Updated various cholesterol tests (#195)

shared/clinical-code-sets/tests/cholesterol/2/README.md

@@ -2,14 +2,25 @@
 
 A patient's total cholesterol as recorded via clinical code and value. This code set only includes codes that are accompanied by a value (`44P.. Serum cholesterol`). It does not include codes that indicate a patient's BMI (`44P3. - Serum cholesterol raised`) without giving the actual value.
 
+Includes fasting and non-fasting cholesterol levels as current guidance is that it does not make a clinically significant difference.
+
 **NB: This code set is intended to indicate a patient's total cholesterol. If you need to know whether a cholesterol was recorded then please use v1 of the code set.**
 
 ## 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 `43.99% - 49.34%` suggests that this code set is likely well defined.
 
+_Update **2024/03/01**: prevalence now `47% - 55%`._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-05-11 | EMIS            | 2606497    | 1146925 (44.00%) |  1146651 (43.99%) |
 | 2021-05-11 | TPP             | 210810     |   98627 (46.78%) |    98627 (46.78%) |
 | 2021-05-11 | Vision          | 334784     |  165186 (49.34%) |   165186 (49.34%) |
+| 2024-03-06 | EMIS            | 2525894    |  1173276 (46.4%) |   1173510 (46.5%) |
+| 2024-03-06 | TPP             | 201753     |     110983 (55%) |      111001 (55%) |
+| 2024-03-06 | Vision          | 335117     |   165017 (49.2%) |    165039 (49.2%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-01

shared/clinical-code-sets/tests/cholesterol/2/cholesterol.ctv3.txt

@@ -4,4 +4,8 @@ XSK14	Total cholesterol measurement
 44P..	Serum cholesterol
 44PZ.	Serum cholesterol NOS
 XE2eD	Serum cholesterol
-XaJe9	Serum total cholesterol level
+XaJe9	Serum total cholesterol level
+X772L	Cholesterol level
+XaFs9	Fasting cholesterol level
+XaIRd	Plasma total cholesterol level
+XaLux	Serum fasting total cholesterol

shared/clinical-code-sets/tests/cholesterol/2/cholesterol.emis.txt

@@ -0,0 +1,12 @@
+^ESCT1192820	Serum fasting total cholesterol
+^ESCT1262075	Cholesterol substance concentration in plasma
+^ESCT1262076	Cholesterol molar concentration in plasma
+^ESCT1262077	Cholesterol substance concentration in serum
+^ESCT1262078	Cholesterol molar concentration in serum
+^ESCTCH829038	Cholesterol level
+^ESCTFA605293	Fasting cholesterol level
+^ESCTSE683159	Serum total cholesterol measurement
+^ESCTSE683160	Serum total cholesterol level
+^ESCTSE846047	Serum fasting total cholesterol level
+^ESCTTO829294	Total cholesterol level
+EGTON456	Fasting serum cholesterol

shared/clinical-code-sets/tests/cholesterol/2/cholesterol.readv2.txt

@@ -1,4 +1,6 @@
 44P..00	Serum cholesterol
 44PZ.00	Serum cholesterol NOS
 44PJ.00	Serum total cholesterol level
-44PH.00	Total cholesterol measurement
+44PH.00	Total cholesterol measurement
+44OE.00	Plasma total cholesterol level
+44PK.00	Serum fasting total cholesterol

shared/clinical-code-sets/tests/cholesterol/2/cholesterol.snomed.txt

@@ -1,4 +1,12 @@
 1005671000000105	Serum cholesterol level
 412808005	Serum total cholesterol level
 121868005	Total cholesterol measurement (procedure)
-994351000000103	Serum total cholesterol level
+994351000000103	Serum total cholesterol level
+1106531000000105	Substance concentration of cholesterol in plasma (observable entity)
+853681000000104	Total cholesterol level (observable entity)
+850981000000101	Cholesterol level (observable entity)
+1017161000000104	Plasma total cholesterol level (observable entity)
+1106541000000101	Substance concentration of cholesterol in serum (observable entity)
+1083761000000106	Serum fasting total cholesterol level (observable entity)
+315017003	Fasting cholesterol level (procedure)
+247801000000106	Serum fasting total cholesterol (procedure)

shared/clinical-code-sets/tests/hdl-cholesterol/1/README.md

@@ -6,8 +6,17 @@ A patient's HDL cholesterol as recorded via clinical code and value. This code s
 
 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 `43.66% - 48.97%` suggests that this code set is likely well defined.
 
