25133001,completed stroke,, +STROKE/TRANSIENT ISCHAEMIC ATTACK,,,, +SUBSTANCE USE DISORDER,66214007,substance abuse,, +SUSPECTED NEOPLASM,,,, +SWELLING,65124004,Swelling (finding),, +THROMBOSIS,439127006,Thrombosis (disorder),, +TINNITUS,60862001,Tinnitus (finding),, +TRANSIENT ISCHAEMIC ATTACK,266257000,Transient ischemic attack (disorder),, +TRANSPLANTATION,161663000,H/O: tissue/organ recipient,, +TREMOR,26079004,Tremor (finding),, +TUBERCULOSIS,56717001,Tuberculosis (disorder),, +UPPER RESPIRATORY TRACT SYMPTOMS (NOT SPECIFIED),,,, +URINARY TRACT INFECTION,68566005,Urinary tract infectious disease (disorder),, +VENTRICULAR ARRHYTHMIA,44103008,Ventricular arrhythmia (disorder),, +VIRAL PNEUMONIA,75570004,Viral pneumonia (disorder),, +VOMITING/NAUSEA,,,, +WEIGHT LOSS,816160009,Measured weight loss (observable entity),, +WHEEZING,56018004,Wheezing (finding),, diff --git a/fhir/codes/SDTM HO FHIR.csv b/fhir/codes/SDTM HO FHIR.csv new file mode 100644 index 0000000..e623256 --- /dev/null +++ b/fhir/codes/SDTM HO FHIR.csv @@ -0,0 +1,126 @@ +SDTM variable,Term,FHIR,code_snomed,label_snomed,comment +STUDYID,,,,, +DOMAIN,,not mapped,,, +USUBJID,,"subject +identifier",,, +HOSEQ,,not mapped,,, +HOREFID,,,,,identifies previous admissions for covid-19 +HOTERM,Consultation for reason related to COVID-19,"class = AMB (ambulatory) +http://terminology.hl7.org/CodeSystem/v3-ActCode",,,relates to follow-up only +HOTERM,,serviceType = 397 (Outpatients) http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Visited a doctor due to COVID-19,"class = AMB (ambulatory) +http://terminology.hl7.org/CodeSystem/v3-ActCode",,,relates to follow-up only +HOTERM,,serviceType = 324 (Doctors) http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Visited a Healthcare Centre Due to COVID-19,"class = AMB (ambulatory) +http://terminology.hl7.org/CodeSystem/v3-ActCode",,,relates to follow-up only +HOTERM,,serviceType = 397 (Outpatients) http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Admission to Hospital Due to COVID-19,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",32485007,Hospital admission (procedure), +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Hospital Admission,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",32485007,Hospital admission (procedure),relates only to previous admissions for covid-19 9130008 Previous (qualifier value) could be added somewhere +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,,reason.use = AD (Admitting Diagnosis) http://hl7.org/fhir/encounter-reason-use,,, +HOTERM,,diagnosis.condition,840539006,Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder), +HOTERM,HOSPITALIZATION,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",32485007,Hospital admission (procedure), +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Hospitalization Due to COVID-19,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode +serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type +reason.use = AD (Admitting Diagnosis) http://hl7.org/fhir/encounter-reason-use",32485007,Hospital admission (procedure),relates to follow-up only +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,,reason.use = AD (Admitting Diagnosis) http://hl7.org/fhir/encounter-reason-use,,, +HOTERM,,diagnosis.condition,840539006,Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder), +HOTERM,Hospitalization due to new COVID-19 infection,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",32485007,Hospital admission (procedure),relates to follow-up only +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,,reason.use = AD (Admitting Diagnosis) http://hl7.org/fhir/encounter-reason-use,,, +HOTERM,,diagnosis.condition,840539006,Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder), +HOTERM,Hospitalization with COVID-19 or Diagnosed with COVID19 during a hospital stay,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",32485007,Hospital admission (procedure), +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Hospitalization With COVID-19 or Diagnosed With COVID-19 During a Hospital Stay,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",32485007,Hospital admission (procedure),relates to follow-up only +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Re-Admission to Hospital or Health Facility,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",417005,Hospital re-admission (procedure),"not sure whether admission.ReAdmission = R (Re-admission indicator) makes sense to use here +http://terminology.hl7.org/CodeSystem/v2-0092" +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Re-admitted to hospital or health facility,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",417005,Hospital re-admission (procedure),"not sure whether admission.ReAdmission = R (Re-admission indicator) makes sense to use here +http://terminology.hl7.org/CodeSystem/v2-0092" +HOTERM,,serviceType = 557 Inpatients http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Transfer to another healthcare facility,,19712007,"Patient transfer, to another health care facility", +HOTERM,Transfer to other facility,,19712007,"Patient transfer, to another health care facility", +HOTERM,Transfer to the Health District,,19712007,"Patient transfer, to another health care facility", +HOTERM,TRANSFERRED TO OTHER FACILITY,,19712007,"Patient transfer, to