From 377a7d7122bdb080f5cfbb3563d0d27e2edd7230 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 14:25:42 +0100 Subject: [PATCH 001/166] Set versions in Python packages --- pyxb_build/ukrdc_schema/__init__.py | 2 +- xsdata_build/setup.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pyxb_build/ukrdc_schema/__init__.py b/pyxb_build/ukrdc_schema/__init__.py index 3bc35c3..ce1305b 100644 --- a/pyxb_build/ukrdc_schema/__init__.py +++ b/pyxb_build/ukrdc_schema/__init__.py @@ -1 +1 @@ -__version__ = "3.4.5" +__version__ = "4.0.0" diff --git a/xsdata_build/setup.py b/xsdata_build/setup.py index 411658d..722a75a 100644 --- a/xsdata_build/setup.py +++ b/xsdata_build/setup.py @@ -1,13 +1,13 @@ -from setuptools import setup -from setuptools import find_packages from pathlib import Path +from setuptools import find_packages +from setuptools import setup # Read the contents of the README file long_description = (Path(__file__).parent / "README.md").read_text() setup( name="ukrdc-xsdata", - version="3.4.5", + version="4.0.0", long_description=long_description, long_description_content_type='text/markdown', author="UK Renal Registry", From 95963340267cff5a9ebcc5ed1cb1c3db00a68822 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 14:32:45 +0100 Subject: [PATCH 002/166] Amend LabOrder schema --- sample_files/ukrdc/fullFile.xml | 5 ----- schema/ukrdc/LabOrders/LabOrder.xsd | 5 +++++ 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/sample_files/ukrdc/fullFile.xml b/sample_files/ukrdc/fullFile.xml index ba4e676..48792e0 100644 --- a/sample_files/ukrdc/fullFile.xml +++ b/sample_files/ukrdc/fullFile.xml @@ -297,11 +297,6 @@ Code82 Description82 - - ODS - Code83 - Description83 - 2006-05-04T18:13:51.0 ODS diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index 6526c0f..aa6507c 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -58,6 +58,11 @@ + + + Requesting Location (as in Hospital, GP, etc.) + + From fbf64f0943f99c50d46855f1ab0da7f3c8f10b7a Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 15:42:11 +0100 Subject: [PATCH 003/166] Update documentation --- docs_build/stylesheet.xsl | 7 +++++++ schema/ukrdc/Patient.xsd | 12 ++++++++++-- schema/ukrdc/Types/RRTypes.xsd | 9 +++++++++ schema/ukrdc/UKRDC.xsd | 31 +++++++++++++++++++------------ 4 files changed, 45 insertions(+), 14 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 205c39a..1fa1609 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -90,6 +90,12 @@ + +
+ +
+ +
@@ -163,6 +169,7 @@ + diff --git a/schema/ukrdc/Patient.xsd b/schema/ukrdc/Patient.xsd index 0bdb42b..ef46d87 100644 --- a/schema/ukrdc/Patient.xsd +++ b/schema/ukrdc/Patient.xsd @@ -16,11 +16,16 @@ - Every Patient should have one MRN type PatientNumber. This should be the primary identifier for the Patient in the sending system and typically not change. If a National Identifier (such as NHS Number) is used as the MRN it should also be submitted as an NI type PatientNumber. - + + UKRRv4,UKRRv5 + + Patient Numbers + + Names + @@ -31,6 +36,9 @@ + + Addresses + diff --git a/schema/ukrdc/Types/RRTypes.xsd b/schema/ukrdc/Types/RRTypes.xsd index 825859a..21fb5f0 100644 --- a/schema/ukrdc/Types/RRTypes.xsd +++ b/schema/ukrdc/Types/RRTypes.xsd @@ -1,5 +1,14 @@ + + + UKRDC Schema Version in 0.0.0 Format + + + + + + diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 15648fe..11dcf3e 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -5,8 +5,8 @@ - + @@ -23,8 +23,10 @@ + + @@ -38,9 +40,9 @@ - + - + @@ -50,15 +52,17 @@ The extract process within the facility which produced this file. - + + Patient Demographics + - Lab Orders. These are measurements taken about a patient that have been processed by a Laboratory. Our EHR structure requires that all test results are associated with a lab order. If the details of the lab order are not received by the renal system then a generic lab order should be created to contain all results with a common sample time. + Lab Orders. These are measurements taken about a patient that have been processed by a Laboratory. Our EHR structure requires that all test results are associated with a lab order. If the details of the lab order are not received by the sending system then a generic lab order should be created to contain all results with a common sample time. - Other Health Related Behaviours. + Other Health Related Behaviours. This element should not be submitted without prior discussion with the UKRR @@ -83,7 +87,7 @@ - Allergies + Allergies. This element should not be submitted without prior discussion with the UKRR @@ -106,8 +110,7 @@ - Primary Renal Diagnosis. These