Update concept sets for UC1 tables 5.15 - 5.19 & UC3 tables

project/R/conceptSets.R

@@ -78,6 +78,117 @@ conceptSets <- list(
       4020812, # source: Plastic repair of aorta and end to end anastomosis of aorta /// concept: Plastic repair of aorta and end-to-end anastomosis of aorta
       4019026, # source: Other specified: plastic repair of aorta /// concept: Plastic repair of aorta
       44510968  # source: Other specified other operations on ventricles of heart /// concept: Other specified other operations on ventricles of heart
+    ),
+
+    # 
+    vitalSigns = c(
+      3027018, # source: Age-dependent HR /// concept: Heart rate
+      3024171, # source: Age-dependent RR /// concept: Respiratory rate
+      3004249, # source: SBP (Systolic Blood Pressure) /// concept: Systolic blood pressure
+      3012888, # source: DBP (Dyastolic Blood Pressure) /// concept: Diastolic blood pressure
+      4020553 # source: SpO2 /// concept: Oxygen saturation measurement
+    ),
+
+    # 5.16 HSJD clinical
+    HSJDClinical = c(
+      3025315, # source: Weight /// concept: Body weight
+      3036277, # source: Height /// concept: Body height
+      4201235, # source: Body Surface Area (BSA) - Combination of weight and height /// concept: body surface area
+      4275564 # source: Cardiac surgeries (Interventions) /// concept: Operation on heart
+    ), 
+
+    # 5.17 HSJD Surgery
+    HSJDSurgery = c(
+      40490494, # source: STAT/EACTS score of surgery /// concept: Society of Thoracic Surgeons risk calculator
+      4301351, # source: Surgery start datetime, end datetime /// concept: Surgical procedure
+      4336464, # source: Cardiac bypass start datetime, end datetime /// concept: Coronary artery bypass graft
+      4201547, # source: Cross-clamping start datetime, end datetime /// concept: Placement of arterial cross clamp
+      37152781, # source: Deep hypothermic circulatory arrest start datetime, end datetime /// concept: Hypothermic circulatory arrest
+      4272324, # source: Antegrade Cerebral Perfusion start datetime, end datetime /// concept: Cardiopulmonary bypass operation
+      4150627 # source: Extubation event /// concept: Removal of endotracheal tube
+    ),
+
+    # 5.18 HSJD Hospitalisations 
+    HSJDHospitalisation = c(
+      44803020, # source: Admission reason /// concept: Primary reason for admission
+      42539650, # source: Vasoactive infusion start datetime, end datetime /// concept: Administration of intravenous vasoactive drug
+      4179206, # source: Postop central venous catheter in/start datetime, out/end datetime /// concept: Central venous catheter
+      37158404, # source: Invasive Mechanical Ventilation LOS /// concept: Invasive mechanical ventilation
+      4177224 # source: Non-Invasive Mechanical Ventilation LOS /// concept: Non-invasive ventilation
+    ),
+
+    # 5.19 HSJD Complications
+    HSJDcomplications = c(
+      4202832, # source: intubation /// concept: Intubation
+      4275564, # source: Cardiac surgeries (interventions) /// concept: Operation on heart
+      4044892, # source: Sternum reopening (procedure undertaken) /// concept: Procedure on sternum
+      4046868, # source: Vocal Cord Dysfunction /// concept: Vocal cord dysfunction
+      4275136, # source: Diaphragmatic Paralysis /// concept: Paralysis of diaphragm
+      253796, # source: Pneumothorax /// concept: Pneumothorax
+      44783799, # source: Tracheostomy /// concept: Exteriorization of trachea
+      44784217, # source: Arrhythmia diagnosis (tachyarrhythmia, bradyarrhythmia, atrial, ventricular etc.) /// concept: Cardiac arrhythmia
+      315643, # source: Arrhythmia diagnosis (tachyarrhythmia, bradyarrhythmia, atrial, ventricular etc.) /// concept: Tachyarrhythmia
+      4228448, # source: Arrhythmia diagnosis (tachyarrhythmia, bradyarrhythmia, atrial, ventricular etc.) /// concept: Bradyarrhythmia
+      4068155, # source: Arrhythmia diagnosis (tachyarrhythmia, bradyarrhythmia, atrial, ventricular etc.) /// concept: Atrial arrhythmia
+      4185572, # source: Arrhythmia diagnosis (tachyarrhythmia, bradyarrhythmia, atrial, ventricular etc.) /// concept: Ventricular arrhythmia
+      46234437, # source: Drugs administered; Arrhythmia therapy (drugs): IV anthyarritmics (ivabradine, amiodarone, flecainide) /// concept: ivabradine
+      1309944, # source: Drugs administered; Arrhythmia therapy (drugs): IV anthyarritmics (ivabradine, amiodarone, flecainide) /// concept: amiodarone
+      1354860, # source: Drugs administered; Arrhythmia therapy (drugs): IV anthyarritmics (ivabradine, amiodarone, flecainide) /// concept: flecainide
+      4353741, # source: Arrhythmia therapy (procedures): Cardioversion, Rapid atrial pacing, temporary pacing, permanent pacing /// concept: Cardioversion
