Update (#205)

shared/clinical-code-sets/tests/alkaline-phosphatase/1/README.md

@@ -8,9 +8,17 @@ Codes retrieved from: https://www.medrxiv.org/content/medrxiv/suppl/2020/05/19/2
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `%57.02 - 60.44%` suggests that this code set is likely well defined.
 
+_Update **2024-03-15**: Prevalence now 58% - 60%._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2022-03-21 | EMIS            | 2658131    | 1515677 (57.02%) |  1515677 (57.02%) |
 | 2022-03-21 | TPP             | 212662     |  128534 (60.44%) |   128534 (60.44%) |
 | 2022-03-21 | Vision          | 341594     |  204911 (59.99%) |   204911 (59.99%) |
+| 2024-03-15 | EMIS            | 2526522    |    1466028 (58%) |     1466176 (58%) |
+| 2024-03-15 | TPP             | 201758     |   118204 (58.6%) |    118215 (58.6%) |
+| 2024-03-15 | Vision          | 335186     |     200958 (60%) |      200975 (60%) |
+
+## Audit log
 
+- Find_missing_codes last run 2024-03-15

shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.ctv3.txt

@@ -1,4 +1,5 @@
 XE2px	Serum alkaline phosphatase
 XE2px	Serum alkaline phosphatase level
 44F3.	Alkaline phosphatase level
-44FZ.	Serum alkaline phosphatase NOS
+44FZ.	Serum alkaline phosphatase NOS
+44F..	Serum alkaline phosphatase

shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.emis.txt

@@ -0,0 +1,2 @@
+^ESCTSE552220	Serum alkaline phosphatase measurement
+^ESCTSE552222	Serum alkal phosphatase level

shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.snomed.txt

@@ -0,0 +1,3 @@
+1000621000000104	Serum alkaline phosphatase level (observable entity)
+997611000000101	Total alkaline phosphatase level (observable entity)
+271234008	Serum alkaline phosphatase measurement (procedure)

shared/clinical-code-sets/tests/corrected-calcium/1/README.md

@@ -8,8 +8,17 @@ Codes from https://getset.ga.
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `38.8% - 45.8%` suggests that this code set is likely well defined, but perhaps missing some EMIS codes.
 
+_Update **2024-03-15**: Prevalence now 43% - 54%._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2022-12-20 | EMIS            | 2438146    |   945836 (38.8%) |    945978 (38.8%) |
 | 2022-12-20 | TPP             | 198637     |    83879 (42.2%) |     89936 (45.3%) |
 | 2022-12-20 | Vision          | 327196     |   149992 (45.8%) |    150003 (45.8%) |
+| 2024-03-15 | EMIS            | 2526522    |  1092432 (43.2%) |   1092562 (43.2%) |
+| 2024-03-15 | TPP             | 201758     |   109306 (54.2%) |    109316 (54.2%) |
+| 2024-03-15 | Vision          | 335186     |   163744 (48.9%) |    163757 (48.9%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-15

shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.ctv3.txt

@@ -2,4 +2,5 @@
 X80Cz	Corrected calcium
 XaIRn	Plasma corrected calcium level
 Xabpk	Serum adjusted calcium concentration
-Xabpr	Plasma adjusted calcium concentration
+Xabpr	Plasma adjusted calcium concentration
+XaZyY	Calcium adjusted level

shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.emis.txt

@@ -1 +1,9 @@
-^ESCTPL833969	Plasma corrected calcium concentration
+^ESCTPL833969	Plasma corrected calcium concentration
+^ESCT1262172	Calcium substance concentration in serum adjusted for albumin
+^ESCT1262173	Calcium molar concentration in serum adjusted for albumin
+^ESCTAD459968	Adjusted serum calcium level
+^ESCTAD728326	Adjusted calcium level
+^ESCTCO459966	Corrected serum calcium measurement
+^ESCTCO459967	Corrected serum calcium level
+^ESCTCO728325	Corrected measurement of calcium
+^ESCTPL651694	Plasma corrected calcium level

shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.readv2.txt

@@ -1,4 +1,5 @@
 44IC.00	Corrected serum calcium level
 44h9.00	Plasma corrected calcium level
 44h9000	Plasma adjusted calcium concentration
-44IC000	Serum adjusted calcium concentration
+44IC000	Serum adjusted calcium concentration
+4Q72100	Calcium adjusted level

shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.snomed.txt

@@ -0,0 +1,11 @@
+166708003 	Corrected serum calcium measurement (procedure)
+390966005 	Plasma corrected calcium level (procedure)
+443796007 	Corrected measurement of calcium (procedure)
+935201000000104 	Plasma adjusted calcium concentration (observable entity)
+998341000000105 	Calcium adjusted level (observable entity)
+443796007 	Corrected measurement of calcium (procedure)
+935051000000108 	Serum adjusted calcium concentration (observable entity)
+6911000237101 	Substance concentration of calcium adjusted in serum (observable entity)
+261000237104 	Substance concentration of calcium adjusted in plasma (observable entity)
+6911000237101 	Substance concentration of calcium adjusted in serum (observable entity)
+1107251000000104 	Substance concentration of calcium in serum adjusted for albumin (observable entity)

shared/clinical-code-sets/tests/haemoglobin/1/README.md

@@ -10,10 +10,17 @@ Haemoglobin codes were retrieved from https://www.medrxiv.org/content/medrxiv/su
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `61% - 68.1%` suggests that this code set is likely well defined.
 
-update:
+_Update **2024-03-15**: Prevalence now 60% - 62%._
 
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
-| 2023-09-18 | EMIS | 2463856 | 1501968 (61%) | 1502094 (61%) | 
-| 2023-09-18 | TPP | 200590 | 136648 (68.1%) | 136654 (68.1%) | 
-| 2023-09-18 | Vision | 332095 | 206665 (62.2%) | 206678 (62.2%) | 
+| 2023-09-18 | EMIS            | 2463856    |    1501968 (61%) |     1502094 (61%) |
+| 2023-09-18 | TPP             | 200590     |   136648 (68.1%) |    136654 (68.1%) |
+| 2023-09-18 | Vision          | 332095     |   206665 (62.2%) |    206678 (62.2%) |
+| 2024-03-15 | EMIS            | 2526522    |  1539133 (60.9%) |   1539250 (60.9%) |
+| 2024-03-15 | TPP             | 201758     |   120785 (59.9%) |    120796 (59.9%) |
+| 2024-03-15 | Vision          | 335186     |   208861 (62.3%) |    208874 (62.3%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-15

shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.emis.txt

@@ -2,4 +2,7 @@
 ^ESCTHA551921	Haemoglobin estimation level
 ^ESCTHB551922	Hb estimation
 ^ESCTHE551919	Hemoglobin estimation level
-^ESCTHE551920	Hemoglobin level estimation
+^ESCTHE551920	Hemoglobin level estimation
+^ESCT1262208	Haemoglobin mass concentration in blood
+^ESCT1262211	Haemoglobin substance concentration in blood
+^ESCT1262212	Haemoglobin molar concentration in blood

shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.snomed.txt

@@ -1,2 +1,4 @@
 1022431000000105	Haemoglobin estimation (observable entity)
-271026005	Hemoglobin level estimation (procedure)
+271026005	Hemoglobin level estimation (procedure)
+1107511000000100	Mass concentration of haemoglobin in blood (observable entity)
+1107531000000108	Substance concentration of haemoglobin in blood (observable entity)

shared/clinical-code-sets/tests/platelets/1/README.md

@@ -6,10 +6,19 @@ Codes retrieved from: https://www.medrxiv.org/content/medrxiv/suppl/2020/05/19/2
 
 ## Prevalence log
 
-By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `%60.7 - 68%` suggests that this code set is likely well defined.
+By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `60.7% - 68%` suggests that this code set is likely well defined.
+
+_Update **2024-03-15**: Prevalence now 59.8% - 62.2%._
 
