diff --git a/_data/codelists/covid_impact_ccu02901_covid-19_pims-ts_ICD10.csv b/_data/codelists/covid_impact_ccu02901_covid-19_pims-ts_ICD10.csv new file mode 100644 index 00000000..f6ea8c72 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_covid-19_pims-ts_ICD10.csv @@ -0,0 +1,31 @@ +Phenotype,Terminology,Code,Description,Position,Filter +covid-19_pims-ts,ICD-10,U075,Emergency use of U07.5,Primary,Include +covid-19_pims-ts,ICD-10,U109,,Primary,Include +covid-19_pims-ts,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Primary,Include +covid-19_pims-ts,ICD-10,R65,Systemic Inflammatory Response Syndrome [SIRS],Primary,Include +covid-19_pims-ts,ICD-10,A01,Typhoid and paratyphoid fevers,Primary,Exclude +covid-19_pims-ts,ICD-10,A02,Other salmonella infections,Primary,Exclude +covid-19_pims-ts,ICD-10,A03,Shigellosis,Primary,Exclude +covid-19_pims-ts,ICD-10,A04,Other bacterial intestinal infections,Primary,Exclude +covid-19_pims-ts,ICD-10,A05,"Other bacterial foodborne intoxications, not elsewhere classified",Primary,Exclude +covid-19_pims-ts,ICD-10,A37,Whooping cough,Primary,Exclude +covid-19_pims-ts,ICD-10,A38,,Primary,Exclude +covid-19_pims-ts,ICD-10,A39,Meningococcal infection,Primary,Exclude +covid-19_pims-ts,ICD-10,A40,Streptococcal sepsis,Primary,Exclude +covid-19_pims-ts,ICD-10,A41,Other sepsis,Primary,Exclude +covid-19_pims-ts,ICD-10,B95,Streptococcus and staphylococcus as the cause of diseases classified to other chapters,Primary,Exclude +covid-19_pims-ts,ICD-10,U075,Emergency use of U07.5,Non-Primary,Include +covid-19_pims-ts,ICD-10,U109,,Non-Primary,Include +covid-19_pims-ts,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Non-Primary,Include +covid-19_pims-ts,ICD-10,R65,Systemic Inflammatory Response Syndrome [SIRS],Non-Primary,Include +covid-19_pims-ts,ICD-10,A01,Typhoid and paratyphoid fevers,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A02,Other salmonella infections,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A03,Shigellosis,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A04,Other bacterial intestinal infections,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A05,"Other bacterial foodborne intoxications, not elsewhere classified",Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A37,Whooping cough,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A38,,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A39,Meningococcal infection,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A40,Streptococcal sepsis,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,A41,Other sepsis,Non-Primary,Exclude +covid-19_pims-ts,ICD-10,B95,Streptococcus and staphylococcus as the cause of diseases classified to other chapters,Non-Primary,Exclude diff --git a/_data/codelists/covid_impact_ccu02901_covid-19_type_a1_ICD10.csv b/_data/codelists/covid_impact_ccu02901_covid-19_type_a1_ICD10.csv new file mode 100644 index 00000000..5fdd1d0f --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_covid-19_type_a1_ICD10.csv @@ -0,0 +1,5 @@ +Phenotype,Terminology,Code,Description,Position,Filter +covid-19_type_a1,ICD-10,U071,Emergency use of U07.1,Primary,Include +covid-19_type_a1,ICD-10,U072,Emergency use of U07.2,Primary,Include +covid-19_type_a1,ICD-10,U073,Emergency use of U07.3,Primary,Include +covid-19_type_a1,ICD-10,U074,Emergency use of U07.4,Primary,Include diff --git a/_data/codelists/covid_impact_ccu02901_covid-19_type_a2_ICD10.csv b/_data/codelists/covid_impact_ccu02901_covid-19_type_a2_ICD10.csv new file mode 100644 index 00000000..82864ac3 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_covid-19_type_a2_ICD10.csv @@ -0,0 +1,95 @@ +Phenotype,Terminology,Code,Description,Position,Filter +covid-19_type_a2,ICD-10,A084,"Viral intestinal infection, unspecified",Primary,Include +covid-19_type_a2,ICD-10,A083,Other viral enteritis,Primary,Include +covid-19_type_a2,ICD-10,A085,Other specified intestinal infections,Primary,Include +covid-19_type_a2,ICD-10,A090,Other and unspecified gastroenteritis and colitis of infectious origin,Primary,Include +covid-19_type_a2,ICD-10,A099,Gastroenteritis and colitis of unspecified origin,Primary,Include +covid-19_type_a2,ICD-10,A419,"Sepsis, unspecified",Primary,Include +covid-19_type_a2,ICD-10,B348,Other viral infections of unspecified site,Primary,Include +covid-19_type_a2,ICD-10,B309,"Viral conjunctivitis, unspecified",Primary,Include +covid-19_type_a2,ICD-10,B338,Other specified viral diseases,Primary,Include +covid-19_type_a2,ICD-10,B349,"Viral infection, unspecified",Primary,Include +covid-19_type_a2,ICD-10,B972,Coronavirus as the cause of diseases classified to other chapters,Primary,Include +covid-19_type_a2,ICD-10,B99,,Primary,Include +covid-19_type_a2,ICD-10,D762,"Haemophagocytic syndrome, infection-associated",Primary,Include +covid-19_type_a2,ICD-10,E86,,Primary,Include +covid-19_type_a2,ICD-10,E87,"Other disorders of fluid, electrolyte and acid-base balance",Primary,Include +covid-19_type_a2,ICD-10,H669,"Otitis media, unspecified",Primary,Include +covid-19_type_a2,ICD-10,I1254,,Primary,Include +covid-19_type_a2,ICD-10,I126,,Primary,Include +covid-19_type_a2,ICD-10,I1471,,Primary,Include +covid-19_type_a2,ICD-10,I254,Coronary artery aneurysm and dissection,Primary,Include +covid-19_type_a2,ICD-10,I26,Pulmonary embolism,Primary,Include +covid-19_type_a2,ICD-10,I288,Other specified diseases of pulmonary vessels,Primary,Include +covid-19_type_a2,ICD-10,I30,Acute pericarditis,Primary,Include +covid-19_type_a2,ICD-10,I31,Other diseases of pericardium,Primary,Include +covid-19_type_a2,ICD-10,I32,Pericarditis in diseases classified elsewhere,Primary,Include +covid-19_type_a2,ICD-10,I33,Acute and subacute endocarditis,Primary,Include +covid-19_type_a2,ICD-10,I40,Acute myocarditis,Primary,Include +covid-19_type_a2,ICD-10,I41,Myocarditis in diseases classified elsewhere,Primary,Include +covid-19_type_a2,ICD-10,I42,Cardiomyopathy,Primary,Include +covid-19_type_a2,ICD-10,I44,Atrioventricular and left bundle-branch block,Primary,Include +covid-19_type_a2,ICD-10,I45,Other conduction disorders,Primary,Include +covid-19_type_a2,ICD-10,I46,Cardiac arrest,Primary,Include +covid-19_type_a2,ICD-10,I47,Paroxysmal tachycardia,Primary,Include +covid-19_type_a2,ICD-10,I48,Atrial fibrillation and flutter,Primary,Include +covid-19_type_a2,ICD-10,I49,Other cardiac arrhythmias,Primary,Include +covid-19_type_a2,ICD-10,I50,Heart failure,Primary,Include +covid-19_type_a2,ICD-10,I51,Complications and ill-defined descriptions of heart disease,Primary,Include +covid-19_type_a2,ICD-10,I63,Cerebral infarction,Primary,Include +covid-19_type_a2,ICD-10,I65,"Occlusion and stenosis of precerebral arteries, not resulting in cerebral infarction",Primary,Include +covid-19_type_a2,ICD-10,I66,"Occlusion and stenosis of cerebral arteries, not resulting in cerebral infarction",Primary,Include +covid-19_type_a2,ICD-10,I67,Other cerebrovascular diseases,Primary,Include +covid-19_type_a2,ICD-10,I880,Nonspecific mesenteric lymphadenitis,Primary,Include +covid-19_type_a2,ICD-10,I9,,Primary,Include +covid-19_type_a2,ICD-10,J00,,Primary,Include +covid-19_type_a2,ICD-10,J01,Acute sinusitis,Primary,Include +covid-19_type_a2,ICD-10,J04,Acute laryngitis and tracheitis,Primary,Include +covid-19_type_a2,ICD-10,J05,Acute obstructive laryngitis [croup] and epiglottitis,Primary,Include +covid-19_type_a2,ICD-10,J06,Acute upper respiratory infections of multiple and unspecified sites,Primary,Include +covid-19_type_a2,ICD-10,J18,"Pneumonia, organism unspecified",Primary,Include +covid-19_type_a2,ICD-10,J22,,Primary,Include +covid-19_type_a2,ICD-10,J40,,Primary,Include +covid-19_type_a2,ICD-10,J80,,Primary,Include +covid-19_type_a2,ICD-10,J81,,Primary,Include +covid-19_type_a2,ICD-10,J83,,Primary,Include +covid-19_type_a2,ICD-10,J90,,Primary,Include +covid-19_type_a2,ICD-10,J93,Pneumothorax,Primary,Include +covid-19_type_a2,ICD-10,J96,"Respiratory failure, not elsewhere classified",Primary,Include +covid-19_type_a2,ICD-10,J98,Other respiratory disorders,Primary,Include +covid-19_type_a2,ICD-10,K297,"Gastritis, unspecified",Primary,Include +covid-19_type_a2,ICD-10,K529,"Noninfective gastroenteritis and colitis, unspecified",Primary,Include +covid-19_type_a2,ICD-10,M255,Pain in joint,Primary,Include +covid-19_type_a2,ICD-10,M791,Myalgia,Primary,Include +covid-19_type_a2,ICD-10,M796,Pain in limb,Primary,Include +covid-19_type_a2,ICD-10,N179,"Acute renal failure, unspecified",Primary,Include +covid-19_type_a2,ICD-10,P928,Other feeding problems of newborn,Primary,Include +covid-19_type_a2,ICD-10,P25,Interstitial emphysema and related conditions originating in the perinatal period,Primary,Include +covid-19_type_a2,ICD-10,P92,Feeding problems of newborn,Primary,Include +covid-19_type_a2,ICD-10,R0,,Primary,Include +covid-19_type_a2,ICD-10,R10,Abdominal and pelvic pain,Primary,Include +covid-19_type_a2,ICD-10,R11,,Primary,Include +covid-19_type_a2,ICD-10,R13,,Primary,Include +covid-19_type_a2,ICD-10,R17,,Primary,Include +covid-19_type_a2,ICD-10,R21,,Primary,Include +covid-19_type_a2,ICD-10,R25,Abnormal involuntary movements,Primary,Include +covid-19_type_a2,ICD-10,R26,Abnormalities of gait and mobility,Primary,Include +covid-19_type_a2,ICD-10,R27,Other lack of coordination,Primary,Include +covid-19_type_a2,ICD-10,R29,Other symptoms and signs involving the nervous and musculoskeletal systems,Primary,Include +covid-19_type_a2,ICD-10,R34,,Primary,Include +covid-19_type_a2,ICD-10,R40,"Somnolence, stupor and coma",Primary,Include +covid-19_type_a2,ICD-10,R41,Other symptoms and signs involving cognitive functions and awareness,Primary,Include +covid-19_type_a2,ICD-10,R42,,Primary,Include +covid-19_type_a2,ICD-10,R43,Disturbances of smell and taste,Primary,Include +covid-19_type_a2,ICD-10,R44,Other symptoms and signs involving general sensations and perceptions,Primary,Include +covid-19_type_a2,ICD-10,R47,"Speech disturbances, not elsewhere classified",Primary,Include +covid-19_type_a2,ICD-10,R5,,Primary,Include +covid-19_type_a2,ICD-10,R6,,Primary,Include +covid-19_type_a2,ICD-10,R768,Other specified abnormal immunological findings in serum,Primary,Include +covid-19_type_a2,ICD-10,R845,Abnormal findings in specimens from respiratory organs and thorax,Primary,Include +covid-19_type_a2,ICD-10,R89,"Abnormal findings in specimens from other organs, systems and tissues",Primary,Include +covid-19_type_a2,ICD-10,R90,Abnormal findings on diagnostic imaging of central nervous system,Primary,Include +covid-19_type_a2,ICD-10,R93,Abnormal findings on diagnostic imaging of other body structures,Primary,Include +covid-19_type_a2,ICD-10,R94,Abnormal results of function studies,Primary,Include +covid-19_type_a2,ICD-10,U049,"Severe acute respiratory syndrome [SARS], unspecified",Primary,Include +covid-19_type_a2,ICD-10,U070,Emergency use of U07.0,Primary,Include diff --git a/_data/codelists/covid_impact_ccu02901_covid-19_type_b1_ICD10.csv b/_data/codelists/covid_impact_ccu02901_covid-19_type_b1_ICD10.csv new file mode 