+_Update **2024/03/01**: prevalence now `46% - 55%%`._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-10-13 | EMIS            | 26929848   | 1168326 (44.42%) |  1168326 (44.42%) |
 | 2021-10-13 | TPP             | 211812     |  100823 (47.60%) |   100823 (47.60%) |
 | 2021-10-13 | Vision          | 338205     |  165935 (49.06%) |   165935 (49.06%) |
+| 2024-03-06 | EMIS            | 2525894    |    1162124 (46%) |     1162354 (46%) |
+| 2024-03-06 | TPP             | 201753     |   110692 (54.9%) |    110708 (54.9%) |
+| 2024-03-06 | Vision          | 335117     |   163929 (48.9%) |    163958 (48.9%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-01

shared/clinical-code-sets/tests/hdl-cholesterol/1/hdl-cholesterol.ctv3.txt

@@ -1,3 +1,6 @@
 44P5.	Serum HDL cholesterol level
 44PC.	Ser random HDL cholesterol lev
-XaEVr	Plasma HDL cholesterol level
+XaEVr	Plasma HDL cholesterol level
+44d2.	Plasma random HDL cholesterol level
+44d3.	Plasma fasting HDL cholesterol level
+44PB.	Serum fasting HDL cholesterol level

shared/clinical-code-sets/tests/hdl-cholesterol/1/hdl-cholesterol.emis.txt

@@ -0,0 +1,5 @@
+^ESCT1262229	HDL (high density lipoprotein) cholesterol substance concentration in plasma
+^ESCT1262230	HDL (high density lipoprotein) cholesterol molar concentration in plasma
+^ESCT1262232	HDL (high density lipoprotein) cholesterol substance concentration in serum
+^ESCT1262233	HDL (high density lipoprotein) cholesterol molar concentration in serum
+^ESCTSE838573	Serum HDL (high density lipoprotein) cholesterol level

shared/clinical-code-sets/tests/hdl-cholesterol/1/hdl-cholesterol.readv2.txt

@@ -1,3 +1,6 @@
 44PC.00	Serum random HDL cholesterol level
 44P5.00	Serum HDL cholesterol level
-44dA.00	Plasma HDL cholesterol level
+44dA.00	Plasma HDL cholesterol level
+44d2.00	Plasma random HDL cholesterol level
+44d3.00	Plasma fasting HDL cholesterol level
+44PB.00	Serum fasting HDL cholesterol level

shared/clinical-code-sets/tests/hdl-cholesterol/1/hdl-cholesterol.snomed.txt

@@ -1,3 +1,8 @@
 1005681000000107	Serum high density lipoprotein cholesterol level (observable entity)
 1010581000000101	Plasma high density lipoprotein cholesterol level (observable entity)
-1026461000000104	Serum random high density lipoprotein cholesterol level (observable entity)
+1026461000000104	Serum random high density lipoprotein cholesterol level (observable entity)
+1107661000000104	Substance concentration of high density lipoprotein cholesterol in plasma (observable entity)
+1028831000000106	Plasma random high density lipoprotein cholesterol level (observable entity)
+1107681000000108	Substance concentration of high density lipoprotein cholesterol in serum (observable entity)
+1026451000000102	Serum fasting high density lipoprotein cholesterol level (observable entity)
+1028841000000102	Plasma fasting high density lipoprotein cholesterol level (observable entity)

shared/clinical-code-sets/tests/ldl-cholesterol/1/README.md

@@ -6,8 +6,17 @@ A patient's LDL cholesterol as recorded via clinical code and value. This code s
 
 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 `41.22% - 45.54%` suggests that this code set is likely well defined.
 