another health care facility", +HOTERM,Admission to Intensive Care (ICU/ITU),"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",305351004,Admission to intensive care unit,"additional snomed mapping to class or type +Pediatric Intensive Care Medicine code 198 also available for those studies where we know were pediatric focussed" +HOTERM,,serviceType = 174 Intensive Care Medicine http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Admitted to intensive care (ICU/ITU),"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",305351004,Admission to intensive care unit,additional snomed mapping to class or type +HOTERM,,serviceType = 174 Intensive Care Medicine http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,ICU OR HIGH DEPENDENCY UNIT,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",305351004,Admission to intensive care unit,additional snomed mapping to class or type +HOTERM,,serviceType = 174 Intensive Care Medicine http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,ICU or High Dependency Unit admission,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",305351004,Admission to intensive care unit,additional snomed mapping to class or type +HOTERM,,serviceType = 174 Intensive Care Medicine http://hl7.org/fhir/ValueSet/service-type,,, +HOTERM,Current admission to ICU/ITU/IMC/HDU,"class = IMP (inpatient encounter) +http://terminology.hl7.org/CodeSystem/v3-ActCode",305351004,Admission to intensive care unit,additional snomed mapping to class or type +HOTERM,,serviceType = 174 Intensive Care Medicine http://hl7.org/fhir/ValueSet/service-type,,, +HODECOD,,"not mapped, HOTERM used for more granularity",,, +HOCAT,,"not mapped, only identifies previous admissions, HOREFID can be used as has an order number included",,, +HOPRESP,,not mapped,,, +HOOCCUR,Y,status,373066001,Yes (qualifier value),FHIR terminology from http://hl7.org/fhir/encounter-status; in-progress | discharged | completed | unknown could be used. Cancelled (failed) and discontinued (abandoned) exist for possibilities for 'N' responses but don't really make sense with our data +,N,status,373067005,No (qualifier value) , +,U,status,261665006,Unknown (qualifier value), +,NA,status,385432009,Not applicable (qualifier value), +HOSTAT,,HOSTAT = not done can be dropped,,, +HOREASND,,"relates to HOSTAT, rows dropped",,, +VISITNUM,,,,,"how to distinguish multiple events with no dates e.g. CVLYDZL patient with 15 rows of Hospitalisation collected as visit days 1-15 each indicating Y +can give a duration from the known data but don't know when pt was discharged and have no dates for actualPeriod" +VISIT,,,,, +VISITDY,,,,, +HOPATT,,,,,number of occurrences of consultations with GP number of readmissions (follow up only incl freestanding) +HODTC,,,,, +HOSTDTC,,actualPeriod,,,no dates for any previous admissions +HOENDTC,,actualPeriod,,, +HODY,,"not mapped, dates used",,, +HOSTDY,,"not mapped, dates used",,, +HOENDY,,"not mapped, dates used",,, +HODUR,,actualPeriod,,,can be used to calculate actualPeriod if one of HOSTDTC or HOENDTC is not provided but HODUR is present +HOTPT,,,,,identifies data collected during follow up +HOTPTREF,,,,,identifies data collected during follow up +HOSTRF,,"not mapped, previous admissions",,, +HOEVINTX,,,,,how to represent different time periods from data capture? +HOCDSTDY,,,,, +HODISOUT,"HOME, SELF CARE","dischargeDisposition = home (Home) +http://terminology.hl7.org/CodeSystem/discharge-disposition",,, +HODISOUT,EXPIRED IN A MEDICAL FACILITY,"dischargeDisposition = exp (Expired) +http://terminology.hl7.org/CodeSystem/discharge-disposition",,, +HODISOUT,SHORT TERM GENERAL HOSPITAL,"dischargeDisposition = other-hcf (Other healthcare facility) +http://terminology.hl7.org/CodeSystem/discharge-disposition",,, +HODISOUT,HOSPICE - MEDICAL FACILITY,"dischargeDisposition = hosp (Hospice) +http://terminology.hl7.org/CodeSystem/discharge-disposition",,, +HODISOUT,INSTITUTION NOT DEFINED,"dischargeDisposition = other-hcf (Other healthcare facility) +http://terminology.hl7.org/CodeSystem/discharge-disposition",,, +HODISOUT,LEFT AGAINST MEDICAL ADVICE OR DISCONTINUED CARE,"dischargeDisposition = aadvice (Left against advice) +http://terminology.hl7.org/CodeSystem/discharge-disposition",,, +HODISOUT,UNKNOWN,,261665006,Unknown (qualifier value), +SELFCARE,BETTER THAN BEFORE ILLNESS,"Observation.category = social-history +effectiveDateTime = HODTC",284773001,Ability to perform personal care activity (observable entity), +SELFCARE,,Observation.valueCodeableConcept,442387004,Increased relative to previous (qualifier value) , +SELFCARE,WORSE THAN BEFORE ILLNESS ,"Observation.category = social-history +effectiveDateTime = HODTC",284773001,Ability to perform personal care activity (observable entity), +SELFCARE,,Observation.valueCodeableConcept,442474009,Decreased relative to previous (qualifier value) , +SELFCARE,SAME AS BEFORE ILLNESS,"Observation.category = social-history +effectiveDateTime = HODTC",284773001,Ability to perform personal care activity (observable entity), +SELFCARE,,Observation.valueCodeableConcept,385630006,Maintained (qualifier value), +SELFCARE,UNKNOWN,"Observation.category = social-history +effectiveDateTime = HODTC",284773001,Ability to perform personal care activity (observable entity), +SELFCARE,,Observation.valueCodeableConcept,261665006,Unknown (qualifier value), +HOINDC,,diagnosis.condition,,,"not well completed, majority relate to ICU admission +can be COVID-19 for all previous admissions" diff --git a/fhir/codes/SDTM MB FHIR.csv b/fhir/codes/SDTM MB FHIR.csv new file mode 100644 index 0000000..1fbd3eb --- /dev/null +++ b/fhir/codes/SDTM MB FHIR.csv @@ -0,0 +1,167 @@ +SDTM variable,Term,FHIR resource,Element,Code,Display,System,code_snomed,label_snomed,code_loinc,label_loinc,IPS,PANGO,Comment, +STUDYID,,,,,,,,,,,,,, +DOMAIN,,not mapped,,,,,,,,,,,, +USUBJID,,Specimen,identifier,,,,,,,,,,Link to related result in observation, +,,Specimen,subject,,,,,,,,,,, +,,Observation,identifier,,,,,,,,,,Link to specimen id using derivedFrom, +,,Observation,subject,,,,,,,,,,, +,,Observation,status,final,Final,http://hl7.org/fhir/observation-status,,,,,,,, +,,Observation,category,laboratory,Laboratory,http://terminology.hl7.org/CodeSystem/observation-category,,,,,,,, +,,Observation,category,,,,116650008,Microbiology finding (navigational concept),LG51017-8,SARSCoV2 detection,,,additional category level to group microbiology results from other lab data LOINC variant type code is a member of this SARSCoV2 detection group, +MBSEQ,,not mapped,,,,,,,,,,,, +MBGRPID,,no data,,,,,,,,,,,, +MBREFID,,no data,,,,,,,,,,,, +MBTESTCD,SARSCOV2,Observation,code,,,,840533007,Severe acute respiratory syndrome coronavirus 2 (organism),,,X,,Where MBTSTDTL = DETECTION, +,SARSCOV2,Observation,code,,,,,,96741-4,SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing,,,Where MBTSTDTL = VARIANT TYPE, +,INFLUVIR,Observation,code,,,,55014007,Family Orthomyxoviridae (organism),,,X,,Where MBTSTDTL = DETECTION, +,SAR2AB,Observation,code,,,,840535000,Antibody to severe acute respiratory syndrome coronavirus 2 (substance),,,,,"Where MBTSTDTL = DETECTION +this is more lab test rather than microbiology so don't categorise as microbiology finding", +,CRONAVIR,Observation,code,,,,84101006,Human coronavirus (organism),,,X,,Where MBTSTDTL = DETECTION, +,OTHRDIND,,,,,,,,,,,,Where MBTSTDTL = DETECTION, +,MCORGIDN,,,,,,,,,,,,Where MBTSTDTL = DETECTION, +,PLSMDM,Observation,code,,,,34706006,Plasmodium (organism),,,X,,Where MBTSTDTL = DETECTION, +,PFALCIP,Observation,code,,,,30020004,Plasmodium falciparum (organism),,,X,,Where MBTSTDTL = DETECTION, +,OTHPHIND,,,,,,,,,,,,Where MBTSTDTL = DETECTION, +,SAR2AG,Observation,code,,,,840536004,Antigen of severe acute respiratory syndrome coronavirus 2 (substance),,,,,"Where MBTSTDTL = DETECTION +this is more lab test rather than microbiology so don't categorise as microbiology finding", +,HIV,Observation,code,,,,19030005,Human immunodeficiency virus (organism),,,X,,Where MBTSTDTL = DETECTION, +MBTEST,,mapped from MBTESTCD,,,,,,,,,,,, +MBMODIFY,,no data,,,,,,,,,,,, +MBTSTDTL,,,,,,,,,,,,,, +MBCAT,,,,,,,,,,,,,, +MBSCAT,,,,,,,,,,,,,, +MBORRES,,,,,,,,,,,,,, +MBORRESU,,,,,,,,,,,,,, +MBSTRESC,INCONCLUSIVE,Observation,valueCodeableConcept,,,,419984006,Inconclusive (qualifier value),,,,,"Where MBTSTDTL = DETECTION +IPS has results Presence Absence binding https://hl7.org/fhir/uv/ips/ValueSet-results-presence-absence-snomed-ct-ips-free-set.html", +,POSITIVE,Observation,valueCodeableConcept,,,,52101004,Present,,,X,,"Where MBTSTDTL = DETECTION +can also use 10828004 Positive (also IPS) or 260373001 Detected (IPS)", +,NEGATIVE,Observation,valueCodeableConcept,,,,2667000,Absent,,,X,,"Where MBTSTDTL = DETECTION +can also use 260385009 Negative (IPS) or 260415000 Not detected (IPS)", +,UNKNOWN,Observation,valueCodeableConcept,,,,261665006,Unknown (qualifier value),,,,,Where MBTSTDTL = DETECTION, +,INDETERMINATE,Observation,valueCodeableConcept,,,,280416009,Indeterminate result (qualifier value),,,,,Where MBTSTDTL = DETECTION, +,BETA - B.1.351,Observation,valueCodeableConcept,,,,,,LA31570-7,SARS-CoV-2 Beta variant (WHO),,B.1.351,"Where MBTSTDTL = VARIANT TYPE +use PANGO lineage code as per label in MBSTRESC reference https://cov-lineages.org/lineage_list.html", +,OMICRON - B.1.1.529,Observation,valueCodeableConcept,,,,,,LA33381-7,SARS-CoV-2 Omicron variant (WHO),,B.1.1.529,Where MBTSTDTL = VARIANT TYPE, +,DELTA - B.1.617.2,Observation,valueCodeableConcept,,,,,,LA32552-4,SARS-CoV-2 Delta variant (WHO),,B.1.617.2,Where MBTSTDTL = VARIANT TYPE, +,OMICRON,Observation,valueCodeableConcept,,,,,,LA33381-7,SARS-CoV-2 Omicron variant (WHO),,B.1.1.529,Where MBTSTDTL = VARIANT TYPE, +,ALPHA - B.1.1.7,Observation,valueCodeableConcept,,,,,,LA31569-9,SARS-CoV-2 Alpha variant (WHO),,B.1.1.7,Where MBTSTDTL = VARIANT TYPE, +,KAPPA - B.1.617.1,,,,,,,,,,,,"Where MBTSTDTL = VARIANT TYPE +does not appear in PANGO resource either kappa or B.1.617.1", +,UNKNOWN,Observation,valueCodeableConcept,,,,261665006,Unknown (qualifier value),,,,,Where MBTSTDTL = VARIANT TYPE, +,use Esteban list in ICC GitHub,,,,,,,,,,,,"Where MBTSTDTL = IDENTIFICATION +IPS has results.microorganism binding for name of microorganism https://hl7.org/fhir/uv/ips/ValueSet-results-microorganism-snomed-ct-ips-free-set.html (snomed codes)", +MBSTRESN,,,,,,,,,,,,,, +MBSTRESU,,,,,,,,,,,,,, +MBSTAT,,,,,,,,,,,,,, +MBREASND,,,,,,,,,,,,,, +MBNAM,,,,,,,,,,,,,, +MBSPEC,SWABBED MATERIAL,Specimen,type,,,,257261003,Swab (specimen),,,X,,"Only use if no detail provided in MBLOC for where swab was taken from +Can collection.bodySite be assigned to any of these