From eb1a9c9a420b41cab01a93760a8c3f5e1da271e3 Mon Sep 17 00:00:00 2001 From: Richard Williams <1234richardwilliams@gmail.com> Date: Fri, 15 Mar 2024 14:13:56 +0000 Subject: [PATCH] Update --- .../tests/alkaline-phosphatase/1/README.md | 8 ++++++++ .../1/alkaline-phosphatase.ctv3.txt | 3 ++- .../1/alkaline-phosphatase.emis.txt | 2 ++ .../1/alkaline-phosphatase.snomed.txt | 3 +++ .../tests/corrected-calcium/1/README.md | 9 +++++++++ .../1/corrected-calcium.ctv3.txt | 3 ++- .../1/corrected-calcium.emis.txt | 10 +++++++++- .../1/corrected-calcium.readv2.txt | 3 ++- .../1/corrected-calcium.snomed.txt | 11 +++++++++++ .../tests/haemoglobin/1/README.md | 15 +++++++++++---- .../tests/haemoglobin/1/haemoglobin.emis.txt | 5 ++++- .../tests/haemoglobin/1/haemoglobin.snomed.txt | 4 +++- .../tests/platelets/1/README.md | 17 +++++++++++++---- .../tests/platelets/1/platelets.ctv3.txt | 2 +- .../tests/platelets/1/platelets.emis.txt | 1 + .../tests/platelets/1/platelets.snomed.txt | 3 ++- .../tests/white-blood-cells/1/README.md | 15 ++++++++++++--- .../1/white-blood-cells.ctv3.txt | 4 +++- .../1/white-blood-cells.readv2.txt | 4 +++- .../1/white-blood-cells.snomed.txt | 7 ++++++- 20 files changed, 107 insertions(+), 22 deletions(-) create mode 100644 shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.emis.txt create mode 100644 shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.snomed.txt create mode 100644 shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.snomed.txt create mode 100644 shared/clinical-code-sets/tests/platelets/1/platelets.emis.txt diff --git a/shared/clinical-code-sets/tests/alkaline-phosphatase/1/README.md b/shared/clinical-code-sets/tests/alkaline-phosphatase/1/README.md index 20e822d5..7da06e03 100644 --- a/shared/clinical-code-sets/tests/alkaline-phosphatase/1/README.md +++ b/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 diff --git a/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.ctv3.txt b/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.ctv3.txt index ecb7e4b0..d6496074 100644 --- a/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.ctv3.txt +++ b/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 \ No newline at end of file +44FZ. Serum alkaline phosphatase NOS +44F.. Serum alkaline phosphatase \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.emis.txt b/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.emis.txt new file mode 100644 index 00000000..5afe0a1c --- /dev/null +++ b/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 \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.snomed.txt b/shared/clinical-code-sets/tests/alkaline-phosphatase/1/alkaline-phosphatase.snomed.txt new file mode 100644 index 00000000..55729e6c --- /dev/null +++ b/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) \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/corrected-calcium/1/README.md b/shared/clinical-code-sets/tests/corrected-calcium/1/README.md index 934c296c..7b4409d1 100644 --- a/shared/clinical-code-sets/tests/corrected-calcium/1/README.md +++ b/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 diff --git a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.ctv3.txt b/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.ctv3.txt index 14ce7637..73531167 100644 --- a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.ctv3.txt +++ b/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 \ No newline at end of file +Xabpr Plasma adjusted calcium concentration +XaZyY Calcium adjusted level \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.emis.txt b/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.emis.txt index cd15025e..ace535b8 100644 --- a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.emis.txt +++ b/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.emis.txt @@ -1 +1,9 @@ -^ESCTPL833969 Plasma corrected calcium concentration \ No newline at end of file +^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 \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.readv2.txt b/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.readv2.txt index 627ed1d6..0c149587 100644 --- a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.readv2.txt +++ b/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 \ No newline at end of file +44IC000 Serum adjusted calcium concentration +4Q72100 Calcium adjusted level \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.snomed.txt b/shared/clinical-code-sets/tests/corrected-calcium/1/corrected-calcium.snomed.txt new file mode 100644 index 00000000..9f18093e --- /dev/null +++ b/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) \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/haemoglobin/1/README.md b/shared/clinical-code-sets/tests/haemoglobin/1/README.md index f03588ee..c6e4fcfa 