100644 index 00000000..e6d53cb4 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_covid-19_type_b1_ICD10.csv @@ -0,0 +1,64 @@ +Phenotype,Terminology,Code,Description,Position,Filter +covid-19_type_b1,ICD-10,A40,Streptococcal sepsis,Primary,Include +covid-19_type_b1,ICD-10,A41,Other sepsis,Primary,Include +covid-19_type_b1,ICD-10,A483,Toxic shock syndrome,Primary,Include +covid-19_type_b1,ICD-10,A49,Bacterial infection of unspecified site,Primary,Include +covid-19_type_b1,ICD-10,A818,Other atypical virus infections of central nervous system,Primary,Include +covid-19_type_b1,ICD-10,A870,Enteroviral meningitis,Primary,Include +covid-19_type_b1,ICD-10,A878,Other viral meningitis,Primary,Include +covid-19_type_b1,ICD-10,A89,,Primary,Include +covid-19_type_b1,ICD-10,A858,Other specified viral encephalitis,Primary,Include +covid-19_type_b1,ICD-10,A86,,Primary,Include +covid-19_type_b1,ICD-10,A879,"Viral meningitis, unspecified",Primary,Include +covid-19_type_b1,ICD-10,B09,,Primary,Include +covid-19_type_b1,ICD-10,B34,Viral infection of unspecified site,Primary,Include +covid-19_type_b1,ICD-10,B95,Streptococcus and staphylococcus as the cause of diseases classified to other chapters,Primary,Include +covid-19_type_b1,ICD-10,B96,Other specified bacterial agents as the cause of diseases classified to other chapters,Primary,Include +covid-19_type_b1,ICD-10,B97,Viral agents as the cause of diseases classified to other chapters,Primary,Include +covid-19_type_b1,ICD-10,E10,Type 1 diabetes mellitus,Primary,Include +covid-19_type_b1,ICD-10,E11,Type 2 diabetes mellitus,Primary,Include +covid-19_type_b1,ICD-10,E14,Unspecified diabetes mellitus,Primary,Include +covid-19_type_b1,ICD-10,E16,Other disorders of pancreatic internal secretion,Primary,Include +covid-19_type_b1,ICD-10,G4,,Primary,Include +covid-19_type_b1,ICD-10,J02,Acute pharyngitis,Primary,Include +covid-19_type_b1,ICD-10,J03,Acute tonsillitis,Primary,Include +covid-19_type_b1,ICD-10,J09,,Primary,Include +covid-19_type_b1,ICD-10,J10,Influenza due to identified seasonal influenza virus,Primary,Include +covid-19_type_b1,ICD-10,J11,"Influenza, virus not identified",Primary,Include +covid-19_type_b1,ICD-10,J12,"Viral pneumonia, not elsewhere classified",Primary,Include +covid-19_type_b1,ICD-10,J13,,Primary,Include +covid-19_type_b1,ICD-10,J14,,Primary,Include +covid-19_type_b1,ICD-10,J15,"Bacterial pneumonia, not elsewhere classified",Primary,Include +covid-19_type_b1,ICD-10,J16,"Pneumonia due to other infectious organisms, not elsewhere classified",Primary,Include +covid-19_type_b1,ICD-10,J17,Pneumonia in diseases classified elsewhere,Primary,Include +covid-19_type_b1,ICD-10,J20,Acute bronchitis,Primary,Include +covid-19_type_b1,ICD-10,J21,Acute bronchiolitis,Primary,Include +covid-19_type_b1,ICD-10,J3,,Primary,Include +covid-19_type_b1,ICD-10,J85,Abscess of lung and mediastinum,Primary,Include +covid-19_type_b1,ICD-10,J86,Pyothorax,Primary,Include +covid-19_type_b1,ICD-10,K859,"Acute pancreatitis, unspecified",Primary,Include +covid-19_type_b1,ICD-10,P22,Respiratory distress of newborn,Primary,Include +covid-19_type_b1,ICD-10,P23,Congenital pneumonia,Primary,Include +covid-19_type_b1,ICD-10,P24,Neonatal aspiration syndromes,Primary,Include +covid-19_type_b1,ICD-10,P26,Pulmonary haemorrhage originating in the perinatal period,Primary,Include +covid-19_type_b1,ICD-10,P27,Chronic respiratory disease originating in the perinatal period,Primary,Include +covid-19_type_b1,ICD-10,P28,Other respiratory conditions originating in the perinatal period,Primary,Include +covid-19_type_b1,ICD-10,P29,Cardiovascular disorders originating in the perinatal period,Primary,Include +covid-19_type_b1,ICD-10,P3,,Primary,Include +covid-19_type_b1,ICD-10,P74,Other transitory neonatal electrolyte and metabolic disturbances,Primary,Include +covid-19_type_b1,ICD-10,R70,Elevated erythrocyte sedimentation rate and abnormality of plasma viscosity,Primary,Include +covid-19_type_b1,ICD-10,R71,,Primary,Include +covid-19_type_b1,ICD-10,R72,,Primary,Include +covid-19_type_b1,ICD-10,R73,Elevated blood glucose level,Primary,Include +covid-19_type_b1,ICD-10,R74,Abnormal serum enzyme levels,Primary,Include +covid-19_type_b1,ICD-10,R79,Other abnormal findings of blood chemistry,Primary,Include +covid-19_type_b1,ICD-10,Z038,Observation for other suspected diseases and conditions,Primary,Include +covid-19_type_b1,ICD-10,Z039,"Observation for suspected disease or condition, unspecified",Primary,Include +covid-19_type_b1,ICD-10,U075,Emergency use of U07.5,Primary,Include +covid-19_type_b1,ICD-10,U109,,Primary,Include +covid-19_type_b1,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Primary,Include +covid-19_type_b1,ICD-10,R65,Systemic Inflammatory Response Syndrome [SIRS],Primary,Include +covid-19_type_b1,ICD-10,U075,Emergency use of U07.5,Non-Primary,Include +covid-19_type_b1,ICD-10,U109,,Non-Primary,Include +covid-19_type_b1,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Non-Primary,Include +covid-19_type_b1,ICD-10,R65,Systemic Inflammatory Response Syndrome [SIRS],Non-Primary,Include diff --git a/_data/codelists/covid_impact_ccu02901_covid-19_type_b2_ICD10.csv b/_data/codelists/covid_impact_ccu02901_covid-19_type_b2_ICD10.csv new file mode 100644 index 00000000..e630042f --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_covid-19_type_b2_ICD10.csv @@ -0,0 +1,113 @@ +Phenotype,Terminology,Code,Description,Position,Filter +covid-19_type_b2,ICD-10,B20,Human immunodeficiency virus [HIV] disease resulting in infectious and parasitic diseases,Primary,Include +covid-19_type_b2,ICD-10,B21,Human immunodeficiency virus [HIV] disease resulting in malignant neoplasms,Primary,Include +covid-19_type_b2,ICD-10,B22,Human immunodeficiency virus [HIV] disease resulting in other specified diseases,Primary,Include +covid-19_type_b2,ICD-10,B24,,Primary,Include +covid-19_type_b2,ICD-10,D3,,Primary,Include +covid-19_type_b2,ICD-10,C,,Primary,Include +covid-19_type_b2,ICD-10,D0,,Primary,Include +covid-19_type_b2,ICD-10,D1,,Primary,Include +covid-19_type_b2,ICD-10,D2,,Primary,Include +covid-19_type_b2,ICD-10,D4,,Primary,Include +covid-19_type_b2,ICD-10,D55,Anaemia due to enzyme disorders,Primary,Include +covid-19_type_b2,ICD-10,D56,Thalassaemia,Primary,Include +covid-19_type_b2,ICD-10,D57,Sickle-cell disorders,Primary,Include +covid-19_type_b2,ICD-10,D58,Other hereditary haemolytic anaemias,Primary,Include +covid-19_type_b2,ICD-10,D59,Acquired haemolytic anaemia,Primary,Include +covid-19_type_b2,ICD-10,D6,,Primary,Include +covid-19_type_b2,ICD-10,D70,,Primary,Include +covid-19_type_b2,ICD-10,D71,,Primary,Include +covid-19_type_b2,ICD-10,D72,Other disorders of white blood cells,Primary,Include +covid-19_type_b2,ICD-10,D730,Hyposplenism,Primary,Include +covid-19_type_b2,ICD-10,D731,Hypersplenism,Primary,Include +covid-19_type_b2,ICD-10,D761,Haemophagocytic lymphohistiocytosis,Primary,Include +covid-19_type_b2,ICD-10,D76,Other specified diseases with participation of lymphoreticular and reticulohistiocytic tissue,Primary,Include +covid-19_type_b2,ICD-10,D8,,Primary,Include +covid-19_type_b2,ICD-10,E10,Type 1 diabetes mellitus,Primary,Include +covid-19_type_b2,ICD-10,E11,Type 2 diabetes mellitus,Primary,Include +covid-19_type_b2,ICD-10,E12,Malnutrition-related diabetes mellitus,Primary,Include +covid-19_type_b2,ICD-10,E13,Other specified diabetes mellitus,Primary,Include +covid-19_type_b2,ICD-10,E14,Unspecified diabetes mellitus,Primary,Include +covid-19_type_b2,ICD-10,E20,Hypoparathyroidism,Primary,Include +covid-19_type_b2,ICD-10,E21,Hyperparathyroidism and other disorders of parathyroid gland,Primary,Include +covid-19_type_b2,ICD-10,E22,Hyperfunction of pituitary gland,Primary,Include +covid-19_type_b2,ICD-10,E23,Hypofunction and other disorders of pituitary gland,Primary,Include +covid-19_type_b2,ICD-10,E24,Cushing syndrome,Primary,Include +covid-19_type_b2,ICD-10,E25,Adrenogenital disorders,Primary,Include +covid-19_type_b2,ICD-10,E26,Hyperaldosteronism,Primary,Include +covid-19_type_b2,ICD-10,E27,Other disorders of adrenal gland,Primary,Include +covid-19_type_b2,ICD-10,E6,,Primary,Include +covid-19_type_b2,ICD-10,E7,,Primary,Include +covid-19_type_b2,ICD-10,E80,Disorders of porphyrin and bilirubin metabolism,Primary,Include +covid-19_type_b2,ICD-10,E81,,Primary,Include +covid-19_type_b2,ICD-10,E82,,Primary,Include +covid-19_type_b2,ICD-10,E83,Disorders of mineral metabolism,Primary,Include +covid-19_type_b2,ICD-10,E84,Cystic fibrosis,Primary,Include +covid-19_type_b2,ICD-10,E850,Non-neuropathic heredofamilial amyloidosis,Primary,Include +covid-19_type_b2,ICD-10,E88,Other metabolic disorders,Primary,Include +covid-19_type_b2,ICD-10,E89,"Postprocedural endocrine and metabolic disorders, not elsewhere classified",Primary,Include +covid-19_type_b2,ICD-10,F7,,Primary,Include +covid-19_type_b2,ICD-10,F8,,Primary,Include +covid-19_type_b2,ICD-10,G1,,Primary,Include +covid-19_type_b2,ICD-10,G2,,Primary,Include +covid-19_type_b2,ICD-10,G3,,Primary,Include +covid-19_type_b2,ICD-10,G7,,Primary,Include +covid-19_type_b2,ICD-10,G8,,Primary,Include +covid-19_type_b2,ICD-10,I10,,Primary,Include +covid-19_type_b2,ICD-10,I11,Hypertensive heart disease,Primary,Include +covid-19_type_b2,ICD-10,I12,Hypertensive renal disease,Primary,Include +covid-19_type_b2,ICD-10,I13,Hypertensive heart and renal disease,Primary,Include +covid-19_type_b2,ICD-10,I15,Secondary hypertension,Primary,Include +covid-19_type_b2,ICD-10,I27,Other pulmonary heart diseases,Primary,Include +covid-19_type_b2,ICD-10,I34,Nonrheumatic mitral valve disorders,Primary,Include +covid-19_type_b2,ICD-10,I35,Nonrheumatic aortic valve disorders,Primary,Include +covid-19_type_b2,ICD-10,I36,Nonrheumatic tricuspid valve disorders,Primary,Include +covid-19_type_b2,ICD-10,I37,Pulmonary valve disorders,Primary,Include +covid-19_type_b2,ICD-10,I42,Cardiomyopathy,Primary,Include +covid-19_type_b2,ICD-10,I43,Cardiomyopathy in diseases classified elsewhere,Primary,Include +covid-19_type_b2,ICD-10,I675,Moyamoya disease,Primary,Include +covid-19_type_b2,ICD-10,J380,Paralysis of vocal cords and larynx,Primary,Include +covid-19_type_b2,ICD-10,J386,Stenosis of larynx,Primary,Include +covid-19_type_b2,ICD-10,J41,Simple and mucopurulent chronic bronchitis,Primary,Include +covid-19_type_b2,ICD-10,J42,,Primary,Include +covid-19_type_b2,ICD-10,J43,Emphysema,Primary,Include +covid-19_type_b2,ICD-10,J44,Other chronic obstructive pulmonary disease,Primary,Include +covid-19_type_b2,ICD-10,J45,Asthma,Primary,Include +covid-19_type_b2,ICD-10,J46,,Primary,Include +covid-19_type_b2,ICD-10,J47,,Primary,Include +covid-19_type_b2,ICD-10,J82,,Primary,Include +covid-19_type_b2,ICD-10,J84,Other interstitial pulmonary diseases,Primary,Include +covid-19_type_b2,ICD-10,J99,Respiratory disorders in diseases classified elsewhere,Primary,Include +covid-19_type_b2,ICD-10,K21,Gastro-oesophageal reflux disease,Primary,Include +covid-19_type_b2,ICD-10,K22,Other diseases of oesophagus,Primary,Include +covid-19_type_b2,ICD-10,K44,Diaphragmatic hernia,Primary,Include +covid-19_type_b2,ICD-10,K50,Crohn disease [regional enteritis],Primary,Include +covid-19_type_b2,ICD-10,K51,Ulcerative colitis,Primary,Include +covid-19_type_b2,ICD-10,K52,Other noninfective gastroenteritis and colitis,Primary,Include +covid-19_type_b2,ICD-10,K71,Toxic liver disease,Primary,Include +covid-19_type_b2,ICD-10,K720,Acute and subacute hepatic failure,Primary,Include +covid-19_type_b2,ICD-10,K721,Chronic hepatic failure,Primary,Include +covid-19_type_b2,ICD-10,K740,Hepatic fibrosis,Primary,Include +covid-19_type_b2,ICD-10,K741,Hepatic sclerosis,Primary,Include +covid-19_type_b2,ICD-10,K744,Secondary biliary cirrhosis,Primary,Include +covid-19_type_b2,ICD-10,K745,"Biliary cirrhosis, unspecified",Primary,Include +covid-19_type_b2,ICD-10,K746,Other and unspecified cirrhosis of liver,Primary,Include +covid-19_type_b2,ICD-10,K75,Other inflammatory liver diseases,Primary,Include +covid-19_type_b2,ICD-10,K76,Other diseases of liver,Primary,Include +covid-19_type_b2,ICD-10,K9,,Primary,Include +covid-19_type_b2,ICD-10,M3,,Primary,Include +covid-19_type_b2,ICD-10,N0,,Primary,Include +covid-19_type_b2,ICD-10,N10,,Primary,Include +covid-19_type_b2,ICD-10,N11,Chronic tubulo-interstitial nephritis,Primary,Include +covid-19_type_b2,ICD-10,N12,,Primary,Include +covid-19_type_b2,ICD-10,N13,Obstructive and reflux uropathy,Primary,Include +covid-19_type_b2,ICD-10,N15,Other renal tubulo-interstitial diseases,Primary,Include +covid-19_type_b2,ICD-10,N18,Chronic kidney disease,Primary,Include +covid-19_type_b2,ICD-10,P0,,Primary,Include +covid-19_type_b2,ICD-10,Q0,,Primary,Include +covid-19_type_b2,ICD-10,Q2,,Primary,Include +covid-19_type_b2,ICD-10,Q3,,Primary,Include +covid-19_type_b2,ICD-10,Q60,Renal agenesis and other reduction defects of kidney,Primary,Include +covid-19_type_b2,ICD-10,Q61,Cystic kidney disease,Primary,Include +covid-19_type_b2,ICD-10,Q9,,Primary,Include +covid-19_type_b2,ICD-10,R161,"Splenomegaly, not elsewhere classified",Primary,Include diff --git a/_data/codelists/covid_impact_ccu02901_covid-19_type_c_ICD10.csv b/_data/codelists/covid_impact_ccu02901_covid-19_type_c_ICD10.csv new file mode 100644 index 00000000..c8720d94 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_covid-19_type_c_ICD10.csv @@ -0,0 +1,193 @@ +Phenotype,Terminology,Code,Description,Position,Filter +covid-19_type_c,ICD-10,A00,Cholera,Primary,Include +covid-19_type_c,ICD-10,A01,Typhoid and paratyphoid fevers,Primary,Include +covid-19_type_c,ICD-10,A02,Other salmonella infections,Primary,Include +covid-19_type_c,ICD-10,A03,Shigellosis,Primary,Include +covid-19_type_c,ICD-10,A04,Other bacterial intestinal infections,Primary,Include +covid-19_type_c,ICD-10,A05,"Other bacterial foodborne intoxications, not elsewhere classified",Primary,Include +covid-19_type_c,ICD-10,A06,Amoebiasis,Primary,Include +covid-19_type_c,ICD-10,A07,Other protozoal intestinal diseases,Primary,Include +covid-19_type_c,ICD-10,A080,Rotaviral enteritis,Primary,Include +covid-19_type_c,ICD-10,A081,Acute gastroenteropathy due to Norwalk agent,Primary,Include +covid-19_type_c,ICD-10,A082,Adenoviral enteritis,Primary,Include +covid-19_type_c,ICD-10,A15,"Respiratory tuberculosis, bacteriologically and histologically confirmed",Primary,Include +covid-19_type_c,ICD-10,A16,"Respiratory tuberculosis, not confirmed bacteriologically or histologically",Primary,Include +covid-19_type_c,ICD-10,A17,Tuberculosis of nervous system,Primary,Include +covid-19_type_c,ICD-10,A18,Tuberculosis of other organs,Primary,Include +covid-19_type_c,ICD-10,A19,Miliary tuberculosis,Primary,Include +covid-19_type_c,ICD-10,A2,,Primary,Include +covid-19_type_c,ICD-10,A3,,Primary,Include +covid-19_type_c,ICD-10,A5,,Primary,Include +covid-19_type_c,ICD-10,A6,,Primary,Include +covid-19_type_c,ICD-10,B00,Herpesviral [herpes simplex] infections,Primary,Include +covid-19_type_c,ICD-10,B01,Varicella [chickenpox],Primary,Include +covid-19_type_c,ICD-10,B02,Zoster [herpes zoster],Primary,Include +covid-19_type_c,ICD-10,B03,,Primary,Include +covid-19_type_c,ICD-10,B04,,Primary,Include +covid-19_type_c,ICD-10,B05,Measles,Primary,Include +covid-19_type_c,ICD-10,B06,Rubella [German measles],Primary,Include +covid-19_type_c,ICD-10,B07,,Primary,Include +covid-19_type_c,ICD-10,B08,"Other viral infections characterized by skin and mucous membrane lesions, not elsewhere classified",Primary,Include +covid-19_type_c,ICD-10,B1,,Primary,Include +covid-19_type_c,ICD-10,B2,,Primary,Include +covid-19_type_c,ICD-10,B3,,Primary,Include +covid-19_type_c,ICD-10,B4,,Primary,Include +covid-19_type_c,ICD-10,B5,,Primary,Include +covid-19_type_c,ICD-10,B6,,Primary,Include +covid-19_type_c,ICD-10,B7,,Primary,Include +covid-19_type_c,ICD-10,B8,,Primary,Include +covid-19_type_c,ICD-10,D50,Iron deficiency anaemia,Primary,Include +covid-19_type_c,ICD-10,D51,Vitamin B₁₂ deficiency anaemia,Primary,Include +covid-19_type_c,ICD-10,D52,Folate deficiency anaemia,Primary,Include +covid-19_type_c,ICD-10,D53,Other nutritional anaemias,Primary,Include +covid-19_type_c,ICD-10,D73,Diseases of spleen,Primary,Include +covid-19_type_c,ICD-10,E0,,Primary,Include +covid-19_type_c,ICD-10,E2,,Primary,Include +covid-19_type_c,ICD-10,E3,,Primary,Include +covid-19_type_c,ICD-10,E5,,Primary,Include +covid-19_type_c,ICD-10,F,,Primary,Include +covid-19_type_c,ICD-10,G0,,Primary,Include +covid-19_type_c,ICD-10,G5,,Primary,Include +covid-19_type_c,ICD-10,G6,,Primary,Include +covid-19_type_c,ICD-10,G9,,Primary,Include +covid-19_type_c,ICD-10,H,,Primary,Include +covid-19_type_c,ICD-10,I0,,Primary,Include +covid-19_type_c,ICD-10,I60,Subarachnoid haemorrhage,Primary,Include +covid-19_type_c,ICD-10,I61,Intracerebral haemorrhage,Primary,Include +covid-19_type_c,ICD-10,I62,Other nontraumatic intracranial haemorrhage,Primary,Include +covid-19_type_c,ICD-10,I7,,Primary,Include +covid-19_type_c,ICD-10,I8,,Primary,Include +covid-19_type_c,ICD-10,J6,,Primary,Include +covid-19_type_c,ICD-10,J95,"Postprocedural respiratory disorders, not elsewhere classified",Primary,Include +covid-19_type_c,ICD-10,K0,,Primary,Include +covid-19_type_c,ICD-10,K1,,Primary,Include +covid-19_type_c,ICD-10,K20,,Primary,Include +covid-19_type_c,ICD-10,K25,Gastric ulcer,Primary,Include +covid-19_type_c,ICD-10,K26,Duodenal ulcer,Primary,Include +covid-19_type_c,ICD-10,K27,"Peptic ulcer, site unspecified",Primary,Include +covid-19_type_c,ICD-10,K28,Gastrojejunal ulcer,Primary,Include +covid-19_type_c,ICD-10,K29,Gastritis and duodenitis,Primary,Include +covid-19_type_c,ICD-10,K3,,Primary,Include +covid-19_type_c,ICD-10,K4,,Primary,Include +covid-19_type_c,ICD-10,K55,Vascular disorders of intestine,Primary,Include +covid-19_type_c,ICD-10,K56,Paralytic ileus and intestinal obstruction without hernia,Primary,Include +covid-19_type_c,ICD-10,K590,Constipation,Primary,Include +covid-19_type_c,ICD-10,K58,Irritable bowel syndrome,Primary,Include +covid-19_type_c,ICD-10,K59,Other functional intestinal disorders,Primary,Include +covid-19_type_c,ICD-10,K6,,Primary,Include +covid-19_type_c,ICD-10,K8,,Primary,Include +covid-19_type_c,ICD-10,K9,,Primary,Include +covid-19_type_c,ICD-10,L0,,Primary,Include +covid-19_type_c,ICD-10,L2,,Primary,Include +covid-19_type_c,ICD-10,L3,,Primary,Include +covid-19_type_c,ICD-10,L4,,Primary,Include +covid-19_type_c,ICD-10,L5,,Primary,Include +covid-19_type_c,ICD-10,L6,,Primary,Include +covid-19_type_c,ICD-10,L72,Follicular cysts of skin and subcutaneous tissue,Primary,Include +covid-19_type_c,ICD-10,L73,Other follicular disorders,Primary,Include +covid-19_type_c,ICD-10,L8,,Primary,Include +covid-19_type_c,ICD-10,L9,,Primary,Include +covid-19_type_c,ICD-10,M0,,Primary,Include +covid-19_type_c,ICD-10,M1,,Primary,Include +covid-19_type_c,ICD-10,M2,,Primary,Include +covid-19_type_c,ICD-10,M4,,Primary,Include +covid-19_type_c,ICD-10,M5,,Primary,Include +covid-19_type_c,ICD-10,M6,,Primary,Include +covid-19_type_c,ICD-10,M7,,Primary,Include +covid-19_type_c,ICD-10,M8,,Primary,Include +covid-19_type_c,ICD-10,M9,,Primary,Include +covid-19_type_c,ICD-10,N141,"Nephropathy induced by other drugs, medicaments and biological substances",Primary,Include +covid-19_type_c,ICD-10,N2,,Primary,Include +covid-19_type_c,ICD-10,N3,,Primary,Include +covid-19_type_c,ICD-10,N39,Other disorders of urinary system,Primary,Include +covid-19_type_c,ICD-10,N4,,Primary,Include +covid-19_type_c,ICD-10,N5,,Primary,Include +covid-19_type_c,ICD-10,N6,,Primary,Include +covid-19_type_c,ICD-10,N7,,Primary,Include +covid-19_type_c,ICD-10,N8,,Primary,Include +covid-19_type_c,ICD-10,N9,,Primary,Include +covid-19_type_c,ICD-10,O,,Primary,Include +covid-19_type_c,ICD-10,P1,,Primary,Include +covid-19_type_c,ICD-10,P20,Intrauterine hypoxia,Primary,Include +covid-19_type_c,ICD-10,P21,Birth asphyxia,Primary,Include +covid-19_type_c,ICD-10,P50,Fetal blood loss,Primary,Include +covid-19_type_c,ICD-10,P51,Umbilical haemorrhage of newborn,Primary,Include +covid-19_type_c,ICD-10,P52,Intracranial nontraumatic haemorrhage of fetus and newborn,Primary,Include +covid-19_type_c,ICD-10,P53,,Primary,Include +covid-19_type_c,ICD-10,P54,Other neonatal haemorrhages,Primary,Include +covid-19_type_c,ICD-10,P55,Haemolytic disease of fetus and newborn,Primary,Include +covid-19_type_c,ICD-10,P56,Hydrops fetalis due to haemolytic disease,Primary,Include +covid-19_type_c,ICD-10,P57,Kernicterus,Primary,Include +covid-19_type_c,ICD-10,P58,Neonatal jaundice due to other excessive haemolysis,Primary,Include +covid-19_type_c,ICD-10,P59,Neonatal jaundice from other and unspecified causes,Primary,Include +covid-19_type_c,ICD-10,P6,,Primary,Include +covid-19_type_c,ICD-10,P70,Transitory disorders of carbohydrate metabolism specific to fetus and newborn,Primary,Include +covid-19_type_c,ICD-10,P71,Transitory neonatal disorders of calcium and magnesium metabolism,Primary,Include +covid-19_type_c,ICD-10,P72,Other transitory neonatal endocrine disorders,Primary,Include +covid-19_type_c,ICD-10,P75,,Primary,Include +covid-19_type_c,ICD-10,P76,Other intestinal obstruction of newborn,Primary,Include +covid-19_type_c,ICD-10,P77,,Primary,Include +covid-19_type_c,ICD-10,P78,Other perinatal digestive system disorders,Primary,Include +covid-19_type_c,ICD-10,P8,,Primary,Include +covid-19_type_c,ICD-10,P90,,Primary,Include +covid-19_type_c,ICD-10,P91,Other disturbances of cerebral status of newborn,Primary,Include +covid-19_type_c,ICD-10,P94,Disorders of muscle tone of newborn,Primary,Include +covid-19_type_c,ICD-10,P95,,Primary,Include +covid-19_type_c,ICD-10,P96,Other conditions originating in the perinatal period,Primary,Include +covid-19_type_c,ICD-10,Q1,,Primary,Include +covid-19_type_c,ICD-10,Q4,,Primary,Include +covid-19_type_c,ICD-10,Q5,,Primary,Include +covid-19_type_c,ICD-10,Q6,,Primary,Include +covid-19_type_c,ICD-10,Q7,,Primary,Include +covid-19_type_c,ICD-10,Q8,,Primary,Include +covid-19_type_c,ICD-10,R12,,Primary,Include +covid-19_type_c,ICD-10,R14,,Primary,Include +covid-19_type_c,ICD-10,R15,,Primary,Include +covid-19_type_c,ICD-10,R19,Other symptoms and signs involving the digestive system and abdomen,Primary,Include +covid-19_type_c,ICD-10,R20,Disturbances of skin sensation,Primary,Include +covid-19_type_c,ICD-10,R22,"Localized swelling, mass and lump of skin and subcutaneous tissue",Primary,Include +covid-19_type_c,ICD-10,R23,Other skin changes,Primary,Include +covid-19_type_c,ICD-10,R29,Other symptoms and signs involving the nervous and musculoskeletal systems,Primary,Include +covid-19_type_c,ICD-10,R30,Pain associated with micturition,Primary,Include +covid-19_type_c,ICD-10,R31,,Primary,Include +covid-19_type_c,ICD-10,R32,,Primary,Include +covid-19_type_c,ICD-10,R33,,Primary,Include +covid-19_type_c,ICD-10,R35,,Primary,Include +covid-19_type_c,ICD-10,R39,Other symptoms and signs involving the urinary system,Primary,Include +covid-19_type_c,ICD-10,R45,Symptoms and signs involving emotional state,Primary,Include +covid-19_type_c,ICD-10,R46,Symptoms and signs involving appearance and behaviour,Primary,Include +covid-19_type_c,ICD-10,R80,,Primary,Include +covid-19_type_c,ICD-10,R81,,Primary,Include +covid-19_type_c,ICD-10,R82,Other abnormal findings in urine,Primary,Include +covid-19_type_c,ICD-10,R93,Abnormal findings on diagnostic imaging of other body structures,Primary,Include +covid-19_type_c,ICD-10,U076,Emergency use of U07.6,Primary,Include +covid-19_type_c,ICD-10,U82,Resistance to betalactam antibiotics,Primary,Include +covid-19_type_c,ICD-10,U83,Resistance to other antibiotics,Primary,Include +covid-19_type_c,ICD-10,S,,Primary,Include +covid-19_type_c,ICD-10,T,,Primary,Include +covid-19_type_c,ICD-10,V,,Primary,Include +covid-19_type_c,ICD-10,W,,Primary,Include +covid-19_type_c,ICD-10,X,,Primary,Include +covid-19_type_c,ICD-10,Y,,Primary,Include +covid-19_type_c,ICD-10,Z,,Primary,Include +covid-19_type_c,ICD-10,B20,Human immunodeficiency virus [HIV] disease resulting in infectious and parasitic diseases,Primary,Exclude +covid-19_type_c,ICD-10,B21,Human immunodeficiency virus [HIV] disease resulting in malignant neoplasms,Primary,Exclude +covid-19_type_c,ICD-10,B22,Human immunodeficiency virus [HIV] disease resulting in other specified diseases,Primary,Exclude +covid-19_type_c,ICD-10,B23,Human immunodeficiency virus [HIV] disease resulting in other conditions,Primary,Exclude +covid-19_type_c,ICD-10,B24,,Primary,Exclude +covid-19_type_c,ICD-10,F7,,Primary,Exclude +covid-19_type_c,ICD-10,F8,,Primary,Exclude +covid-19_type_c,ICD-10,H669,"Otitis media, unspecified",Primary,Exclude +covid-19_type_c,ICD-10,K44,Diaphragmatic hernia,Primary,Exclude +covid-19_type_c,ICD-10,Y4,,Primary,Exclude +covid-19_type_c,ICD-10,Y5,,Primary,Exclude +covid-19_type_c,ICD-10,Z038,Observation for other suspected diseases and conditions,Primary,Exclude +covid-19_type_c,ICD-10,Z039,"Observation for suspected disease or condition, unspecified",Primary,Exclude +covid-19_type_c,ICD-10,U075,Emergency use of U07.5,Primary,Exclude +covid-19_type_c,ICD-10,U109,,Primary,Exclude +covid-19_type_c,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Primary,Exclude +covid-19_type_c,ICD-10,R65,Systemic Inflammatory Response Syndrome [SIRS],Primary,Exclude +covid-19_type_c,ICD-10,U075,Emergency use of U07.5,Non-Primary,Exclude +covid-19_type_c,ICD-10,U109,,Non-Primary,Exclude +covid-19_type_c,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Non-Primary,Exclude +covid-19_type_c,ICD-10,R65,Systemic Inflammatory Response Syndrome [SIRS],Non-Primary,Exclude diff --git a/_data/codelists/covid_impact_ccu02901_green_book_arthritis_and_connective_tissue_diseases_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_arthritis_and_connective_tissue_diseases_ICD10.csv new file mode 100644 index 00000000..5a33c66f --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_arthritis_and_connective_tissue_diseases_ICD10.csv @@ -0,0 +1,9 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M05,Seropositive rheumatoid arthritis,Include, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M06,Other rheumatoid arthritis,Include, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M07,Psoriatic and enteropathic arthropathies,Include, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M08,Juvenile arthritis,Include, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M09,Juvenile arthritis in diseases classified elsewhere,Include, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M3,,Include, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Filter, +green_book_arthritis_and_connective_tissue_diseases,ICD-10,M357,Hypermobility syndrome,Filter, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_blood_disorders_and_immune_deficiencies_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_blood_disorders_and_immune_deficiencies_ICD10.csv new file mode 100644 index 00000000..68822d34 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_blood_disorders_and_immune_deficiencies_ICD10.csv @@ -0,0 +1,15 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_blood_disorders_and_immune_deficiencies,ICD-10,B20,Human immunodeficiency virus [HIV] disease resulting in infectious and parasitic diseases,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,B21,Human immunodeficiency virus [HIV] disease resulting in malignant neoplasms,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,B22,Human immunodeficiency virus [HIV] disease resulting in other specified diseases,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,B24,,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D56,Thalassaemia,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D57,Sickle-cell disorders,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D58,Other hereditary haemolytic anaemias,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D61,Other aplastic anaemias,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D71,,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D730,Hyposplenism,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D731,Hypersplenism,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D8,,Include, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D898,"Other specified disorders involving the immune mechanism, not elsewhere classified",Filter, +green_book_blood_disorders_and_immune_deficiencies,ICD-10,D899,"Disorder involving the immune mechanism, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_cancer_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_cancer_ICD10.csv new file mode 100644 index 00000000..68f78079 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_cancer_ICD10.csv @@ -0,0 +1,5 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_cancer,ICD-10,C,,Include,5 years +green_book_cancer,ICD-10,D0,,Include,5 years +green_book_cancer,ICD-10,D4,,Include,5 years +green_book_cancer,ICD-10,D473,Essential (haemorrhagic) thrombocythaemia,Filter,5 years diff --git a/_data/codelists/covid_impact_ccu02901_green_book_congenital_syndromes_and_anomalies_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_congenital_syndromes_and_anomalies_ICD10.csv new file mode 100644 index 00000000..b7311edb --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_congenital_syndromes_and_anomalies_ICD10.csv @@ -0,0 +1,14 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_congenital_syndromes_and_anomalies,ICD-10,Q0,,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q2,,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q3,,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q9,,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q60,Renal agenesis and other reduction defects of kidney,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q61,Cystic kidney disease,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q4,,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q79,"Congenital malformations of the musculoskeletal system, not elsewhere classified",Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q80,Congenital ichthyosis,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q81,Epidermolysis bullosa,Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q897,"Multiple congenital malformations, not elsewhere classified",Include, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q245,Malformation of coronary vessels,Filter, +green_book_congenital_syndromes_and_anomalies,ICD-10,Q38,"Other congenital malformations of tongue, mouth and pharynx",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_digestive_and_liver_diseases_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_digestive_and_liver_diseases_ICD10.csv new file mode 100644 index 00000000..6f12fd68 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_digestive_and_liver_diseases_ICD10.csv @@ -0,0 +1,35 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_digestive_and_liver_diseases,ICD-10,K44,Diaphragmatic hernia,Include, +green_book_digestive_and_liver_diseases,ICD-10,K50,Crohn disease [regional enteritis],Include, +green_book_digestive_and_liver_diseases,ICD-10,K51,Ulcerative colitis,Include, +green_book_digestive_and_liver_diseases,ICD-10,K52,Other noninfective gastroenteritis and colitis,Include, +green_book_digestive_and_liver_diseases,ICD-10,K71,Toxic liver disease,Include, +green_book_digestive_and_liver_diseases,ICD-10,K721,Chronic hepatic failure,Include, +green_book_digestive_and_liver_diseases,ICD-10,K740,Hepatic fibrosis,Include, +green_book_digestive_and_liver_diseases,ICD-10,K741,Hepatic sclerosis,Include, +green_book_digestive_and_liver_diseases,ICD-10,K744,Secondary biliary cirrhosis,Include, +green_book_digestive_and_liver_diseases,ICD-10,K745,"Biliary cirrhosis, unspecified",Include, +green_book_digestive_and_liver_diseases,ICD-10,K754,Autoimmune hepatitis,Include, +green_book_digestive_and_liver_diseases,ICD-10,K75,Other inflammatory liver diseases,Include, +green_book_digestive_and_liver_diseases,ICD-10,K90,Intestinal malabsorption,Include, +green_book_digestive_and_liver_diseases,ICD-10,K21,Gastro-oesophageal reflux disease,Include,5 years +green_book_digestive_and_liver_diseases,ICD-10,K22,Other diseases of oesophagus,Include,5 years +green_book_digestive_and_liver_diseases,ICD-10,K210,Gastro-oesophageal reflux disease with oesophagitis,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K219,Gastro-oesophageal reflux disease without oesophagitis,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K220,Achalasia of cardia,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K221,Ulcer of oesophagus,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K222,Oesophageal obstruction,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K223,Perforation of oesophagus,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K224,Dyskinesia of oesophagus,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K225,"Diverticulum of oesophagus, acquired",Filter, +green_book_digestive_and_liver_diseases,ICD-10,K226,Gastro-oesophageal laceration-haemorrhage syndrome,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K227,Barrett