confidently?", +,,Specimen,collection.method,,,,129323009,Scraping - action,,,X,,, +,bile,Specimen,type,BIFL,Bile Fluid,http://terminology.hl7.org/CodeSystem/v2-0487,119341000,Bile specimen (specimen),,,X,,, +,,Specimen,collection.method,,,,,,,,,,, +,BLOOD,Specimen,type,,,,119297000,Blood sample (specimen),,,X,,, +,,Specimen,collection.method,,,,129300006,Puncture - action,,,X,,, +,LAVAGE FLUID,Specimen,type,KELOI,Lavage,http://terminology.hl7.org/CodeSystem/v2-0487,440674008,Specimen obtained by lavage (specimen),,,,,IPS = Bronchoalveolar lavage fluid specimen 258607008, +,,Specimen,collection.method,,,,,,,,,,, +,SPUTUM,Specimen,type,SPT,Sputum,http://terminology.hl7.org/CodeSystem/v2-0487,119334006,Sputum sample (specimen),,,X,,or Coughed sputum specimen 119335007 (also IPS), +,,Specimen,collection.method,,,,386089008,Collection of coughed sputum,,,X,,, +,tracheal aspirate,Specimen,type,TASP,"Aspirate, Tracheal",http://terminology.hl7.org/CodeSystem/v2-0487,122877000,Upper respiratory fluid specimen obtained by tracheal aspiration (specimen),,,,,, +,,Specimen,collection.method,,,,129316008,Aspiration - action,,,X,,, +,op swab,Specimen,type,,,,4.61911E+14,Swab specimen from oropharynx (specimen),,,,,, +,,Specimen,collection.method,,,,129323009,Scraping - action,,,X,,, +,tissue,Specimen,type,TISS,Tissue,http://terminology.hl7.org/CodeSystem/v2-0487,119376003,Tissue specimen (specimen),,,X,,, +,,Specimen,collection.method,,,,129314006,Biopsy - action,,,X,,, +,rapid covid serology ovios,,,,,,,,,,,,, +,URINE,Specimen,type,UR,Urine,http://terminology.hl7.org/CodeSystem/v2-0487,122575003,Urine specimen (specimen),,,X,,, +,,Specimen,collection.method,,,,73416001,"Urine specimen collection, clean catch",,,X,,"also exists; Timed urine collection, Urine specimen collection, catheterized", +,oropharyngeal swab,Specimen,type,,,,4.61911E+14,Swab specimen from oropharynx (specimen),,,,,, +,,Specimen,collection.method,,,,129323009,Scraping - action,,,X,,, +,tracheal aspiration,Specimen,type,TASP,"Aspirate, Tracheal",http://terminology.hl7.org/CodeSystem/v2-0487,122877000,Upper respiratory fluid specimen obtained by tracheal aspiration (specimen),,,,,, +,,Specimen,collection.method,,,,129316008,Aspiration - action,,,X,,, +MBSPCCND,,no data - check complete file,,,,,,,,,,,, +MBLOC,NASAL CAVITY/NASOPHARYNX,Specimen,type,,,,,,,,,,Combine as multiple i.e. one set for nasal cavity one set for nasopharynx?, +,NASAL CAVITY/NASOPHARYNX/THROAT,Specimen,type,,,,,,,,,,, +,THROAT,Specimen,type,,,,258529004,Throat swab (specimen),,,,,When MBSPEC = SWABBED MATERIAL, +,LOWER RESPIRATORY SYSTEM,Specimen,type,,,,258606004,Lower respiratory tract specimen (specimen),,,,,, +,NASAL CAVITY/NASOPHARYNX AND THROAT,Specimen,type,,,,,,,,,,, +MBMETHOD,antibody rapid test,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,This is the parent of rapid antigen detection immunoassay. Rapid antibody test is a chromatographic immunoassay technique but this term not located in snomed, +,Confirmed by physician through CT scan,,,,,,,,,,,,CT scan only references whole body 169072007, +,COVID confirmed through CT scan,,,,,,,,,,,,CT scan only references whole body 169072007, +,covid rapid test,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,covid rtk antibody,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,covid-19 ag,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,covid-19 rapid serology,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,Ct scan,,,,,,,,,,,,CT scan only references whole body 169072007, +,dengu serology,,,,,,,,,,,,, +,"dengue igm, igg, ns1 antigen",,,,,,,,,,,,, +,dengue ns1 antigen,,,,,,,,,,,,, +,dengue serology,,,,,,,,,,,,, +,Drive through,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,gene xpert,Observation,method,,,,1156878000,Molecular nucleic acid amplification technique (qualifier value),,,,,, +,IMMUNOASSAY,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,lateral flow test,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,MICROBIAL CULTURE,Observation,method,,,,702658000,Microbial culture technique (qualifier value),,,,,, +,mtb genexpert,Observation,method,,,,1156878000,Molecular nucleic acid amplification technique (qualifier value),,,,,, +,"not sure, done in thompson hospital",,,,,,,,,,,,, +,nps for influenza pcr,Observation,method,,,,258066000,Polymerase chain reaction technique (qualifier value),,,,,, +,POLYMERASE CHAIN REACTION,Observation,method,,,,258066000,Polymerase chain reaction technique (qualifier value),,,,,, +,rapid covid serology ovios,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rapid antigen,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,rapid antigen test,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,rapid covid serology,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,RAPID IMMUNOASSAY,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rapid test,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rapid test kit,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rapid test kit for coid 119 antibody ,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk anitgen sars cov 2,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,rtk ab,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk ab sars cov 2,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk ag,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,rtk antibody,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk antibody ,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk antibody covid,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk antibody sars cov 2,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk antibody sars cov2,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk antibody sars-cov 2,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk antigen,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,rtk antobody,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,rtk-ag,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,rtk-antigen,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,Self testing kit,Observation,method,,,,1156860005,Rapid antigen detection immunoassay technique (qualifier value),,,,,, +,serology,,,,,,,,,,,,, +,serology covid 19,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,serology rapid test,Observation,method,,,,708099001,Rapid immunoassay technique (qualifier value),,,,,, +,UNKNOWN,,,,,,261665006,Unknown (qualifier value),,,,,, +VISITNUM,,,,,,,,,,,,,, +VISIT,,,,,,,,,,,,,, +VISITDY,,,,,,,,,,,,,, +EPOCH,,,,,,,,,,,,,, +MBDTC,,Specimen,collectedDateTime,,,,,,,,,,, +,,Observation,effectiveDateTime,,,,,,,,,,, +MBDY,,,,,,,,,,,,,, +MBTPT,,,,,,,,,,,,,, +MBTPTNUM,,,,,,,,,,,,,, +MBELTM,,,,,,,,,,,,,, +MBTPTREF,,,,,,,,,,,,,, +MBSTRF,,,,,,,,,,,,,, +MBEVINTX,DURING THIS ILLNESS EPISODE,,,,,,,,,,,,, +,WITHIN 7-10 DAYS OF FIRST BECOMING UNWELL,,,,,,,,,,,,, +,SINCE LAST FOLLOW-UP,,,,,,708353007,Since last encounter (qualifier value),,,,,, +,AT ANY OTHER TIME,,,,,,,,,,,,, +,BEFORE HOSPITAL ADMISSION,,,,,,281379000,Pre-admission (qualifier value),,,,,, +,AT ANY TIME DURING HOSPITALIZATION,,,,,,307168008,During admission (qualifier value),,,,,, +MBSTRTPT,,,,,,,,,,,,,, +MBSTTPT,,,,,,,,,,,,,, +MBCDSTDY,,,,,,,,,,,,,, +MBRPOC,,,,,,,,,,,,,, +,,,,,,,,,,,,,, +additional sample type/test type/pathogen type combined LOINC codes for SARS-CoV-2,,,,,,,,,96119-3,SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay,,,, +,,,,,,,,,94763-0,SARS-CoV-2 (COVID-19) [Presence] in Specimen by Organism specific culture,,,, +,,,,,,,,,94558-4,SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay,,,, +,,,,,,,,,97097-0,SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay,,,, +,,,,,,,,,98069-8,SARS-CoV-2 (COVID-19) Ab [Presence] in Saliva (oral fluid) by Rapid immunoassay,,,, +,,,,,,,,,94762-2,SARS-CoV-2 (COVID-19) Ab [Presence] in Serum or Plasma by Immunoassay,,,, +,,,,,,,,,95542-7,"SARS-CoV-2 (COVID-19) Ab [Presence] in Serum, Plasma or Blood by Rapid Immunoassay",,,, diff --git a/fhir/codes/SDTM PO FHIR.csv b/fhir/codes/SDTM PO FHIR.csv new file mode 100644 index 0000000..b8dce2d --- /dev/null +++ b/fhir/codes/SDTM PO FHIR.csv @@ -0,0 +1,37 @@ +SDTM variable,Term,FHIR resource,Data element,Code,Display,System,code_snomed,label_snomed,code_loinc,label_loinc,code_icd11,label_icd11,code_nci,label_nci,ucum_code,ucum_display,IG,comment +STUDYID,,,,,,,,,,,,,,,,,, +DOMAIN,,Observation,category,social-history,Social History,,,,,,,,,,,,,category not used in US PH +USUBJID,,Observation,subject,,,,,,,,,,,,,,, +POSEQ,,not mapped,,,,,,,,,,,,,,,, +POTERM,Born Alive | Live Birth,Observation,value,,,,281050002,Livebirth (finding),LA14270-5,Live birth,,,,,,,, +,Pregnancy,not mapped directly,,,,,,,,,,,,,,,, +,Stillbirth | Still Birth,Observation,value,,,,237364002,Stillbirth (finding),LA14271-3,Stillborn,,,,,,,, +,UNKNOWN,Observation,value,,,,261665006,Unknown (qualifier value),,,,,,,,,, +POMODIFY,{blank},not mapped,,,,,,,,,,,,,,,, +POCAT,PREGNANCY OUTCOME,Observation,code,,,,,,63893-2,Outcome of pregnancy,,,,,,,US PH, +,{blank},not mapped,,,,,,,,,,,,,,,, +POPRESP,{blank},not mapped,,,,,,,,,,,,,,,, +POOCCUR,{blank},not mapped,,,,,,,,,,,,,,,, +POSTAT,{blank},not mapped,,,,,,,,,,,,,,,, +POREASND,{blank},not mapped,,,,,,,,,,,,,,,, +VISITNUM,1,,,,,,,,,,,,,,,,, +,{blank},,,,,,,,,,,,,,,,, +VISIT,Day 0,,,,,,,,,,,,,,,,, +,Hospital Discharge,,,,,,,,,,,,,,,,, +,{blank},,,,,,,,,,,,,,,,, +VISITDY,1,,,,,,,,,,,,,,,,, +,{blank},,,,,,,,,,,,,,,,, +EPOCH,{blank},not mapped,,,,,,,,,,,,,,,, +PODTC,Date | DateTime,,,,,,,,,,,,,,,,, +POSTDTC,Date,Observation,effectiveDateTime,,,,,,,,,,,,,,, +POENDTC,Date,not mapped (same as POSTDTC),,,,,,,,,,,,,,,, +PODY,integer,not mapped,,,,,,,,,,,,,,,, +POSTDY,integer,,,,,,,,,,,,,,,,, +POENDY,integer,not mapped,,,,,,,,,,,,,,,, +POSTRF,{blank},not mapped,,,,,,,,,,,,,,,, +POENRF,{blank},not mapped,,,,,,,,,,,,,,,, +POEVINTX,{blank},not mapped,,,,,,,,,,,,,,,, +POFETNUM,{blank},not mapped,,,,,,,,,,,,,,,, +POFTINID,{blank},not mapped,,,,,,,,,,,,,,,, +POMODDLV,{blank},not mapped,,,,,,,,,,,,,,,, +POSETTNG,{blank},not mapped,,,,,,,,,,,,,,,, diff --git a/fhir/codes/SDTM RP FHIR.csv b/fhir/codes/SDTM RP FHIR.csv new file mode 100644 index 0000000..05ee393 --- /dev/null +++ b/fhir/codes/SDTM RP FHIR.csv @@ -0,0 +1,48 @@ +SDTM variable,Term,FHIR resource,Data element,Code,Display,System,code_snomed,label_snomed,code_loinc,label_loinc,code_icd11,label_icd11,code_nci,label_nci,ucum_code,ucum_display,IG,comment +STUDYID,,,,,,,,,,,,,,,,,, +DOMAIN,,Observation,category,social-history,Social History,http://terminology.hl7.org/CodeSystem/observation-category,,,,,,,,,,,GECCO,not required per IPS +USUBJID,,Observation,subject (reference