+_Update **2024/03/01**: prevalence now `43% - 48%%`._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-10-13 | EMIS            | 26929848   | 1102872 (41.94%) |  1102872 (41.94%) |
 | 2021-10-13 | TPP             | 211812     |   91673 (43.28%) |    91673 (43.28%) |
 | 2021-10-13 | Vision          | 338205     |  154055 (45.55%) |   154055 (45.55%) |
+| 2024-03-06 | EMIS            | 2525894    |    1086503 (43%) |     1086736 (43%) |
+| 2024-03-06 | TPP             | 201753     |      96837 (48%) |       96849 (48%) |
+| 2024-03-06 | Vision          | 335117     |   149075 (44.5%) |    149103 (44.5%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-01

shared/clinical-code-sets/tests/ldl-cholesterol/1/ldl-cholesterol.ctv3.txt

@@ -1,3 +1,7 @@
 44P6.	Serum LDL cholesterol level
 XaIp4	Calculated LDL cholesterol lev
-XaEVs	Plasma LDL cholesterol level
+XaEVs	Plasma LDL cholesterol level
+44d4.	Plasma random LDL cholesterol levell
+44d5.	Plasma fasting LDL cholesterol level
+44PD.	Serum fasting LDL cholesterol level
+44PE.	Serum random LDL cholesterol level

shared/clinical-code-sets/tests/ldl-cholesterol/1/ldl-cholesterol.emis.txt

@@ -0,0 +1,5 @@
+^ESCT1262339	LDL-C (low density lipoprotein cholesterol) substance concentration in plasma
+^ESCT1262340	LDL-C (low density lipoprotein cholesterol) molar concentration in plasma
+^ESCT1262341	LDL-C (low density lipoprotein cholesterol) substance concentration in serum
+^ESCT1262342	LDL-C (low density lipoprotein cholesterol) molar concentration in serum
+^ESCTSE840392	Serum LDL (low density lipoprotein) cholesterol level

shared/clinical-code-sets/tests/ldl-cholesterol/1/ldl-cholesterol.readv2.txt

@@ -1,3 +1,7 @@
 44PI.00	Calculated LDL cholesterol level
 44P6.00	Serum LDL cholesterol level
-44dB.00	Plasma LDL cholesterol level
+44dB.00	Plasma LDL cholesterol level
+44d4.00	Plasma random LDL cholesterol level
+44d5.00	Plasma fasting LDL cholesterol level
+44PD.00	Serum fasting LDL cholesterol level
+44PE.00	Serum random LDL cholesterol level

shared/clinical-code-sets/tests/ldl-cholesterol/1/ldl-cholesterol.snomed.txt

@@ -1,3 +1,11 @@
 1010591000000104	Plasma low density lipoprotein cholesterol level (observable entity)
 1014501000000104	Calculated low density lipoprotein cholesterol level (observable entity)
-1022191000000100	Serum low density lipoprotein cholesterol level (observable entity)
+1022191000000100	Serum low density lipoprotein cholesterol level (observable entity)
+1026471000000106	Serum fasting low density lipoprotein cholesterol level (observable entity)
+1026481000000108	Serum random low density lipoprotein cholesterol level (observable entity)
+53981000237105	Substance concentration of low density lipoprotein cholesterol in plasma (observable entity)
+1108541000000100	Substance concentration of low density lipoprotein cholesterol in plasma (observable entity)
+1108551000000102	Substance concentration of low density lipoprotein cholesterol in serum (observable entity)
+1028861000000101	Plasma fasting low density lipoprotein cholesterol level (observable entity)
+1028851000000104	Plasma random low density lipoprotein cholesterol level (observable entity)
+55621000237101	Substance concentration of low density lipoprotein cholesterol in serum (observable entity)

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

@@ -1,15 +1,24 @@
 # Triglyceride (level)
 
-A patient's triglyceride level as recorded via clinical code and value. This code set only includes codes that are accompanied by a value (`44Q..00 - Serum triglycerides`). It does not include codes that indicate a patient's creatinine (`44Q3.00 - Serum triglycerides raised') without giving the actual value.
+A patient's triglyceride level as recorded via clinical code and value. This code set only includes codes that are accompanied by a value (`44Q..00 - Serum triglycerides`). It does not include codes that indicate a patient's triglyceride level (`44Q3.00 - Serum triglycerides raised') without giving the actual value.
 