oesophagus,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K228,Other specified diseases of oesophagus,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K521,Toxic gastroenteritis and colitis,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K522,Allergic and dietetic gastroenteritis and colitis,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K528,Other specified noninfective gastroenteritis and colitis,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K529,"Noninfective gastroenteritis and colitis, unspecified",Filter, +green_book_digestive_and_liver_diseases,ICD-10,K750,Abscess of liver,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K751,Phlebitis of portal vein,Filter, +green_book_digestive_and_liver_diseases,ICD-10,K904,"Malabsorption due to intolerance, not elsewhere classified",Filter, +green_book_digestive_and_liver_diseases,ICD-10,K908,Other intestinal malabsorption,Filter, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_endocrine_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_endocrine_conditions_ICD10.csv new file mode 100644 index 00000000..a8710122 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_endocrine_conditions_ICD10.csv @@ -0,0 +1,22 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_endocrine_conditions,ICD-10,E10,Type 1 diabetes mellitus,Include, +green_book_endocrine_conditions,ICD-10,E11,Type 2 diabetes mellitus,Include, +green_book_endocrine_conditions,ICD-10,E12,Malnutrition-related diabetes mellitus,Include, +green_book_endocrine_conditions,ICD-10,E13,Other specified diabetes mellitus,Include, +green_book_endocrine_conditions,ICD-10,E14,Unspecified diabetes mellitus,Include, +green_book_endocrine_conditions,ICD-10,E22,Hyperfunction of pituitary gland,Include, +green_book_endocrine_conditions,ICD-10,E23,Hypofunction and other disorders of pituitary gland,Include, +green_book_endocrine_conditions,ICD-10,E24,Cushing syndrome,Include, +green_book_endocrine_conditions,ICD-10,E25,Adrenogenital disorders,Include, +green_book_endocrine_conditions,ICD-10,E26,Hyperaldosteronism,Include, +green_book_endocrine_conditions,ICD-10,E27,Other disorders of adrenal gland,Include, +green_book_endocrine_conditions,ICD-10,E7,,Include, +green_book_endocrine_conditions,ICD-10,E80,Disorders of porphyrin and bilirubin metabolism,Include, +green_book_endocrine_conditions,ICD-10,E81,,Include, +green_book_endocrine_conditions,ICD-10,E82,,Include, +green_book_endocrine_conditions,ICD-10,E88,Other metabolic disorders,Include, +green_book_endocrine_conditions,ICD-10,E89,"Postprocedural endocrine and metabolic disorders, not elsewhere classified",Include, +green_book_endocrine_conditions,ICD-10,E84,Cystic fibrosis,Include, +green_book_endocrine_conditions,ICD-10,E231,Drug-induced hypopituitarism,Filter, +green_book_endocrine_conditions,ICD-10,E232,Diabetes insipidus,Filter, +green_book_endocrine_conditions,ICD-10,E739,"Lactose intolerance, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_hypertension_and_cardiac_valves_and_cardiomyopathy_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_hypertension_and_cardiac_valves_and_cardiomyopathy_ICD10.csv new file mode 100644 index 00000000..d90f103d --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_hypertension_and_cardiac_valves_and_cardiomyopathy_ICD10.csv @@ -0,0 +1,13 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I10,,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I11,Hypertensive heart disease,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I12,Hypertensive renal disease,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I13,Hypertensive heart and renal disease,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I15,Secondary hypertension,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I27,Other pulmonary heart diseases,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I34,Nonrheumatic mitral valve disorders,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I35,Nonrheumatic aortic valve disorders,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I36,Nonrheumatic tricuspid valve disorders,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I37,Pulmonary valve disorders,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I42,Cardiomyopathy,Include, +green_book_hypertension_and_cardiac_valves_and_cardiomyopathy,ICD-10,I43,Cardiomyopathy in diseases classified elsewhere,Include, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_obesity_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_obesity_ICD10.csv new file mode 100644 index 00000000..b8642a4f --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_obesity_ICD10.csv @@ -0,0 +1,2 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_obesity,ICD-10,E66,Obesity,Include, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_pregnancy_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_pregnancy_ICD10.csv new file mode 100644 index 00000000..ec828b1e --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_pregnancy_ICD10.csv @@ -0,0 +1,2 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_pregnancy,ICD-10,O,,Include,9 months diff --git a/_data/codelists/covid_impact_ccu02901_green_book_renal_diseases_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_renal_diseases_ICD10.csv new file mode 100644 index 00000000..2fd64dd0 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_renal_diseases_ICD10.csv @@ -0,0 +1,7 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_renal_diseases,ICD-10,N0,,Include, +green_book_renal_diseases,ICD-10,N11,Chronic tubulo-interstitial nephritis,Include, +green_book_renal_diseases,ICD-10,N12,,Include, +green_book_renal_diseases,ICD-10,N13,Obstructive and reflux uropathy,Include, +green_book_renal_diseases,ICD-10,N15,Other renal tubulo-interstitial diseases,Include, +green_book_renal_diseases,ICD-10,N18,Chronic kidney disease,Include, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_severe_neurological_and_developmental_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_severe_neurological_and_developmental_conditions_ICD10.csv new file mode 100644 index 00000000..a23da298 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_severe_neurological_and_developmental_conditions_ICD10.csv @@ -0,0 +1,24 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_severe_neurological_and_developmental_conditions,ICD-10,F7,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F80,Specific developmental disorders of speech and language,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F82,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F83,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F84,Pervasive developmental disorders,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F85,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F86,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F87,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F88,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,F89,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G1,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G20,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G21,Secondary parkinsonism,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G22,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G23,Other degenerative diseases of basal ganglia,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G24,Dystonia,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G26,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G27,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G28,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G29,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G3,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G7,,Include, +green_book_severe_neurological_and_developmental_conditions,ICD-10,G8,,Include, diff --git a/_data/codelists/covid_impact_ccu02901_green_book_severe_respiratory_diseases_ICD10.csv b/_data/codelists/covid_impact_ccu02901_green_book_severe_respiratory_diseases_ICD10.csv new file mode 100644 index 00000000..36c0a52e --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_green_book_severe_respiratory_diseases_ICD10.csv @@ -0,0 +1,11 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +green_book_severe_respiratory_diseases,ICD-10,J380,Paralysis of vocal cords and larynx,Include, +green_book_severe_respiratory_diseases,ICD-10,J386,Stenosis of larynx,Include, +green_book_severe_respiratory_diseases,ICD-10,J44,Other chronic obstructive pulmonary disease,Include, +green_book_severe_respiratory_diseases,ICD-10,J45,Asthma,Include, +green_book_severe_respiratory_diseases,ICD-10,J46,,Include, +green_book_severe_respiratory_diseases,ICD-10,J47,,Include, +green_book_severe_respiratory_diseases,ICD-10,J82,,Include, +green_book_severe_respiratory_diseases,ICD-10,J84,Other interstitial pulmonary diseases,Include, +green_book_severe_respiratory_diseases,ICD-10,J99,Respiratory disorders in diseases classified elsewhere,Include, +green_book_severe_respiratory_diseases,ICD-10,P27,Chronic respiratory disease originating in the perinatal period,Include,5 years diff --git a/_data/codelists/covid_impact_ccu02901_uhc_blood_disorders_and_immune_deficiencies_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_blood_disorders_and_immune_deficiencies_ICD10.csv new file mode 100644 index 00000000..3bc5ad0d --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_blood_disorders_and_immune_deficiencies_ICD10.csv @@ -0,0 +1,24 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_blood_disorders_and_immune_deficiencies,ICD-10,B2,,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D55,Anaemia due to enzyme disorders,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D56,Thalassaemia,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D57,Sickle-cell disorders,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D58,Other hereditary haemolytic anaemias,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D60,Acquired pure red cell aplasia [erythroblastopenia],Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D61,Other aplastic anaemias,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D64,Other anaemias,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D66,,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D67,,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D680,Von Willebrand disease,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D681,Hereditary factor XI deficiency,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D682,Hereditary deficiency of other clotting factors,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D71,,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D730,Hyposplenism,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D731,Hypersplenism,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D8,,Include, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,B25,Cytomegaloviral disease,Filter, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,B26,Mumps,Filter, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,B27,Infectious