+      4117045, # source: Arrhythmia therapy (procedures): Cardioversion, Rapid atrial pacing, temporary pacing, permanent pacing /// concept: Atrial overdrive pacing
+      4049398, # source: Arrhythmia therapy (procedures): Cardioversion, Rapid atrial pacing, temporary pacing, permanent pacing /// concept: Temporary cardiac pacemaker procedure
+      4051940, # source: Arrhythmia therapy (procedures): Cardioversion, Rapid atrial pacing, temporary pacing, permanent pacing /// concept: Permanent cardiac pacemaker procedure
+      609312 # source: Listed for heart transplantation /// concept: Awaiting transplantation of heart
+      ),
+
+    # 5.28 Patient characteristics 
+    UC3PateintCharacteristics = c(
+      434007, # source: hemophilia A diagnosis /// concept: hereditary factor VIII deficiency disease
+      4094223, # source: hemophilia A subtype/ severity /// concept: mild hereditary factor VIII deficiency disease
+      4140661, # source: hemophilia A subtype/ severity /// concept: moderate hereditary factor VIII deficiency disease
+      4056830, # source: hemophilia A subtype/ severity /// concept: severe hereditary factor VIII deficiency disease
+      3003694, # source: blood group /// concept: ABO and Rh group [Type] in Blood
+      37393608, # source: factor VIII inhibitor status /// concept: factor VIII inhibitor activity
+      4126681, # source: factor VIII inhibitor status /// concept: detected
+      9190 # source: factor VIII inhibitor status /// concept: not detected
+    ),
+
+    # 5.29 Lab Measurements
+    UC3LabMeasurements = c(
+      3024942, # source: factor VIII inhibitor titer /// concept: coagulation factor VIII inhibitor [Units/volume] in platelet poor plasma by coagulation assay
+      3022520, # source: factor VIII activity measurement /// concept: coagulation factor VIII activated [Units/volume] in platelet poor plasma by coagulation assay
+      3011832, # source: factor VIII activity measurement /// concept: coagulation factor VIII activity [Units/volume] in platelet poor plasma by Chromogenic assay
+      43534000, # source: Von Willebrand factor activity measurement /// concept: von Willebrand factor (vWf) activity [Units/volume] in platelet poor plasma by Immunoassay
+      3002124, # source: Von Willebrand factor antigen measurement /// concept: von Willebrand factor (vWf) Ag [Units/volume] in platelet poor plasma by Immunoassay
+      3023693, # source: Von Willebrand factor propeptide measurement /// concept: von Willebrand factor (vWf) multimers in platelet poor plasma by Immunoblot
+      3042349, # source: Von Willebrand factor propeptide measurement /// concept: von Willebrand factor (vWf) cleaving protease inhibitor [Units/volume] in platelet poor plasma
+      4175016, # source: activated partial thromboplastin time (APTT) /// concept: partial thromboplastin time, activated
+      3034426, # source: Prothrombin time (PT) /// concept: prothrombin time (PT)
+      4267147, # source: platelet count /// concept: platelet count
+      3009542, # source: hematocrit /// concept: Hematocrit [Volume Fraction] of Blood
+      3016407, # source: fibrinogen /// concept: fibrinogen [mass/volume] in platelet poor plasma by coagulation assay
+      3006923, # source: ALT /// concept: alanine aminotransferase [enzymatic activity/volume] in serum or plasma
+      3013721 # source: AST /// concept: aspartate aminotransferase [enzymatic activity/volume] in serum or plasma
+    ),
+
+    # 5.30 Treatments 
+    UC3Treatments = c(
+      1352213, # source: factor VIII /// concept: factor VIII (umbrella term)
+      793042, # source: factor VIII /// concept: emicizumab (umbrella term)
+      40492862, # source: factor VIII dose is continuous infusion or bolus dose /// concept: mode of drug administration
+      4129275, # source: factor VIII dose is continuous infusion or bolus dose /// concept: continuous infusion
+      4265597, # source: factor VIII dose is continuous infusion or bolus dose /// concept: by bolus infusions
+      1517070 # source: desmopressin /// concept: desmopressin
+    ),
+
+    # 5.31 Surgery-specific parameters
+    UC3Surgery = c(
+      4172515, # source: Medical/ surgical procedure /// concept: Therapeutic procedure
+      967823, # source: NaCl administration during surgery /// concept: sodium chloride
+      4028665, # source: plasma administration during surgery /// concept: plasma transfusion
+      4160439, # source: datetime start anesthesia /// concept: Administration of anesthesia
+      4308716, # source: blood loss during surgery /// concept: intraoperative hemorrhage
+      37017589 # source: blood transfusion during surgery /// concept: Bleeding during surgery requiring transfusion
     )
   )
 )

