diff --git a/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv b/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv index 22630353..342ddd89 100644 --- a/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv +++ b/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv @@ -21,4 +21,4 @@ FIELD,plausibleTemporalAfter,The number and percent of records with a value in t FIELD,plausibleDuringLife,"If yes, the number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_during_life.sql,plausibleDuringLife=='Yes' FIELD,withinVisitDates,The number and percent of records not within one week on either side of the corresponding visit occurrence start and end date,Verification,Conformance,,field_within_visit_dates.sql,withinVisitDates=='Yes' CONCEPT,plausibleGender,"For a CONCEPT_ID @conceptId (@conceptName), the number and percent of records associated with patients with an implausible gender (correct gender = @plausibleGender).",Validation,Plausibility,Atemporal,concept_plausible_gender.sql,plausibleGender!='' -CONCEPT,plausibleUnitConceptIds,"The number and percent of records for a given CONCEPT_ID @conceptId (@conceptName) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (@plausibleUnitConceptIds)).",Verification,Plausibility,Atemporal,concept_plausible_unit_concept_ids.sql,plausibleUnitConceptIdsThreshold!='' \ No newline at end of file +CONCEPT,plausibleUnitConceptIds,"The number and percent of records for a given CONCEPT_ID @conceptId (@conceptName) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN (@plausibleUnitConceptIds), '-1' means unit_concept_id can be null).",Verification,Plausibility,Atemporal,concept_plausible_unit_concept_ids.sql,plausibleUnitConceptIdsThreshold!='' diff --git a/inst/csv/OMOP_CDMv5.4_Concept_Level.csv b/inst/csv/OMOP_CDMv5.4_Concept_Level.csv index cd7b4f83..9de41101 100644 --- a/inst/csv/OMOP_CDMv5.4_Concept_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Concept_Level.csv @@ -348,15 +348,15 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013721,Aspartate aminotransferase [Enzymatic MEASUREMENT,MEASUREMENT_CONCEPT_ID,3019198,Lymphocytes [#/volume] in Blood,,,,,,,,,,,,,,,,,,,,,"8784,8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3034426,Prothrombin time (PT),,,,,,,,,,,,,,,,,,,,,8555,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3043688,Hemoglobin [Mass/volume] in Body fluid,,,,,,,,,,,,,,,,,,,,,8713,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3046485,Urea nitrogen/Creatinine [Mass Ratio] in Blood,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3046485,Urea nitrogen/Creatinine [Mass Ratio] in Blood,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4216098,Eosinophil count,,,,,,,,,,,,,,,,,,,,,"8784,8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4245152,Potassium measurement,,,,,,,,,,,,,,,,,,,,,"8736,8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,43055141,Pain severity - 0-10 verbal numeric rating [Score] - Reported,,,,,,,,,,,,,,,,,,,,,NA,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,43055141,Pain severity - 0-10 verbal numeric rating [Score] - Reported,,,,,,,,,,,,,,,,,,,,,-1,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3006923,Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8645,8923",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3021044,Iron binding capacity [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8837,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3024171,Respiratory rate,,,,,,,,,,,,,,,,,,,,,"8483,8541",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3027114,Cholesterol [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,40762499,Oxygen saturation in Arterial blood by Pulse oximetry,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,40762499,Oxygen saturation in Arterial blood by Pulse oximetry,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3000963,Hemoglobin [Mass/volume] in Blood,,,,,,,,,,,,,,,,,,,,,"8636,8713",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3001604,Monocytes [#/volume] in Blood,,,,,,,,,,,,,,,,,,,,,"8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3019069,Monocytes/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -371,12 +371,12 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3028615,Eosinophils [#/volume] in Blood by Au MEASUREMENT,MEASUREMENT_CONCEPT_ID,3051205,Crystals [#/area] in Urine sediment by Microscopy high power field,,,,,,,,,,,,,,,,,,,,,8786,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4098046,Pulse oximetry,,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3005131,Glucose mean value [Mass/volume] in Blood Estimated from glycated hemoglobin,,,,,,,,,,,,,,,,,,,,,"8840,9028",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3011163,Cholesterol.total/Cholesterol in HDL [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8529,8554,8596,8606,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3011163,Cholesterol.total/Cholesterol in HDL [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8529,8554,8596,8606,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3044491,Cholesterol non HDL [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8576,8840,9028",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4017361,Blood urea nitrogen measurement,,,,,,,,,,,,,,,,,,,,,"8753,8840",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3006504,Eosinophils/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3000483,Glucose [Mass/volume] in Blood,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3033543,Specific gravity of Urine,,,,,,,,,,,,,,,,,,,,,"8523,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3033543,Specific gravity of Urine,,,,,,,,,,,,,,,,,,,,,"8523,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3045716,Anion gap in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4101713,High density lipoprotein cholesterol measurement,,,,,,,,,,,,,,,,,,,,,"8636,8736,8753,8840",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4103762,Anion gap measurement,,,,,,,,,,,,,,,,,,,,,"8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -390,14 +390,14 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3035995,Alkaline phosphatase [Enzymatic activ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3038553,Body mass index (BMI) [Ratio],,,,,,,,,,,,,,,,,,,,,9531,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,35610320,Diastolic arterial pressure,,,,,,,,,,,,,,,,,,,,,8876,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3001490,Nucleated erythrocytes [#/volume] in Blood,,,,,,,,,,,,,,,,,,,,,"8784,8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,4195214,Cholesterol/HDL ratio measurement,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,4195214,Cholesterol/HDL ratio measurement,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,36306178,"Glomerular filtration rate/1.73 sq M.predicted among blacks [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)",,,,,,,,,,,,,,,,,,,,,"720870,8795",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,37393850,MCHC - Mean corpuscular haemoglobin concentration,,,,,,,,,,,,,,,,,,,,,"8636,8713",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3004501,Glucose [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3008598,Thyroxine (T4) free [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8817,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3018010,Neutrophils/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3018010,Neutrophils/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3022192,Triglyceride [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,4151768,Pack years,,,,,,,,,,,,,,,,,,,,,"9448,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,4151768,Pack years,,,,,,,,,,,,,,,,,,,,,"9448,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4197602,Serum TSH measurement,,,,,,,,,,,,,,,,,,,,,"8719,9040,9093",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,46236952,"Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (MDRD)",,,,,,,,,,,,,,,,,,,,,"720870,8795",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3006906,Calcium [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -416,7 +416,7 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3040168,Immature granulocytes [#/volume] in B MEASUREMENT,MEASUREMENT_CONCEPT_ID,4097430,Sodium measurement,,,,,,,,,,,,,,,,,,,,,"8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3005424,Body surface area,,,,,,,,,,,,,,,,,,,,,8617,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013603,Prostate specific Ag [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8748,8842",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3020509,Albumin/Globulin [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3020509,Albumin/Globulin [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3036277,Body height,,,,,,,,,,,,,,,,,,,,,"8582,9327,9330,9546",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4301868,Pulse rate,,,,,,,,,,,,,,,,,,,,,"8483,8541,8581",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,40762636,Body mass index (BMI) [Percentile],,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -424,10 +424,10 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,40765040,25-Hydroxyvitamin D3+25-Hydroxyvitam MEASUREMENT,MEASUREMENT_CONCEPT_ID,3024386,Platelet mean volume [Entitic volume] in Blood by Rees-Ecker,,,,,,,,,,,,,,,,,,,,,8583,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3009201,Thyrotropin [Units/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"44777578,8719,9040,9093",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3024731,MCV [Entitic volume],,,,,,,,,,,,,,,,,,,,,8583,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3050479,Immature granulocytes/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3050479,Immature granulocytes/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4012479,Low density lipoprotein cholesterol measurement,,,,,,,,,,,,,,,,,,,,,"8636,8753,8840",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4152194,Systolic blood pressure,,,,,,,,,,,,,,,,,,,,,8876,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,37393840,Haematocrit,,,,,,,,,,,,,,,,,,,,,"44777604,8523,8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,37393840,Haematocrit,,,,,,,,,,,,,,,,,,,,,"44777604,8523,8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3000593,Cobalamin (Vitamin B12) [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8845,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3002888,Erythrocyte distribution width [Entitic volume],,,,,,,,,,,,,,,,,,,,,8583,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3010910,Erythrocytes [#/volume] in Body fluid,,,,,,,,,,,,,,,,,,,,,"8647,8785,8815,8931",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -439,7 +439,7 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3023103,Potassium [Moles/volume] in Serum or MEASUREMENT,MEASUREMENT_CONCEPT_ID,4030871,Red blood cell count,,,,,,,,,,,,,,,,,,,,,"8734,8815,8931,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4154790,Diastolic blood pressure,,,,,,,,,,,,,,,,,,,,,8876,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4217013,Systolic arterial pressure,,,,,,,,,,,,,,,,,,,,,8876,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3001318,Cholesterol.total/Cholesterol in HDL [Percentile],,,,,,,,,,,,,,,,,,,,,"8554,8596,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3001318,Cholesterol.total/Cholesterol in HDL [Percentile],,,,,,,,,,,,,,,,,,,,,"8554,8596,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3004249,Systolic blood pressure,,,,,,,,,,,,,,,,,,,,,8876,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3009596,Cholesterol in VLDL [Mass/volume] in Serum or Plasma by calculation,,,,,,,,,,,,,,,,,,,,,"8576,8840",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3025315,Body weight,,,,,,,,,,,,,,,,,,,,,"8739,9346,9373,9529",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -449,11 +449,11 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,36303797,"Glomerular filtration rate/1.73 sq MEASUREMENT,MEASUREMENT_CONCEPT_ID,37398460,Serum alkaline phosphatase level,,,,,,,,,,,,,,,,,,,,,"32995,8645,8923",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013682,Urea nitrogen [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3026361,Erythrocytes [#/volume] in Blood,,,,,,,,,,,,,,,,,,,,,"32706,8785,8815,8931",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3027018,Heart rate,,,,,,,,,,,,,,,,,,,,,"8483,8541,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3027018,Heart rate,,,,,,,,,,,,,,,,,,,,,"8483,8541,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4013965,"Oxygen saturation measurement, arterial",,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,"8784,8816,8848,8961,9436,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3023599,MCV [Entitic volume] by Automated count,,,,,,,,,,,,,,,,,,,,,8583,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3036588,Neutrophil cytoplasmic Ab.perinuclear [Presence] in Serum,,,,,,,,,,,,,,,,,,,,,"8525,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3036588,Neutrophil cytoplasmic Ab.perinuclear [Presence] in Serum,,,,,,,,,,,,,,,,,,,,,"8525,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4298431,White blood cell count,,,,,,,,,,,,,,,,,,,,,"8848,8961",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3017732,Neutrophils [#/volume] in Blood,,,,,,,,,,,,,,,,,,,,,"8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3024561,Albumin [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8636,8713",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -475,14 +475,14 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,4313591,Respiratory rate,,,,,,,,,,,,,,,,,,,,, MEASUREMENT,MEASUREMENT_CONCEPT_ID,37393851,MCV - Mean corpuscular volume,,,,,,,,,,,,,,,,,,,,,8583,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,1619025,"Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI 2021)",,,,,,,,,,,,,,,,,,,,,"720870,8795",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013869,Basophils/100 leukocytes in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3035472,Albumin/Protein.total in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3035472,Albumin/Protein.total in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3039000,Anion gap in Blood,,,,,,,,,,,,,,,,,,,,,"8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3000905,Leukocytes [#/volume] in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,"8816,8848,8961,9436,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3015632,"Carbon dioxide, total [Moles/volume] in Serum or Plasma",,,,,,,,,,,,,,,,,,,,,"8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3032710,Calcium.ionized/Calcium.total corrected for albumin in Blood,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3032710,Calcium.ionized/Calcium.total corrected for albumin in Blood,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4197971,HbA1c measurement (DCCT aligned),,,,,,,,,,,,,,,,,,,,,"8554,8632,8737",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,42869452,Immature granulocytes/100 leukocytes in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3002109,Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8596,8606,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,42869452,Immature granulocytes/100 leukocytes in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3002109,Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8596,8606,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3004327,Lymphocytes [#/volume] in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,"8784,8816,8848,8961,9436,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3006322,Oral temperature,,,,,,,,,,,,,,,,,,,,,586323,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3008342,Neutrophils/100 leukocytes in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -494,17 +494,17 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3010457,Eosinophils/100 leukocytes in Blood b MEASUREMENT,MEASUREMENT_CONCEPT_ID,4192368,Platelet mean volume determination,,,,,,,,,,,,,,,,,,,,,8583,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3014576,Chloride [Moles/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8753,9557",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3024128,Bilirubin.total [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3018311,Urea nitrogen/Creatinine [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3018311,Urea nitrogen/Creatinine [Mass Ratio] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,"8523,8554,8596,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3020891,Body temperature,,,,,,,,,,,,,,,,,,,,,"586323,9289",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3037556,Urate [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,37399332,Serum TSH (thyroid stimulating hormone) level,,,,,,,,,,,,,,,,,,,,,"44777578,9040",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3011904,Phosphate [Mass/volume] in Serum or Plasma,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,3019897,Erythrocyte distribution width [Ratio] by Automated count,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,3019897,Erythrocyte distribution width [Ratio] by Automated count,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3025255,Bacteria [#/area] in Urine sediment by Microscopy high power field,,,,,,,,,,,,,,,,,,,,,8786,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4076704,High density lipoprotein measurement,,,,,,,,,,,,,,,,,,,,,"8753,8840",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4172647,Basophil count,,,,,,,,,,,,,,,,,,,,,"8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,37393531,Serum alanine aminotransferase level,,,,,,,,,,,,,,,,,,,,,"32995,8645,8923",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,40771529,Immature granulocytes/100 leukocytes in Body fluid,,,,,,,,,,,,,,,,,,,,,"8554,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,40771529,Immature granulocytes/100 leukocytes in Body fluid,,,,,,,,,,,,,,,,,,,,,"8554,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3000034,Microalbumin [Mass/volume] in Urine,,,,,,,,,,,,,,,,,,,,,"8576,8723,8751,8840,8859",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3035124,Erythrocytes [#/area] in Urine sediment by Microscopy high power field,,,,,,,,,,,,,,,,,,,,,"8786,8889",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3002030,Lymphocytes/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,"8554,8848",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID @@ -514,7 +514,7 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3022174,Leukocytes [#/volume] in Body fluid,, MEASUREMENT,MEASUREMENT_CONCEPT_ID,3024929,Platelets [#/volume] in Blood by Automated count,,,,,,,,,,,,,,,,,,,,,"8816,8848,8961,9436,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3049187,"Glomerular filtration rate/1.73 sq M.predicted among non-blacks [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (MDRD)",,,,,,,,,,,,,,,,,,,,,"720870,8795",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,37398676,Basophil count,,,,,,,,,,,,,,,,,,,,,8848,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID -MEASUREMENT,MEASUREMENT_CONCEPT_ID,4112223,BUN/Creatinine ratio,,,,,,,,,,,,,,,,,,,,,"8523,8596,NA",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID +MEASUREMENT,MEASUREMENT_CONCEPT_ID,4112223,BUN/Creatinine ratio,,,,,,,,,,,,,,,,,,,,,"8523,8596,-1",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3017250,Creatinine [Mass/volume] in Urine,,,,,,,,,,,,,,,,,,,,,"8576,8840",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,4191837,Calculated LDL cholesterol level,,,,,,,,,,,,,,,,,,,,,8840,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID MEASUREMENT,MEASUREMENT_CONCEPT_ID,3022096,Basophils/100 leukocytes in Blood,,,,,,,,,,,,,,,,,,,,,8554,5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID diff --git a/inst/sql/sql_server/concept_plausible_unit_concept_ids.sql b/inst/sql/sql_server/concept_plausible_unit_concept_ids.sql index 99dcfb18..964e2449 100644 --- a/inst/sql/sql_server/concept_plausible_unit_concept_ids.sql +++ b/inst/sql/sql_server/concept_plausible_unit_concept_ids.sql @@ -39,7 +39,7 @@ FROM AND c.cohort_definition_id = @cohortDefinitionId } WHERE m.@cdmFieldName = @conceptId - AND COALESCE (m.unit_concept_id, -1) NOT IN (replace (@plausibleUnitConceptIds, 'NA', '-1')) -- '-1' stands for the cases when unit_concept_id is null + AND COALESCE (m.unit_concept_id, -1) NOT IN (@plausibleUnitConceptIds) -- '-1' stands for the cases when unit_concept_id is null AND m.value_as_number IS NOT NULL /*violatedRowsEnd*/ ) violated_rows