mononucleosis,Filter, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,B28,,Filter, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,B29,,Filter, +uhc_blood_disorders_and_immune_deficiencies,ICD-10,D649,"Anaemia, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_cancer_and_neoplasms_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_cancer_and_neoplasms_ICD10.csv new file mode 100644 index 00000000..a1b2482d --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_cancer_and_neoplasms_ICD10.csv @@ -0,0 +1,5 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_cancer_and_neoplasms,ICD-10,C,,Include,5 years +uhc_cancer_and_neoplasms,ICD-10,D0,,Include,5 years +uhc_cancer_and_neoplasms,ICD-10,D4,,Include,5 years +uhc_cancer_and_neoplasms,ICD-10,D473,Essential (haemorrhagic) thrombocythaemia,Filter,5 years diff --git a/_data/codelists/covid_impact_ccu02901_uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease_ICD10.csv new file mode 100644 index 00000000..115a55ee --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease_ICD10.csv @@ -0,0 +1,25 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,P27,Chronic respiratory disease originating in the perinatal period,Include,5 years +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I05,Rheumatic mitral valve diseases,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I06,Rheumatic aortic valve diseases,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I07,Rheumatic tricuspid valve diseases,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I08,Multiple valve diseases,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I10,,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I11,Hypertensive heart disease,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I12,Hypertensive renal disease,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I13,Hypertensive heart and renal disease,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I14,,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I15,Secondary hypertension,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I21,Acute myocardial infarction,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I22,Subsequent myocardial infarction,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I27,Other pulmonary heart diseases,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I28,Other diseases of pulmonary vessels,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I34,Nonrheumatic mitral valve disorders,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I35,Nonrheumatic aortic valve disorders,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I36,Nonrheumatic tricuspid valve disorders,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I37,Pulmonary valve disorders,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I42,Cardiomyopathy,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I43,Cardiomyopathy in diseases classified elsewhere,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,I44,Atrioventricular and left bundle-branch block,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,Q2,,Include, +uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease,ICD-10,Q245,Malformation of coronary vessels,Filter, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_digestive_and_liver_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_digestive_and_liver_conditions_ICD10.csv new file mode 100644 index 00000000..0a5c0ed1 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_digestive_and_liver_conditions_ICD10.csv @@ -0,0 +1,23 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_digestive_and_liver_conditions,ICD-10,K44,Diaphragmatic hernia,Include, +uhc_digestive_and_liver_conditions,ICD-10,K50,Crohn disease [regional enteritis],Include, +uhc_digestive_and_liver_conditions,ICD-10,K51,Ulcerative colitis,Include, +uhc_digestive_and_liver_conditions,ICD-10,K52,Other noninfective gastroenteritis and colitis,Include, +uhc_digestive_and_liver_conditions,ICD-10,K71,Toxic liver disease,Include, +uhc_digestive_and_liver_conditions,ICD-10,K721,Chronic hepatic failure,Include, +uhc_digestive_and_liver_conditions,ICD-10,K740,Hepatic fibrosis,Include, +uhc_digestive_and_liver_conditions,ICD-10,K741,Hepatic sclerosis,Include, +uhc_digestive_and_liver_conditions,ICD-10,K744,Secondary biliary cirrhosis,Include, +uhc_digestive_and_liver_conditions,ICD-10,K745,"Biliary cirrhosis, unspecified",Include, +uhc_digestive_and_liver_conditions,ICD-10,K75,Other inflammatory liver diseases,Include, +uhc_digestive_and_liver_conditions,ICD-10,K754,Autoimmune hepatitis,Include, +uhc_digestive_and_liver_conditions,ICD-10,K90,Intestinal malabsorption,Include, +uhc_digestive_and_liver_conditions,ICD-10,Q35,Cleft palate,Include, +uhc_digestive_and_liver_conditions,ICD-10,Q36,Cleft lip,Include, +uhc_digestive_and_liver_conditions,ICD-10,Q37,Cleft palate with cleft lip,Include, +uhc_digestive_and_liver_conditions,ICD-10,Q39,Congenital malformations of oesophagus,Include, +uhc_digestive_and_liver_conditions,ICD-10,Q4,,Include, +uhc_digestive_and_liver_conditions,ICD-10,K21,Gastro-oesophageal reflux disease,Include,5 years +uhc_digestive_and_liver_conditions,ICD-10,K22,Other diseases of oesophagus,Include, +uhc_digestive_and_liver_conditions,ICD-10,K528,Other specified noninfective gastroenteritis and colitis,Filter, +uhc_digestive_and_liver_conditions,ICD-10,K529,"Noninfective gastroenteritis and colitis, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_endocrine_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_endocrine_conditions_ICD10.csv new file mode 100644 index 00000000..440d3c3b --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_endocrine_conditions_ICD10.csv @@ -0,0 +1,13 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_endocrine_conditions,ICD-10,E0,,Include, +uhc_endocrine_conditions,ICD-10,E1,,Include, +uhc_endocrine_conditions,ICD-10,E2,,Include, +uhc_endocrine_conditions,ICD-10,E3,,Include, +uhc_endocrine_conditions,ICD-10,E4,,Include, +uhc_endocrine_conditions,ICD-10,E7,,Include, +uhc_endocrine_conditions,ICD-10,E8,,Include, +uhc_endocrine_conditions,ICD-10,E231,Drug-induced hypopituitarism,Filter, +uhc_endocrine_conditions,ICD-10,E232,Diabetes insipidus,Filter, +uhc_endocrine_conditions,ICD-10,E86,,Filter, +uhc_endocrine_conditions,ICD-10,E87,"Other disorders of fluid, electrolyte and acid-base balance",Filter, +uhc_endocrine_conditions,ICD-10,E162,"Hypoglycaemia, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_muscle_and_skin_and_arthritis_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_muscle_and_skin_and_arthritis_ICD10.csv new file mode 100644 index 00000000..002479d9 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_muscle_and_skin_and_arthritis_ICD10.csv @@ -0,0 +1,36 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_muscle_and_skin_and_arthritis,ICD-10,L1,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,L4,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,L85,Other epidermal thickening,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,L93,Lupus erythematosus,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,L94,Other localized connective tissue disorders,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M0,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M1,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M3,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M41,Scoliosis,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M42,Spinal osteochondrosis,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M43,Other deforming dorsopathies,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q65,Congenital deformities of hip,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q66,Congenital deformities of feet,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q67,"Congenital musculoskeletal deformities of head, face, spine and chest",Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q68,Other congenital musculoskeletal deformities,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q69,Polydactyly,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q7,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q8,,Include, +uhc_muscle_and_skin_and_arthritis,ICD-10,M01,Direct infections of joint in infectious and parasitic diseases classified elsewhere,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,M02,Reactive arthropathies,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,M03,Postinfective and reactive arthropathies in diseases classified elsewhere,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,M04,,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,M303,Mucocutaneous lymph node syndrome [Kawasaki],Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q668,Other congenital deformities of feet,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q690,Accessory finger(s),Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q691,Accessory thumb(s),Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q692,Accessory toe(s),Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q699,"Polydactyly, unspecified",Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q700,Fused fingers,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q701,Webbed fingers,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q702,Fused toes,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q703,Webbed toes,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q825,Congenital non-neoplastic naevus,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q828,Other specified congenital malformations of skin,Filter, +uhc_muscle_and_skin_and_arthritis,ICD-10,Q829,"Congenital malformation of skin, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_neurological_and_developmental_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_neurological_and_developmental_conditions_ICD10.csv new file mode 100644 index 00000000..ee58072e --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_neurological_and_developmental_conditions_ICD10.csv @@ -0,0 +1,50 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_neurological_and_developmental_conditions,ICD-10,F7,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,F8,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,F9,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G1,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G2,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G3,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G4,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G5,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G6,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G7,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G8,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,G9,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H17,Corneal scars and opacities,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H18,Other disorders of cornea,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H19,Disorders of sclera and cornea in diseases classified