project/data/phems_variable_list/5.15_vital_signs.csv

@@ -1,4 +1,4 @@
-sourceCode,concept_id
+sourceCode,concept_id
 Age-dependent HR ,4239408 
 Age-dependent HR ,8483 
 Age-dependent RR ,4313591 
@@ -7,7 +7,7 @@ SBP (Systolic Blood Pressure) ,4152194 
 SBP (Systolic Blood Pressure) ,8876 
 DBP (Dyastolic Blood Pressure) ,4154790 
 DBP (Dyastolic Blood Pressure) ,8876 
-SpO2 ,4096101 
+SpO2 ,4020553 
 SpO2 ,8554 
 ,
 ,

project/data/phems_variable_list/5.17_hsjd_surgery.csv

@@ -1,10 +1,10 @@
-sourceCode,concept_id
+sourceCode,concept_id
 Aristotle's score of surgery ,0 
 STAT/EACTS score of surgery ,40490494 
 "Surgery start datetime, end datetime ",4301351 
 "Cardiac bypass start datetime, end datetime ",4336464 
 "Cross-clamping start datetime, end datetime ",4201547 
-"Deep hypothermic circulatory arrest start datetime, end datetime ",44790138 
+"Deep hypothermic circulatory arrest start datetime, end datetime ",37152781 
 "Antegrade Cerebral Perfusion start datetime, end datetime ",4272324 
 Extubation event ,4150627 
 ,

project/data/phems_variable_list/5.18_hsjd_hospitalisation.csv

@@ -1,9 +1,8 @@
-sourceCode,concept_id
+sourceCode,concept_id
 Admission reason ,44803020 
 ventilation ,0 
 "Vasoactive infusion start datetime, end datetime ",42539650 
 Type of vasoactive infusion ,0 
-Dose of vasoactive infusion (rate - mcg/kg/hr) ,794078 
 VIS score of vasoactive infusion ,0 
 "Postop central venous catheter in/start datetime, out/ end datetime ",4179206 
 "Total ventilation start datetime, end datetime ",0 