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
-| 2023-09-19 | EMIS | 2466262 | 1495899 (60.7%) | 1496040 (60.7%) | 
-| 2023-09-19 | TPP | 200680 | 136474 (68%) | 136481 (68%) | 
-| 2023-09-19 | Vision | 332105 | 205855 (62%) | 205868 (62%) | 
+| 2023-09-19 | EMIS            | 2466262    |  1495899 (60.7%) |   1496040 (60.7%) |
+| 2023-09-19 | TPP             | 200680     |     136474 (68%) |      136481 (68%) |
+| 2023-09-19 | Vision          | 332105     |     205855 (62%) |      205868 (62%) |
+| 2024-03-15 | EMIS            | 2526522    |  1534744 (60.7%) |   1534877 (60.8%) |
+| 2024-03-15 | TPP             | 201758     |   120690 (59.8%) |    120700 (59.8%) |
+| 2024-03-15 | Vision          | 335186     |   208318 (62.1%) |    208331 (62.2%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-15

shared/clinical-code-sets/tests/platelets/1/platelets.ctv3.txt

@@ -1,2 +1,2 @@
 42P..	Platelet count
-42PZ.	Platelet count NOS
+42PZ.	Platelet count NOS

shared/clinical-code-sets/tests/platelets/1/platelets.emis.txt

@@ -0,0 +1 @@
+^ESCT1262279	Platelet count in blood

shared/clinical-code-sets/tests/platelets/1/platelets.snomed.txt

@@ -1 +1,2 @@
-1022651000000100	Platelet count (observable entity)
+1022651000000100	Platelet count (observable entity)
+1108041000000107	Platelet count in blood (observable entity)

shared/clinical-code-sets/tests/white-blood-cells/1/README.md

@@ -8,8 +8,17 @@ Codes retrieved from: https://www.medrxiv.org/content/medrxiv/suppl/2020/05/19/2
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `59.9% - 68.1%` suggests that this code set is likely well defined.
 
+_Update **2024-03-15**: Prevalence now 60% - 68%._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
-| 2023-09-18 | EMIS | 2463856 | 1476970 (59.9%) | 1475393 (59.9%) | 
-| 2023-09-18 | TPP | 200590 | 136584 (68.1%) | 136587 (68.1%) | 
-| 2023-09-18 | Vision | 332095 | 208915 (62.9%) | 208785 (62.9%) | 
+| 2023-09-18 | EMIS            | 2463856    |  1476970 (59.9%) |   1475393 (59.9%) |
+| 2023-09-18 | TPP             | 200590     |   136584 (68.1%) |    136587 (68.1%) |
+| 2023-09-18 | Vision          | 332095     |   208915 (62.9%) |    208785 (62.9%) |
+| 2024-03-15 | EMIS            | 2526522    |  1507457 (59.7%) |   1507583 (59.7%) |
+| 2024-03-15 | TPP             | 201758     |   137046 (67.9%) |    137053 (67.9%) |
+| 2024-03-15 | Vision          | 335186     |   210897 (62.9%) |    210909 (62.9%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-15

shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.ctv3.txt

@@ -1,4 +1,6 @@
 XaIdY	Total white blood count
 42H..	White blood cell count
 42H..	White blood cell count - observation
-42HZ.	Total white cell count NOS
+42HZ.	Total white cell count NOS
+XaIdZ	Total WBC (IMM)
+XaKKg	Leucocyte count

shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.readv2.txt

@@ -2,4 +2,6 @@
 42H..11	White blood count
 42H..12	White cell count
 42H7.00	Total white blood count
-42HZ.00	Total white cell count NOS
+42HZ.00	Total white cell count NOS
+42H8.00	Total WBC (IMM)
+42MG.00	Leucocyte count

shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.snomed.txt

@@ -1 +1,6 @@
-1022541000000102	Total white cell count (observable entity)
+1022541000000102	Total white cell count (observable entity)
+11701000237105	Count of white blood cells in cerebrospinal fluid (observable entity)
+42331000237103	Count of white blood cells in urine (observable entity)
+16181000237107	Count of white blood cells in fluid (observable entity)
+1027691000000105	Leucocyte count (observable entity)
+767002	White blood cell count (procedure)