Patient),,,,,,,,,,,,,,, +RPSEQ,integer,not mapped,,,,,,,,,,,,,,,, +RPTESTCD,PREGIND,mapped from RPTEST,,,,,,,,,,,,,,,, +,EGESTAGE,mapped from RPTEST,,,,,,,,,,,,,,,, +RPTEST,Pregnant Indicator,Observation,code,,,,,,82810-3,Pregnancy status,,,,,,,IPS | GECCO, +,Estimated Gestational Age,Observation,code,,,,57036006,Fetal gestational age (observable entity),49051-6,Gestational age in weeks,,,,,,,, +RPCAT,{blank},not mapped,,,,,,,,,,,,,,,, +RPSCAT,{blank},not mapped,,,,,,,,,,,,,,,, +RPORRES,Currently pregnant | Y | Yes,Observation,valueCodeableConcept,,,,77386006,Pregnant(finding),LA15173-0,Pregnant,,,,,,,IPS | GECCO, +,Don't know | Not known | U | Unknown,Observation,valueCodeableConcept,,,,261665006,Unknown (qualifier value),LA4489-6,Unknown,,,,,,,IPS | GECCO,"Loinc code mapped to Possible pregnancy in IPS IG, although mapped snomed code here appears invalid. Possible pregnancy (situation) 146799005 is a valid term and used in US Core" +,In the postpartum period,Observation,valueCodeableConcept,,,,60001007,Not pregnant (finding),LA26683-5,Not pregnant,,,,,,,,Indicate as post-partum elsewhere? +,N | No,Observation,valueCodeableConcept,,,,60001007,Not pregnant (finding),LA26683-5,Not pregnant,,,,,,,IPS | GECCO, +,N/A | NA | Not applicable | NC,,,,,,,,,,,,,,,,, +,Numerical (decimal | integer),,valueQuantity.value,,,,,,,,,,,,,,, +RPORRESU,WEEKS,Observation,valueQuantity.unit,,,,,,,,,,,,wk,weeks,, +RPSTRESC,Y,mapped from RPORRES,,,,,,,,,,,,,,,, +,N,mapped from RPORRES,,,,,,,,,,,,,,,, +,NA,mapped from RPORRES,,,,,,,,,,,,,,,, +,U,mapped from RPORRES,,,,,,,,,,,,,,,, +,Numerical (decimal | integer),mapped from RPORRES,,,,,,,,,,,,,,,, +RPSTRESN,Numerical (decimal | integer),mapped from RPORRES,,,,,,,,,,,,,,,, +RPSTRESU,WEEKS,mapped from RPORRESU,,,,,,,,,,,,,,,, +RPSTAT,NOT DONE,not mapped,,,,,,,,,,,,,,,,drop where indicated NOT DONE +,{blank},not mapped,,,,,,,,,,,,,,,, +RPREASND,MISSING IN DATABASE,not mapped,,,,,,,,,,,,,,,, +,NOT ASKED,not mapped,,,,,,,,,,,,,,,, +,{blank},not mapped,,,,,,,,,,,,,,,, +RPMETHOD,{blank},not mapped,,,,,,,,,,,,,,,, +VISITNUM,1,,,,,,,,,,,,,,,,, +VISIT,Day 0,,,,,,,,,,,,,,,,, +,Hospital Discharge,,,,,,,,,,,,,,,,, +VISITDY,1,,,,,,,,,,,,,,,,, +EPOCH,{blank},not mapped,,,,,,,,,,,,,,,, +RPDTC,date | dateTime,Observation,effectiveDateTime,,,,,,,,,,,,,,IPS | GECCO, +RPDY,integer,,,,,,,,,,,,,,,,, +RPDUR,{blank},not mapped,,,,,,,,,,,,,,,, +RPTPT,FOLLOW-UP,,,,,,,,,,,,,,,,, +,{blank},not mapped,,,,,,,,,,,,,,,, +RPTPTREF,ACUTE COVID-19 ILLNESS,,,,,,,,,,,,,,,,, +,{blank},not mapped,,,,,,,,,,,,,,,, +RPSTRF,{blank},not mapped,,,,,,,,,,,,,,,, +RPEVINTX,{blank},not mapped,,,,,,,,,,,,,,,, +RPSTRTPT,{blank},not mapped,,,,,,,,,,,,,,,, +RPSTTPT,{blank},not mapped,,,,,,,,,,,,,,,, +RPCDSTDY,{blank},not mapped,,,,,,,,,,,,,,,, diff --git a/fhir/codes/SDTM RS FHIR.csv b/fhir/codes/SDTM RS FHIR.csv new file mode 100644 index 0000000..30df790 --- /dev/null +++ b/fhir/codes/SDTM RS FHIR.csv @@ -0,0 +1,60 @@ +SDTM variable,Term,FHIR,Snomed,Snomed label,Loinc,Loinc label,NCI,NCI label +STUDYID,,Identifier for observation,,,,,, +STUDYID,,"status = final +http://hl7.org/fhir/observation-status",,,,,, +STUDYID,,"category = survey +http://terminology.hl7.org/CodeSystem/observation-category",,,,,, +DOMAIN,,Not mapped,,,,,, +USUBJID,,Subject,,,,,, +RSSEQ,,Not mapped,,,,,, +RSTESTCD,,Not mapped,,,,,, +RSTEST,APCH1-Total APACHE II Score,code,,,9264-3,Apache II score,, +RSTEST,AVPU01-Responsiveness,code,449159002,Alert voice pain unresponsive scale (assessment scale),67775-7,Level of responsiveness,, +RSTEST,BCS01-Total Score,code,,,,,, +RSTEST,CFS01-Total Score,code,763264000,Canadian Study of Health and Aging Clinical Frailty Scale score (observable entity),,,, +RSTEST,GCS01-Total Score,code,248241002,Glasgow coma score (observable entity),9269-2,Glasgow coma score total,, +RSTEST,MBLTY01-Best Physical Mobility,code,,,,,, +RSTEST,PELOD01-Score,code,,,,,, +RSTEST,PRISM01-Total Score,code,273683007,Pediatric risk of mortality (assessment scale),,,, +RSTEST,RASS01-Score,code,,,,,C171419,RASS - Score +RSTEST,SAPSII-Total Score,code,273812009,Simplified acute physiology scale II (assessment scale),,,, +RSTEST,SAS01-Score,code,,,,,C171420,SAS - Score +RSTEST,SOFA-Total Score,code,1187491009,Sequential Organ Failure Assessment score (observable entity),96790-1,SOFA Total Score,, +RSCAT,,Not mapped,,,,,, +RSSCAT,SIGNS AND SYMPTOMS AT HOSPITAL ADMISSION,additional category?,278307001,On admission (qualfier value),,,, +RSSCAT,SIGNS AND SYMPTOMS AT ICU ADMISSION,additional category?,737586005,Assesment for admission to adult intensive care (procedure),,,, +RSSCAT,SIGNS AND SYMPTOMS AT FOLLOW UP,additional category?,,,,,, +RSSCAT,{blank},additional category?,307168008,During admission (qualifier value),,,, +RSORRES,,"not mapped, all data present in RSSTRESC mapped",,,,,, +RSORRESU,,"no data, not mapped - to check full file",,,,,, +RSSTRESC,,valueInteger,,,,,, +RSSTRESC,ALERT,valueCodeableConcept,,,LA9340-6,Alert,, +RSSTRESC,VERBAL,valueCodeableConcept,,,LA17108-4,Verbal,, +RSSTRESC,PAINFUL,valueCodeableConcept,,,LA17107-6,Painful,, +RSSTRESC,UNRESPONSIVE,valueCodeableConcept,,,LA9343-0,Unresponsive,, +RSSTRESC,UNKNOWN,valueCodeableConcept,261665006,Unknown (qualifier value),,,, +RSSTRESN,,"not mapped, all data present in RSSTRESC mapped",,,,,, +RSSTRESU,,"no data, not mapped - to check full