project/data/phems_variable_list/5.28_uc3_patient_characteristics.csv

@@ -0,0 +1,15 @@
+sourceCode,concept_id
+body weight,3025315
+body weight,9529
+body weight,8504
+height,3036277
+height,8582
+height,9546
+hemophilia A diagnosis,434007
+hemophilia A subtype/ severity,4094223
+hemophilia A subtype/ severity,4140661
+hemophilia A subtype/ severity,4056830
+blood group,3003694
+factor VIII inhibitor status,37393608
+factor VIII inhibitor status,4126681
+factor VIII inhibitor status,9190

project/data/phems_variable_list/5.29_uc3_lab_measurements.csv

@@ -0,0 +1,37 @@
+sourceCode,concept_id
+factor VIII inhibitor titer,3024942
+factor VIII inhibitor titer,44777562
+factor VIII activity measurement,3022520
+factor VIII activity measurement,3011832
+factor VIII activity measurement,8985
+factor VIII activity measurement,9332
+factor VIII activity measurement,8554
+Von Willebrand factor activity measurement,43534000
+Von Willebrand factor activity measurement,8985
+Von Willebrand factor activity measurement,9332
+Von Willebrand factor activity measurement,8554
+Von Willebrand factor antigen measurement,3002124
+Von Willebrand factor antigen measurement,8985
+Von Willebrand factor antigen measurement,9332
+Von Willebrand factor antigen measurement,8554
+Von Willebrand factor propeptide measurement,3023693
+Von Willebrand factor propeptide measurement,3042349
+Von Willebrand factor propeptide measurement,8763
+activated partial thromboplastin time (APTT),4175016
+activated partial thromboplastin time (APTT),8555
+activated partial thromboplastin time (APTT),8523
+Prothrombin time (PT),3034426
+Prothrombin time (PT),8555
+Prothrombin time (PT),8523
+Prothrombin time (PT),8554
+platelet count,4267147
+platelet count,44777588
+hematocrit,3009542
+hematocrit,44777604
+hematocrit,8554
+fibrinogen,3016407
+fibrinogen,8636
+ALT,3006923
+ALT,8645
+AST,3013721
+AST,8645

project/data/phems_variable_list/5.30_uc3_treatments.csv

@@ -0,0 +1,42 @@
+sourceCode,concept_id
+factor VIII,35766745
+factor VIII,35771058
+factor VIII,35754324
+factor VIII,35758435
+factor VIII,35771055
+factor VIII,43515206
+factor VIII,35762625
+factor VIII,21154209
+factor VIII,21085384
+factor VIII,21075681
+factor VIII,21124454
+factor VIII,21095190
+factor VIII,2061062
+factor VIII,2061050
+factor VIII,2061030
+factor VIII,2061007
+factor VIII,2061102
+factor VIII,35771458
+factor VIII,35758810
+factor VIII,35758809
+factor VIII,35754712
+factor VIII,2923922
+factor VIII,43290877
+factor VIII,2923914
+factor VIII,43269176
+factor VIII,2923932
+factor VIII,43263693
+factor VIII,2923927
+factor VIII,43258267
+factor VIII,40745282
+factor VIII,43026972
+factor VIII,40745288
+factor VIII,43026968
+factor VIII,8985
+factor VIII dose is continuous infusion or bolus dose,40492862
+factor VIII dose is continuous infusion or bolus dose,4129275
+factor VIII dose is continuous infusion or bolus dose,4265597
+desmopressin,1517070
+desmopressin,9655
+desmopressin,8576
+desmopressin,9662

project/data/phems_variable_list/5.31_uc3_surgery.csv

@@ -0,0 +1,8 @@
+sourceCode,concept_id
+Medical/ surgical procedure,4172515
+NaCl administration during surgery,967823
+NaCl administration during surgery,8587
+plasma administration during surgery,4028665
+datetime start anesthesia,4160439
+blood loss during surgery,4308716
+blood transfusion during surgery,37017589