-Codes taken from: https://www.medrxiv.org/content/medrxiv/suppl/2020/05/19/2020.05.14.20101626.DC1/2020.05.14.20101626-1.pdf
+Codes taken from: https://www.medrxiv.org/content/medrxiv/suppl/2020/05/19/2020.05.14.20101626.DC1/2020.05.14.20101626-1.pdf and the NHS PCD refsets.
 
 ## 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 `43.18% - 48.34%` suggests that this code set is likely well defined.
 
+_Update **2024/03/01**: prevalence now `45% - 54%%`._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-10-13 | EMIS            | 26929848   | 1135572 (43.18%) |  1135572 (43.18%) |
 | 2021-10-13 | TPP             | 211812     |   99188 (46.82%) |    99188 (46.82%) |
 | 2021-10-13 | Vision          | 338205     |  163502 (48.34%) |   163502 (48.34%) |
+| 2024-03-06 | EMIS            | 2525894    |  1146848 (45.4%) |   1147073 (45.4%) |
+| 2024-03-06 | TPP             | 201753     |   109632 (54.3%) |    109648 (54.3%) |
+| 2024-03-06 | Vision          | 335117     |   162700 (48.6%) |    162729 (48.6%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-01

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

@@ -1,4 +1,10 @@
 XE2q9	Serum triglycerides
 XE2q9	Serum triglyceride levels
 44Q4.	Serum fasting triglyceride level
-44QZ.	Serum triglycerides NOS
+44QZ.	Serum triglycerides NOS
+44e..	Plasma triglyceride level
+44e0.	Plasma random triglyceride level
+44e1.	Plasma fasting triglyceride level
+44Q..	Serum triglycerides
+44Q5.	Serum random triglyceride level
+X772O	Triglyceride level

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

@@ -0,0 +1,8 @@
+^ESCT1262496	Triglyceride substance concentration in plasma
+^ESCT1262497	Triglyceride molar concentration in plasma
+^ESCT1262498	Triglyceride substance concentration in serum
+^ESCT1262499	Triglyceride molar concentration in serum
+^ESCTFI627911	Finding of serum triglyceride levels
+^ESCTSE627910	Serum triglyceride levels
+^ESCTME552241	Measurement of serum triglyceride level
+^ESCTSE552242	Serum triglyceride levels

shared/clinical-code-sets/tests/triglycerides/1/triglycerides.readv2.txt

@@ -1,4 +1,8 @@
 44Q..00	Serum triglycerides
 44Q4.00	Serum fasting triglyceride level
 44Q5.00	Serum random triglyceride level
-44QZ.00	Serum triglycerides NOS
+44QZ.00	Serum triglycerides NOS
+44e..00	Plasma triglyceride level
+44e0.00	Plasma random triglyceride level
+44e1.00	Plasma fasting triglyceride level
+4QA1.00	Triglyceride level

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

@@ -0,0 +1,12 @@
+1028871000000108	Plasma random triglyceride level (observable entity)
+1031321000000109	Plasma fasting triglyceride level (observable entity)
+850991000000104	Triglyceride level (observable entity)
+1005691000000109	Serum triglycerides level (observable entity)
+1109831000000104	Substance concentration of triglyceride in serum (observable entity)
+1026491000000105	Serum fasting triglyceride level (observable entity)
+1010601000000105	Plasma triglyceride level (observable entity)
+1461000237101	Substance concentration of triglyceride in serum (observable entity)
+1026501000000104	Serum random triglyceride level (observable entity)
+1109821000000101	Substance concentration of triglyceride in plasma (observable entity)
+365796000	Finding of serum triglyceride levels (finding)
+271245006	Measurement of serum triglyceride level (procedure)