file",,,,,, +RSSTAT,,drop rows where RSSTAT = NOT DONE,,,,,, +RSREASND,,"associated with RSSTAT, dropped",,,,,, +VISITNUM,,"no data, not mapped - to check full file",,,,,, +VISIT,,"no data, not mapped - to check full file",,,,,, +VISITDY,,"no data, not mapped - to check full file",,,,,, +EPOCH,,"no data, not mapped - to check full file",,,,,, +RSDTC,,effectiveDateTime,,,,,, +RSDY,,"not mapped, date from RSDTC will be mapped as effectiveDateTime",,,,,, +RSTPT,FOLLOW-UP,,,,,,, +RSTPT,{blank},,,,,,, +RSTPTNUM,,"no data, not mapped - to check full file",,,,,, +RSTPTREF,ACUTE COVID-19 ILLNESS,,,,,,, +RSTPTREF,{blank},,,,,,, +RSSTRF,,"no data, not mapped - to check full file",,,,,, +RSEVINTX,00:00-24:00 ON DAY OF ASSESSMENT,accounted for by RSSCAT,,,,,, +RSEVINTX,WITHIN 24 HOURS OF ADMISSION,,,,,,, +RSEVINTX,WITHIN 24 HOURS OF HOSPITAL ADMISSION,,,,,,, +RSEVINTX,WITHIN 24HRS OF FIRST ICU ADMISSION,,,,,,, +RSEVINTX,{blank},,,,,,, +RSSTRTPT,,"no data, not mapped - to check full file",,,,,, +RSSTTPT,,"no data, not mapped - to check full file",,,,,, +RSCDSTDY,,study day of assessment - how to map?,,,,,, +RSRPOC,,"no data, not mapped - to check full file",,,,,, diff --git a/fhir/codes/SDTM SC FHIR.csv b/fhir/codes/SDTM SC FHIR.csv new file mode 100644 index 0000000..29d2c0a --- /dev/null +++ b/fhir/codes/SDTM SC FHIR.csv @@ -0,0 +1,52 @@ +SDTM variable,Term,FHIR,code_snomed,label_snomed,code_loinc,label_loinc,code_icd11,label_icd11,code_nci,label_nci,comment +STUDYID,,,,,,,,,,, +DOMAIN,,not mapped,,,,,,,,, +USUBJID,,"Observation.identifier +Observation.subject",,,,,,,,, +USUBJID,,"Observation.status = final +http://hl7.org/fhir/observation-status",,,,,,,,, +USUBJID,,"Observation.category = social-history +http://terminology.hl7.org/CodeSystem/observation-category",,,,,,,,, +SCSEQ,,not mapped,,,,,,,,, +SCTESTCD,,not mapped,,,,,,,,, +SCTEST,Appropriate Developmental Age Indicator,Observation.code,23397005,Normal growth and development for age (finding),,,,,,, +SCTEST,,,,,,,,,C171499,Appropriate Developmental Age Indicator,nci codes from https://ncim.nci.nih.gov/ +SCTEST,Appropriate Developmental Age Indicator??,Observation.code,23397005,Normal growth and development for age (finding),,,,,,, +SCTEST,,,,,,,,,C171499,Appropriate Developmental Age Indicator, +SCTEST,Breast Fed Indicator,Observation.code,,,77318-4,Is the patient breastfed,,,,, +SCTEST,Income Decile,,,,,,,,,, +SCTEST,Index of Multiple Deprivation Decile,,,,,,,,,, +SCTEST,Index of Multiple Deprivation Quintile,,,,,,,,,, +SCTEST,Index of Multiple Deprivation Rank,,,,,,,,,, +SCTEST,Infant Less Than One Year Indicator,Observation.code,,,,,,,C171513,Infant Less Than One Year Indicator, +SCTEST,Lower-Layer Super Output Area Code,,,,,,,,,, +SCTEST,Premature Birth Indicator,Observation.code,395507008,Premature infant (finding) - Finding of neonate,,,KA21.4Z,"Preterm newborn, unspecified",,, +SCMODIFY,,no data,,,,,,,,, +SCCAT,,no data,,,,,,,,, +SCSCAT,,no data,,,,,,,,, +SCORRES,Breastfeeding Discontinued,Observation.valueCodeableConcept,169746009,Breastfeeding stopped (finding),,,,,,,use for breastfeeding indicator for additional granularity +SCORRES,Currently Breastfed,Observation.valueCodeableConcept,413711008,Breastfeeding (infant) (observable entity),,,,,,, +SCORRES,N/A,Observation.valueCodeableConcept,385432009,Not applicable (qualifier value),,,,,,, +SCORRES,No,Observation.valueCodeableConcept,373067005,No (qualifier value),,,,,,, +SCORRES,Unknown,Observation.valueCodeableConcept,261665006,Unknown (qualifier value),,,,,,, +SCORRES,Yes,Observation.valueCodeableConcept,413711008,Breastfeeding (infant) (observable entity),,,,,,, +SCORRES,Yes - Breastfeeding Discontinued ,Observation.valueCodeableConcept,169746009,Breastfeeding stopped (finding),,,,,,, +SCORRES,Yes - Currently Breastfed,Observation.valueCodeableConcept,413711008,Breastfeeding (infant) (observable entity),,,,,,, +SCORRES,Yes - Currently Breastfeeding,Observation.valueCodeableConcept,413711008,Breastfeeding (infant) (observable entity),,,,,,, +SCORRES,Yes-currently,Observation.valueCodeableConcept,413711008,Breastfeeding (infant) (observable entity),,,,,,, +SCORRESU,,no data,,,,,,,,, +SCSTRESC,Y,Observation.valueCodeableConcept,373066001,Yes (qualifier value),,,,,,, +SCSTRESC,N,Observation.valueCodeableConcept,373067005,No (qualifier value),,,,,,, +SCSTRESC,U,Observation.valueCodeableConcept,261665006,Unknown (qualifier value),,,,,,, +SCSTRESC,NA,Observation.valueCodeableConcept,385432009,Not applicable (qualifier value),,,,,,, +SCSTRESN,,SCSTRESC/SCORRES can be used,,,,,,,,, +SCSTRESU,,no data,,,,,,,,, +SCSTAT,,no data,,,,,,,,, +SCREASND,,no data,,,,,,,,, +SCMETHOD,,no data,,,,,,,,, +VISITNUM,,no data,,,,,,,,, +VISIT,,no data,,,,,,,,, +VISITDY,,no data,,,,,,,,, +EPOCH,,no data,,,,,,,,, +SCDTC,,Observation.effectiveDateTime,,,,,,,,, +SCDY,,use SCDTC,,,,,,,,, diff --git a/fhir/codes/VS_mappings.csv b/fhir/codes/VS_mappings.csv new file mode 100644 index 0000000..5be2304 --- /dev/null +++ b/fhir/codes/VS_mappings.csv @@ -0,0 +1,16 @@ +name,code_snomed,nname_snomed,code_icd10,name_icd10 +Temperature,386725007,Body temperature (observable entity),, +Heart Rate,364075005,Heart rate (observable entity),, +Respiratory Rate,86290005,Respiratory rate (observable entity),, +Systolic Blood Pressure,271649006,Systolic blood pressure (observable