100644 --- a/shared/clinical-code-sets/tests/haemoglobin/1/README.md +++ b/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%) | \ No newline at end of file +| 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 diff --git a/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.emis.txt b/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.emis.txt index 8d3dce90..00a8a91d 100644 --- a/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.emis.txt +++ b/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 \ No newline at end of file +^ESCTHE551920 Hemoglobin level estimation +^ESCT1262208 Haemoglobin mass concentration in blood +^ESCT1262211 Haemoglobin substance concentration in blood +^ESCT1262212 Haemoglobin molar concentration in blood \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.snomed.txt b/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.snomed.txt index 02a362c0..14306512 100644 --- a/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.snomed.txt +++ b/shared/clinical-code-sets/tests/haemoglobin/1/haemoglobin.snomed.txt @@ -1,2 +1,4 @@ 1022431000000105 Haemoglobin estimation (observable entity) -271026005 Hemoglobin level estimation (procedure) \ No newline at end of file +271026005 Hemoglobin level estimation (procedure) +1107511000000100 Mass concentration of haemoglobin in blood (observable entity) +1107531000000108 Substance concentration of haemoglobin in blood (observable entity) \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/platelets/1/README.md b/shared/clinical-code-sets/tests/platelets/1/README.md index c595aeb4..b8344eb0 100644 --- a/shared/clinical-code-sets/tests/platelets/1/README.md +++ b/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%) | \ No newline at end of file +| 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 diff --git a/shared/clinical-code-sets/tests/platelets/1/platelets.ctv3.txt b/shared/clinical-code-sets/tests/platelets/1/platelets.ctv3.txt index 02a5da31..b4fd6acd 100644 --- a/shared/clinical-code-sets/tests/platelets/1/platelets.ctv3.txt +++ b/shared/clinical-code-sets/tests/platelets/1/platelets.ctv3.txt @@ -1,2 +1,2 @@ 42P.. Platelet count -42PZ. Platelet count NOS \ No newline at end of file +42PZ. Platelet count NOS diff --git a/shared/clinical-code-sets/tests/platelets/1/platelets.emis.txt b/shared/clinical-code-sets/tests/platelets/1/platelets.emis.txt new file mode 100644 index 00000000..6cc901c9 --- /dev/null +++ b/shared/clinical-code-sets/tests/platelets/1/platelets.emis.txt @@ -0,0 +1 @@ +^ESCT1262279 Platelet count in blood \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/platelets/1/platelets.snomed.txt b/shared/clinical-code-sets/tests/platelets/1/platelets.snomed.txt index 296c5c9a..c94b6abb 100644 --- a/shared/clinical-code-sets/tests/platelets/1/platelets.snomed.txt +++ b/shared/clinical-code-sets/tests/platelets/1/platelets.snomed.txt @@ -1 +1,2 @@ -1022651000000100 Platelet count (observable entity) \ No newline at end of file +1022651000000100 Platelet count (observable entity) +1108041000000107 Platelet count in blood (observable entity) \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/white-blood-cells/1/README.md b/shared/clinical-code-sets/tests/white-blood-cells/1/README.md index 55993c79..0b7eb13e 100644 --- a/shared/clinical-code-sets/tests/white-blood-cells/1/README.md +++ b/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 diff --git a/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.ctv3.txt b/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.ctv3.txt index fdba0022..3db27ffc 100644 --- a/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.ctv3.txt +++ b/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 \ No newline at end of file +42HZ. Total white cell count NOS +XaIdZ Total WBC (IMM) +XaKKg Leucocyte count diff --git a/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.readv2.txt b/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.readv2.txt index 00afb46b..e989d27d 100644 --- a/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.readv2.txt +++ b/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 \ No newline at end of file +42HZ.00 Total white cell count NOS +42H8.00 Total WBC (IMM) +42MG.00 Leucocyte count \ No newline at end of file diff --git a/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.snomed.txt b/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.snomed.txt index 115d4090..b8e2b57d 100644 --- a/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.snomed.txt +++ b/shared/clinical-code-sets/tests/white-blood-cells/1/white-blood-cells.snomed.txt @@ -1 +1,6 @@ -1022541000000102 Total white cell count (observable entity) \ No newline at end of file +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) \ No newline at end of file