elsewhere,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H26,Other cataract,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H33,Retinal detachments and breaks,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H35,Other retinal disorders,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H40,Glaucoma,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H42,Glaucoma in diseases classified elsewhere,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H46,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H47,Other disorders of optic [2nd] nerve and visual pathways,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H48,Disorders of optic [2nd] nerve and visual pathways in diseases classified elsewhere,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H54,Visual impairment including blindness (binocular or monocular),Include, +uhc_neurological_and_developmental_conditions,ICD-10,H90,Conductive and sensorineural hearing loss,Include, +uhc_neurological_and_developmental_conditions,ICD-10,H91,Other hearing loss,Include, +uhc_neurological_and_developmental_conditions,ICD-10,I673,Progressive vascular leukoencephalopathy,Include, +uhc_neurological_and_developmental_conditions,ICD-10,I675,Moyamoya disease,Include, +uhc_neurological_and_developmental_conditions,ICD-10,I69,Sequelae of cerebrovascular disease,Include, +uhc_neurological_and_developmental_conditions,ICD-10,P21,Birth asphyxia,Include, +uhc_neurological_and_developmental_conditions,ICD-10,Q0,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,Q1,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,Q9,,Include, +uhc_neurological_and_developmental_conditions,ICD-10,R62,Lack of expected normal physiological development,Include, +uhc_neurological_and_developmental_conditions,ICD-10,F93,Emotional disorders with onset specific to childhood,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,F94,Disorders of social functioning with onset specific to childhood and adolescence,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,F98,Other behavioural and emotional disorders with onset usually occurring in childhood and adolescence,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,F99,,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G25,Other extrapyramidal and movement disorders,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G43,Migraine,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G44,Other headache syndromes,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G45,Transient cerebral ischaemic attacks and related syndromes,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G46,Vascular syndromes of brain in cerebrovascular diseases,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G92,,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G93,Other disorders of brain,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G96,Other disorders of central nervous system,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G97,"Postprocedural disorders of nervous system, not elsewhere classified",Filter, +uhc_neurological_and_developmental_conditions,ICD-10,G98,,Filter, +uhc_neurological_and_developmental_conditions,ICD-10,H471,"Papilloedema, unspecified",Filter, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_obesity_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_obesity_ICD10.csv new file mode 100644 index 00000000..d816c00c --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_obesity_ICD10.csv @@ -0,0 +1,2 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_obesity,ICD-10,E66,Obesity,Include, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_pregnancy_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_pregnancy_ICD10.csv new file mode 100644 index 00000000..789c1d22 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_pregnancy_ICD10.csv @@ -0,0 +1,2 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_pregnancy,ICD-10,O,,Include,9 months diff --git a/_data/codelists/covid_impact_ccu02901_uhc_prematurity_and_low_birth_weight_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_prematurity_and_low_birth_weight_ICD10.csv new file mode 100644 index 00000000..dee35d54 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_prematurity_and_low_birth_weight_ICD10.csv @@ -0,0 +1,3 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_prematurity_and_low_birth_weight,ICD-10,P05,Slow fetal growth and fetal malnutrition,Include,5 years +uhc_prematurity_and_low_birth_weight,ICD-10,P07,"Disorders related to short gestation and low birth weight, not elsewhere classified",Include,5 years diff --git a/_data/codelists/covid_impact_ccu02901_uhc_renal_and_genitourinary_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_renal_and_genitourinary_conditions_ICD10.csv new file mode 100644 index 00000000..104795bc --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_renal_and_genitourinary_conditions_ICD10.csv @@ -0,0 +1,15 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_renal_and_genitourinary_conditions,ICD-10,N0,,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N11,Chronic tubulo-interstitial nephritis,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N12,,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N13,Obstructive and reflux uropathy,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N15,Other renal tubulo-interstitial diseases,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N18,Chronic kidney disease,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N31,"Neuromuscular dysfunction of bladder, not elsewhere classified",Include, +uhc_renal_and_genitourinary_conditions,ICD-10,N32,Other disorders of bladder,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,Q5,,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,Q60,Renal agenesis and other reduction defects of kidney,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,Q61,Cystic kidney disease,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,Q62,Congenital obstructive defects of renal pelvis and congenital malformations of ureter,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,Q63,Other congenital malformations of kidney,Include, +uhc_renal_and_genitourinary_conditions,ICD-10,Q64,Other congenital malformations of urinary system,Include, diff --git a/_data/codelists/covid_impact_ccu02901_uhc_respiratory_conditions_ICD10.csv b/_data/codelists/covid_impact_ccu02901_uhc_respiratory_conditions_ICD10.csv new file mode 100644 index 00000000..f0bf3cc1 --- /dev/null +++ b/_data/codelists/covid_impact_ccu02901_uhc_respiratory_conditions_ICD10.csv @@ -0,0 +1,19 @@ +Phenotype,Terminology,Code,Description,Filter,Lookback +uhc_respiratory_conditions,ICD-10,E84,Cystic fibrosis,Include, +uhc_respiratory_conditions,ICD-10,J380,Paralysis of vocal cords and larynx,Include, +uhc_respiratory_conditions,ICD-10,J386,Stenosis of larynx,Include, +uhc_respiratory_conditions,ICD-10,J41,Simple and mucopurulent chronic bronchitis,Include, +uhc_respiratory_conditions,ICD-10,J42,,Include, +uhc_respiratory_conditions,ICD-10,J43,Emphysema,Include, +uhc_respiratory_conditions,ICD-10,J44,Other chronic obstructive pulmonary disease,Include, +uhc_respiratory_conditions,ICD-10,J45,Asthma,Include, +uhc_respiratory_conditions,ICD-10,J46,,Include, +uhc_respiratory_conditions,ICD-10,J47,,Include, +uhc_respiratory_conditions,ICD-10,J82,,Include, +uhc_respiratory_conditions,ICD-10,J84,Other interstitial pulmonary diseases,Include, +uhc_respiratory_conditions,ICD-10,J99,Respiratory disorders in diseases classified elsewhere,Include, +uhc_respiratory_conditions,ICD-10,Q30,Congenital malformations of nose,Include, +uhc_respiratory_conditions,ICD-10,Q31,Congenital malformations of larynx,Include, +uhc_respiratory_conditions,ICD-10,Q32,Congenital malformations of trachea and bronchus,Include, +uhc_respiratory_conditions,ICD-10,Q33,Congenital malformations of lung,Include, +uhc_respiratory_conditions,ICD-10,Q34,Other congenital malformations of respiratory system,Include, diff --git a/_phenotypes/covid_impact_ccu01301_COVID19-infection.md b/_phenotypes/covid_impact_ccu01301_COVID19-infection.md index 2873198a..19fc363c 100644 --- a/_phenotypes/covid_impact_ccu01301_COVID19-infection.md +++ b/_phenotypes/covid_impact_ccu01301_COVID19-infection.md @@ -33,13 +33,14 @@ sex: - Female - Male author: - - Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas + - Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas, on behalf of the Longitudinal Health and Wellbeing COVID-19 National Core Study and the CVD-COVID-UK/COVID-IMPACT Consortium + publications: - - "Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination." + - "COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records." status: FINAL date: 2021-11-09 -modified_date: 2021-11-09 -version: Revision 1 +modified_date: 2022-09-08 +version: Revision 2 --- @@ -60,8 +61,8 @@ version: Revision 1 ### Publication -Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination +COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records -Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas +Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas, on behalf of theLongitudinal Health and Wellbeing COVID-19 National Core Study and the CVD-COVID-UK/COVID-IMPACT Consortium -medRxiv 2021.11.08.21265312; doi: [https://doi.org/10.1101/2021.11.08.21265312](https://doi.org/10.1101/2021.11.08.21265312) +Lancet Digital Health. 