entity),, +Diastolic Blood Pressure,271650006,Diastolic blood pressure (observable entity),, +Oxygen Saturation,104847001,Oxygen saturation measurement (procedure),, +Pulse Rate,78564009,Heart rate measured at systemic artery (observable entity),, +Mean Arterial Pressure,1285244000,Mean arterial pressure (observable entity),, +Height,1153637007,Body height (observable entity),, +Weight,248345008,Body weight (observable entity),, +Estimated Weight,,,,could use Estimated (qualifier value) 414135002 somehow along with Body weight code and/or loinc 8335-2 Body weight Estimated +Estimated Height,1162418000,Estimated body height (observable entity),, +Body Mass Index,162859006,Body mass index (observable entity),, +Birth Weight,47340003,Birth weight finding (finding),, +Capillary Refill Time,15527001,"Capillary filling, function (observable entity)",, diff --git a/fhir/ethnic_grouping_sdtm_isaric.py b/fhir/ethnic_grouping_sdtm_isaric.py new file mode 100644 index 0000000..a0443a0 --- /dev/null +++ b/fhir/ethnic_grouping_sdtm_isaric.py @@ -0,0 +1,259 @@ +ethnic_sdtm_isaric = [ + ( + "Arab", + [ + r"arab(?:ique|ic|e)?", + r"alg[e,é]ri(?:an|en|enne)", + r"comor[o,e]s", + "egyptian", + r"iraqi?", + r"leban(?:ese|on)", + r"palestin(?:a|e|ian)", + r"jordan(?:ia|ian)?", + r"maurit(?:ian|us)", + r"maro[c,cc,kk][o,a]?n?", + r"morr?occ?(?:o|an)", + r"middle\s?east(ern)?", + r"saudi\s?arabian", + r"sudan(ese)?", + r"syrian?", + r"tunisian?", + r"y[e,a]mani?", + ], + ), + ( + "Black", + [ + "black", + r"african?", + r"afro(-)?american", + r"afro(-)?caribe[e,a]n", + r"cape\s?verd(?:e|ean|ian)", + r"chan?d", + "creole", + r"east\s?african", + "ethiopian", + r"eritrean?", + "gambian", + "guinean", + "ivoirien", # cote d'ivoire + "kami", # tanzania + "kaapverdian", # cape verde + "liberia", + "madagascar", + "malagache", # madagascar + "mauritius", + "negro", + r"nigerian?", + "noir", + "pari", # sudan + r"senegal(?:ise|ese)?", + r"sierra leonn?e", + r"somalian?", + ], + ), + ( + "Central_Asian", + [ + "kazakhstan", + r"kyrgyz?(stan)?", + ], + ), + ( + "East_Asian", + [ + r"east[\s,_]?asian?" + r"amarel[a,o]", # "yellow", term in brazil for ethnic east asian + r"chin(?:a|ese)", + r"japan(ese)?", + "taiwanese", + "korean", + r"tibet(ian)?", + ], + ), + ( + "South_Asian", + [ + r"south[\s,_]?asian?", + r"afghan(istan)?", + r"banga?la?deshi?", + r"indian?", + r"nepa(?:l|ll)?(?:i|ese)?", + "maldivian", + r"pakistani?", + r"sri lankan?", + "agrawal", + "bish?w[o,a]karma", # nepali + "chauhan", + "chaurasia", + "chepang", # indian caste + "dalit", + "damai", # nepali caste + "dangi", + "danuwar", + "devi", + "gurung", # nepalese + "sinha", + "jain", # west india + "kathariya", # nepal + "kumal", # nepal + "kunwar", # nepalese/indian + "lama", # nepal + "lamgade", # nepal + "lepcha", # india + "magar", # nepal + "majhi", # nepal + "malik", # pakistani + "oriisa", # india + "parashar", + "pariyar", + "rana", # nepal, subgroup of tharu + "saru", + "sunar", + "thami", + ], + ), + ( + "South_East_Asian", + [ + r"sou?t?h[\s,_]?eas[t,e][\s,_]?asian?", + r"indon?es[i,e]an?", + r"malay(sian)?", + r"cambodian?", + r"brunei(an)?", + r"thai(land)?", + r"phill?ip[p,h]?in[e,o]s?", + r"fill?ipin[o,es]", + r"vietnam(ese)?", + r"mya[n,m]mar", + r"rohin?g?n?yan?", + r"bur(na)?m(?:a|ese)?", + "bajau", + "bidayuh", + "bugis", + r"cambodian?", + "dusun", # borneo + "iban", # malaysia + "kadazan", # malaysia + "kedayan", # brunei + "kemboja", + "melanau", # malaysia + "murut", # borneo + r"singapore(an)?", + "siamese", # thai + "laos", + "sarawak", + "suluk", + ], + ), + ( + "West_Asian", + [ + r"west(ern)?[\s,_]?asian?", + r"armenian?", + r"tur(?:c|key|que)", + r"turkis[h,k]", + r"tyrkia", + r"iran(?ese|ian)?", + r"azerbaijani?", + r"kurde?", + ], + ), + ( + "Latin_American", + [ + r"latino?[\s,_]?america(?:n|os)?", + "latine", + "antillean", + "barbados", + "caribbean" r"cura[ç,c]ao(an)?", + "chile", + r"columbian?", + "cuba", + "dominican", + "ecuador", + r"el\s?salvador", + "guyana", + r"ha[i,ï]ti(?:an|enne)?", + "martiniquaise", + r"pard[a,o]", # Brazilian for 'mixed origin' historically + r"peru(vian)?", + r"suri?nam(?:e|es|ese|esian)?", + "trinidad", + r"west\s?indies", + ], + ), + ( + "White", + [ + "white", + "caucasi[a,e]n", + "eur(?:opean|asian)", + r"alban(?:ise|ia|ian)", + r"american?", + "amerique", + r"austrian?", + r"bosnian?", + r"bulgar(?ian|ia|y)", + "british", + "canadian", + "cigano", # portuguese romani + r"croat(ian)?", + r"czech\s?republic", + "dutch", + r"finn(ish)?", + r"french", + r"german(ic)?", + r"georgian?", + "greek", + r"hungar(?:y|ian)", + "irish", + r"israeli", + r"ital(?:y|ian|iano)", + "jewish", + "mediterranean", + "macedonian", + "maltese", + "moldova", + "muldave", + "polish", + r"portug[u,e]?ese?", + r"rou?ma?(?:ni|nia|ian|nian)?", + r"russian?", + r"serbian?", + r"slovakian?", + "slovenia", + "spanish", + "ukrainian", + "juegoslavie", + r"yug[o,u]slav(?:ia|ian)?", + ], + ), + ( + "Oceania", + [ + r"cook islands?", + r"australian?", + r"new\s?zealand", + r"f[i,u]ji(an)?", + "guinee", + "micronesian", + "pacifica", + "samoan", + "niuean", # polynesian + "tongan", + "melanesian", + ], + )( + "Aboriginal_First_Nations_Indigenous", + [ + "aboriginal", + r"first[\s,_]?nations?", + "indigenous", + "maori", + "bajau", + "indigena", + "metis", + ], + ), +]