Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PR for adding sdtm->snomed mapping codes #204

Draft
wants to merge 18 commits into
base: main
Choose a base branch
from
Draft
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@
*.csv
*.xlsx

# except those storing codes
!fhir/codes/*.csv

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
Expand Down Expand Up @@ -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

Expand Down
4 changes: 4 additions & 0 deletions fhir/codes/LB_LBSPEC_snomed_codes.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
name,FHIR Resource,code_snomed,label_snomed
Arterial blood,,4635002,
Capillary blood,,31675002,
Venous blood,,53130003,
77 changes: 77 additions & 0 deletions fhir/codes/LB_LBTEST_snomed_codes.csv
Original file line number Diff line number Diff line change
@@ -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,,
9 changes: 9 additions & 0 deletions fhir/codes/RP_PO_mappings.csv
Original file line number Diff line number Diff line change
@@ -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
208 changes: 208 additions & 0 deletions fhir/codes/SA_complications_SS_codes.csv
Original file line number Diff line number Diff line change
@@ -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,,
Loading