2022;4(7):e542-e557. Published Online June 8, 2022; doi: [https://doi.org/10.1016/S2589-7500(22)00091-7](https://doi.org/10.1016/S2589-7500(22)00091-7) diff --git a/_phenotypes/covid_impact_ccu02901_COVID19-admission-types.md b/_phenotypes/covid_impact_ccu02901_COVID19-admission-types.md new file mode 100644 index 00000000..57dff1c9 --- /dev/null +++ b/_phenotypes/covid_impact_ccu02901_COVID19-admission-types.md @@ -0,0 +1,60 @@ +--- +layout: phenotype +title: CCU029_01 COVID-19 admission types +name: CCU029_01 COVID-19 admission types +phenotype_id: +type: Disease or Syndrome +group: Disease or Syndrome +sources: + - bhfcvdcoviduk +data_sources: + - Trusted Research Environments for CVD-COVID-UK / COVID-IMPACT + - Hospital Episode Statistics Admitted Patient Care +clinical_terminologies: + - ICD-10 + +valid_event_data_range: 01/07/2020 - 31/03/2022 +codelists: + - covid_impact_ccu02901_covid-19_type_c_ICD10.csv + - covid_impact_ccu02901_covid-19_pims-ts_ICD10.csv + - covid_impact_ccu02901_covid-19_type_a1_ICD10.csv + - covid_impact_ccu02901_covid-19_type_a2_ICD10.csv + - covid_impact_ccu02901_covid-19_type_b1_ICD10.csv + - covid_impact_ccu02901_covid-19_type_b2_ICD10.csv + +sex: + - Female + - Male +author: + - Harrison Wilde, Christopher Tomlinson, Bilal A Mateen, David Selby, Hari Krishnan Kanthimathinathan, Padmanabhan Ramnarayan, Pascale Du Pre, Mae Johnson, Nazima Pathan, Arturo Gonzalez-Izquierdo, Alvina G Lai, Deepti Gurdasani, Christina Pagel, Spiros Denaxas, Sebastian Vollmer, Katherine Brown, On behalf of the CVD-COVID-UK/COVID-IMPACT consortium +publications: + - "Hospital admissions linked to SARS-CoV-2 infection in children: a cohort study of 3.2 million first ascertained infections in England" +status: DRAFT +date: 2022-09-15 +modified_date: 2022-09-15 +version: Version 1 + +--- + +### Phenotypes + +#### England hospitalization EHR: COVID-19 admission - Type C +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_covid-19_type_c_ICD10 %} +#### England hospitalization EHR: COVID-19 admission - PIMS-TS +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_covid-19_pims-ts_ICD10 %} +#### England hospitalization EHR: COVID-19 admission - Type A1 +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_covid-19_type_a1_ICD10 %} +#### England hospitalization EHR: COVID-19 admission - Type A2 +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_covid-19_type_a2_ICD10 %} +#### England hospitalization EHR: COVID-19 admission - Type B1 +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_covid-19_type_b1_ICD10 %} +#### England hospitalization EHR: COVID-19 admission - Type B2 +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_covid-19_type_b2_ICD10 %} + +### Publication + +Hospital admissions linked to SARS-CoV-2 infection in children: a cohort study of 3.2 million first ascertained infections in England + +Harrison Wilde, Christopher Tomlinson, Bilal A Mateen, David Selby, Hari Krishnan Kanthimathinathan, Padmanabhan Ramnarayan, Pascale Du Pre, Mae Johnson, Nazima Pathan, Arturo Gonzalez-Izquierdo, Alvina G Lai, Deepti Gurdasani, Christina Pagel, Spiros Denaxas, Sebastian Vollmer, Katherine Brown, On behalf of the CVD-COVID-UK/COVID-IMPACT consortium + +Journal 2022.MM.DD; doi: [https://doi.org/](https://doi.org/) diff --git a/_phenotypes/covid_impact_ccu02901_green_book_conditions.md b/_phenotypes/covid_impact_ccu02901_green_book_conditions.md new file mode 100644 index 00000000..7c557546 --- /dev/null +++ b/_phenotypes/covid_impact_ccu02901_green_book_conditions.md @@ -0,0 +1,77 @@ +--- +layout: phenotype +title: CCU029_01 Green Book Conditions +name: CCU029_01 Green Book Conditions +phenotype_id: +type: Disease or Syndrome +group: Disease or Syndrome +sources: + - bhfcvdcoviduk +data_sources: + - Trusted Research Environments for CVD-COVID-UK / COVID-IMPACT + - Hospital Episode Statistics Admitted Patient Care +clinical_terminologies: + - ICD-10 + +valid_event_data_range: 01/07/2003 - 31/03/2022 +codelists: + - covid_impact_ccu02901_green_book_arthritis_and_connective_tissue_diseases_ICD10.csv + - covid_impact_ccu02901_green_book_blood_disorders_and_immune_deficiencies_ICD10.csv + - covid_impact_ccu02901_green_book_cancer_ICD10.csv + - covid_impact_ccu02901_green_book_congenital_syndromes_and_anomalies_ICD10.csv + - covid_impact_ccu02901_green_book_digestive_and_liver_diseases_ICD10.csv + - covid_impact_ccu02901_green_book_endocrine_conditions_ICD10.csv + - covid_impact_ccu02901_green_book_hypertension_and_cardiac_valves_and_cardiomyopathy_ICD10.csv + - covid_impact_ccu02901_green_book_obesity_ICD10.csv + - covid_impact_ccu02901_green_book_pregnancy_ICD10.csv + - covid_impact_ccu02901_green_book_renal_diseases_ICD10.csv + - covid_impact_ccu02901_green_book_severe_neurological_and_developmental_conditions_ICD10.csv + - covid_impact_ccu02901_green_book_severe_respiratory_diseases_ICD10.csv +sex: + - Female + - Male +author: + - Harrison Wilde, Christopher Tomlinson, Bilal A Mateen, David Selby, Hari Krishnan Kanthimathinathan, Padmanabhan Ramnarayan, Pascale Du Pre, Mae Johnson, Nazima Pathan, Arturo Gonzalez-Izquierdo, Alvina G Lai, Deepti Gurdasani, Christina Pagel, Spiros Denaxas, Sebastian Vollmer, Katherine Brown, On behalf of the CVD-COVID-UK/COVID-IMPACT consortium +publications: + - "Hospital admissions linked to SARS-CoV-2 infection in children: a cohort study of 3.2 million first ascertained infections in England" +status: DRAFT +date: 2022-09-15 +modified_date: 2022-09-15 +version: Version 1 + +--- + +### Phenotypes + +#### England hospitalization EHR: Arthritis & connective tissue diseases +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_arthritis_and_connective_tissue_diseases_ICD10 %} +#### England hospitalization EHR: Blood disorders & immune deficiencies +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_blood_disorders_and_immune_deficiencies_ICD10 %} +#### England hospitalization EHR: Cancer +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_cancer_ICD10 %} +#### England hospitalization EHR: Congenital syndromes & anomalies +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_congenital_syndromes_and_anomalies_ICD10 %} +#### England hospitalization EHR: Digestive & liver diseases +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_digestive_and_liver_diseases_ICD10 %} +#### England hospitalization EHR: Endocrine conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_endocrine_conditions_ICD10 %} +#### England hospitalization EHR: Hypertension and cardiac valves and cardiomyopathy +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_hypertension_and_cardiac_valves_and_cardiomyopathy_ICD10 %} +#### England hospitalization EHR: Obesity +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_obesity_ICD10 %} +#### England hospitalization EHR: Pregnancy +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_pregnancy_ICD10 %} +#### England hospitalization EHR: Renal diseases +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_renal_diseases_ICD10 %} +#### England hospitalization EHR: Severe neurological & developmental conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_severe_neurological_and_developmental_conditions_ICD10 %} +#### England hospitalization EHR: Severe respiratory diseases +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_green_book_severe_respiratory_diseases_ICD10 %} + +### Publication + +Hospital admissions linked to SARS-CoV-2 infection in children: a cohort study of 3.2 million first ascertained infections in England + +Harrison Wilde, Christopher Tomlinson, Bilal A Mateen, David Selby, Hari Krishnan Kanthimathinathan, Padmanabhan Ramnarayan, Pascale Du Pre, Mae Johnson, Nazima Pathan, Arturo Gonzalez-Izquierdo, Alvina G Lai, Deepti Gurdasani, Christina Pagel, Spiros Denaxas, Sebastian Vollmer, Katherine Brown, On behalf of the CVD-COVID-UK/COVID-IMPACT consortium + +Journal 2022.MM.DD; doi: [https://doi.org/](https://doi.org/) diff --git a/_phenotypes/covid_impact_ccu02901_underlying_health_conditions.md b/_phenotypes/covid_impact_ccu02901_underlying_health_conditions.md new file mode 100644 index 00000000..e4a0e864 --- /dev/null +++ b/_phenotypes/covid_impact_ccu02901_underlying_health_conditions.md @@ -0,0 +1,77 @@ +--- +layout: phenotype +title: CCU029_01 Underlying Health Conditions +name: CCU029_01 Underlying Health Conditions +phenotype_id: +type: Disease or Syndrome +group: Disease or Syndrome +sources: + - bhfcvdcoviduk +data_sources: + - Trusted Research Environments for CVD-COVID-UK / COVID-IMPACT + - Hospital Episode Statistics Admitted Patient Care +clinical_terminologies: + - ICD-10 + +valid_event_data_range: 01/07/2003 - 31/03/2022 +codelists: + - covid_impact_ccu02901_uhc_blood_disorders_and_immune_deficiencies_ICD10.csv + - covid_impact_ccu02901_uhc_cancer_and_neoplasms_ICD10.csv + - covid_impact_ccu02901_uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease_ICD10.csv + - covid_impact_ccu02901_uhc_digestive_and_liver_conditions_ICD10.csv + - covid_impact_ccu02901_uhc_endocrine_conditions_ICD10.csv + - covid_impact_ccu02901_uhc_muscle_and_skin_and_arthritis_ICD10.csv + - covid_impact_ccu02901_uhc_neurological_and_developmental_conditions_ICD10.csv + - covid_impact_ccu02901_uhc_obesity_ICD10.csv + - covid_impact_ccu02901_uhc_pregnancy_ICD10.csv + - covid_impact_ccu02901_uhc_prematurity_and_low_birth_weight_ICD10.csv + - covid_impact_ccu02901_uhc_renal_and_genitourinary_conditions_ICD10.csv + - covid_impact_ccu02901_uhc_respiratory_conditions_ICD10.csv +sex: + - Female + - Male +author: + - Harrison Wilde, Christopher Tomlinson, Bilal A Mateen, David Selby, Hari Krishnan Kanthimathinathan, Padmanabhan Ramnarayan, Pascale Du Pre, Mae Johnson, Nazima Pathan, Arturo Gonzalez-Izquierdo, Alvina G Lai, Deepti Gurdasani, Christina Pagel, Spiros Denaxas, Sebastian Vollmer, Katherine Brown, On behalf of the CVD-COVID-UK/COVID-IMPACT consortium +publications: + - "Hospital admissions linked to SARS-CoV-2 infection in children: a cohort study of 3.2 million first ascertained infections in England" +status: DRAFT +date: 2022-09-15 +modified_date: 2022-09-15 +version: Version 1 + +--- + +### Phenotypes + +#### England hospitalization EHR: Blood disorders & immune deficiencies +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_blood_disorders_and_immune_deficiencies_ICD10 %} +#### England hospitalization EHR: Cancer & neoplasms +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_cancer_and_neoplasms_ICD10 %} +#### England hospitalization EHR: Congenital heart disease and hypertension and acquired heart disease +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_congenital_heart_disease_and_hypertension_and_acquired_heart_disease_ICD10 %} +#### England hospitalization EHR: Digestive & liver conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_digestive_and_liver_conditions_ICD10 %} +#### England hospitalization EHR: Endocrine conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_endocrine_conditions_ICD10 %} +#### England hospitalization EHR: Muscle and skin and arthritis +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_muscle_and_skin_and_arthritis_ICD10 %} +#### England hospitalization EHR: Neurological & developmental conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_neurological_and_developmental_conditions_ICD10 %} +#### England hospitalization EHR: Obesity +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_obesity_ICD10 %} +#### England hospitalization EHR: Pregnancy +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_pregnancy_ICD10 %} +#### England hospitalization EHR: Prematurity & low birth weight +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_prematurity_and_low_birth_weight_ICD10 %} +#### England hospitalization EHR: Renal & genitourinary conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_renal_and_genitourinary_conditions_ICD10 %} +#### England hospitalization EHR: Respiratory conditions +{% include csv.html csvdata=site.data.codelists.covid_impact_ccu02901_uhc_respiratory_conditions_ICD10 %} + +### Publication + +Hospital admissions linked to SARS-CoV-2 infection in children: a cohort study of 3.2 million first ascertained infections in England + +Harrison Wilde, Christopher Tomlinson, Bilal A Mateen, David Selby, Hari Krishnan Kanthimathinathan, Padmanabhan Ramnarayan, Pascale Du Pre, Mae Johnson, Nazima Pathan, Arturo Gonzalez-Izquierdo, Alvina G Lai, Deepti Gurdasani, Christina Pagel, Spiros Denaxas, Sebastian Vollmer, Katherine Brown, On behalf of the CVD-COVID-UK/COVID-IMPACT consortium + +Journal 2022.MM.DD; doi: [https://doi.org/](https://doi.org/)