should be used to record the Primary Renal Disease (defined in the ERA-EDTA PRD spreadsheet, notes for users, sections: 'Description of PRD' and 'Selection of the most appropriate PRD' http://www.era-edta-reg.org/prd.jsp ) for analysis by the UKRR, SRR and ERA. In order for the data to be comparable across countries it needs to be coded in using the EDTA code lists. Consequently we expect that some conditions may appear both as PRD objects and as generic diagnoses coded in SNOMED. Patients who started RRT after 01/01/2014 should be coded using the 2012 "EDTA2" code list. Patients who started before then can continue to be submitted using the older EDTA list. Systems should not automatically convert the older codes to the newer ones as this results in a loss of accuracy. - + Renal Diagnoses @@ -115,7 +118,7 @@ - Medications. All recorded medications should be submitted whether or not prescribed for the purposes of renal care. + Medications @@ -141,7 +144,11 @@ - + + + Procedures (not otherwise Specified) + + Dialysis Sessions @@ -149,7 +156,7 @@ - Transplant Procedures.These should be used to record any Transplants. A single Procedure should be recorded for each organ being transplanted, with multiple organ transplants being identified by multiple transplants occurring on the same day. The record also contains information about the source donor for each transplant. + Transplant Procedures From 662d522b8a51570d52a8189abae4dad906db2013 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 15:46:35 +0100 Subject: [PATCH 004/166] . --- docs_build/stylesheet.xsl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 1fa1609..553539e 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -90,7 +90,7 @@ - +
@@ -169,7 +169,7 @@ - + From d1359fbbbb61241ff6ba6d00d8ca9b937e847e0d Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 16:02:18 +0100 Subject: [PATCH 005/166] . --- docs_build/stylesheet.xsl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 553539e..e503e11 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -169,7 +169,7 @@ - + From 981b4d77ddb2387424d993099333c16d74996567 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 16:08:32 +0100 Subject: [PATCH 006/166] . --- docs_build/stylesheet.xsl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index e503e11..c66f4aa 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -169,7 +169,6 @@ - @@ -243,6 +242,7 @@ + From 69201d248d333b5f4197ec42ebfdf017b958537e Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 16:11:21 +0100 Subject: [PATCH 007/166] . --- docs_build/stylesheet.xsl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index c66f4aa..d20c56b 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -90,7 +90,7 @@ - +
@@ -242,7 +242,7 @@ - + From d2a558cb8dc384b164b894a1e7be530af879bdf3 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 16:53:23 +0100 Subject: [PATCH 008/166] . --- docs_build/stylesheet.xsl | 4 +++- schema/ukrdc/Patient.xsd | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index d20c56b..df6e90f 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -92,13 +92,15 @@
- + Should be submitted for: +
+
diff --git a/schema/ukrdc/Patient.xsd b/schema/ukrdc/Patient.xsd index ef46d87..c0f20c8 100644 --- a/schema/ukrdc/Patient.xsd +++ b/schema/ukrdc/Patient.xsd @@ -14,7 +14,7 @@ - + UKRRv4,UKRRv5 From 01c28db52fab0fa95f52a83b22823e64888a41de Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 17:17:20 +0100 Subject: [PATCH 009/166] . --- docs_build/stylesheet.xsl | 4 ++-- schema/ukrdc/Types/SendingFacility.xsd | 13 +++++++++++++ schema/ukrdc/UKRDC.xsd | 19 ++----------------- 3 files changed, 17 insertions(+), 19 deletions(-) create mode 100644 schema/ukrdc/Types/SendingFacility.xsd diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index df6e90f..bd37c61 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -93,14 +93,14 @@
Should be submitted for: - +
- +
diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd new file mode 100644 index 0000000..de097e9 --- /dev/null +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -0,0 +1,13 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 11dcf3e..5bd9a05 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -25,28 +25,13 @@ + - - - - - - - - - - - - - - - - - + The extract process within the facility which produced this file. From c343507d00e531a25b366bdf8aa0adcb4dc90297 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sat, 17 Jun 2023 17:21:24 +0100 Subject: [PATCH 010/166] . --- schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd | 4 +++- schema/ukrdc/Types/SendingFacility.xsd | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd b/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd index a19fed6..687d662 100644 --- a/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd +++ b/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd @@ -1,7 +1,9 @@ - + + UKRRv5 + diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd index de097e9..3c29cd9 100644 --- a/schema/ukrdc/Types/SendingFacility.xsd +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -1,6 +1,6 @@ - From 43c211132f18dc7dfbc070a534bc166bb637dc76 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 19:27:44 +0100 Subject: [PATCH 011/166] Try to generate links in the XSL --- docs_build/stylesheet.xsl | 4 +++- schema/ukrdc/Patient.xsd | 1 + schema/ukrdc/UKRDC.xsd | 10 +++++----- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index bd37c61..4819030 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -255,7 +255,9 @@ - + + + diff --git a/schema/ukrdc/Patient.xsd b/schema/ukrdc/Patient.xsd index c0f20c8..2b726c2 100644 --- a/schema/ukrdc/Patient.xsd +++ b/schema/ukrdc/Patient.xsd @@ -12,6 +12,7 @@ + diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 5bd9a05..f4cd57a 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -31,16 +31,16 @@ - - + + The extract process within the facility which produced this file. - + Patient Demographics - + Lab Orders. These are measurements taken about a patient that have been processed by a Laboratory. Our EHR structure requires that all test results are associated with a lab order. If the details of the lab order are not received by the sending system then a generic lab order should be created to contain all results with a common sample time. @@ -51,7 +51,7 @@ - + From f74561cf996d5cf994688eef5abd14f813d87041 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 19:47:46 +0100 Subject: [PATCH 012/166] Type to improve stylesheet --- docs_build/stylesheet.xsl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 4819030..e31829b 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -255,7 +255,10 @@ - + + + + From c3e4f52e79ae5cdaa4c0acac4acab9c8c5c7d4f6 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 20:05:30 +0100 Subject: [PATCH 013/166] Fix stylesheet --- docs_build/stylesheet.xsl | 4 ++-- schema/ukrdc/UKRDC.xsd | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index e31829b..061cf2d 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -257,8 +257,8 @@ - - + + diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index f4cd57a..32510a9 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -37,15 +37,15 @@ The extract process within the facility which produced this file. - + Patient Demographics - + Lab Orders. These are measurements taken about a patient that have been processed by a Laboratory. Our EHR structure requires that all test results are associated with a lab order. If the details of the lab order are not received by the sending system then a generic lab order should be created to contain all results with a common sample time. - + Other Health Related Behaviours. This element should not be submitted without prior discussion with the UKRR From a651424808c7a88e462b96aa5229208d98ae8ca2 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 20:10:20 +0100 Subject: [PATCH 014/166] Improve stylesheet.xsl --- docs_build/stylesheet.xsl | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 061cf2d..7a71d7f 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -257,10 +257,17 @@ - - - - + + + + + + + + + + + From e7a8c7431e2c4d5e087b95c346f2a043b278868b Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 20:16:54 +0100 Subject: [PATCH 015/166] Fix stylesheet --- schema/ukrdc/Types/SendingFacility.xsd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd index 3c29cd9..845380a 100644 --- a/schema/ukrdc/Types/SendingFacility.xsd +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -1,5 +1,7 @@ + + From 7ad4f5dd93a63e0601835c64881fa4c6f68e621f Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 20:20:55 +0100 Subject: [PATCH 016/166] . --- schema/ukrdc/Types/SendingFacility.xsd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd index 845380a..08f2e46 100644 --- a/schema/ukrdc/Types/SendingFacility.xsd +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -1,6 +1,6 @@ - + From f49fce807633f6fcf5b290ab7166d793706e9ef1 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 20:47:07 +0100 Subject: [PATCH 017/166] Fix typo --- schema/ukrdc/UKRDC.xsd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 32510a9..ed18fe6 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -32,7 +32,7 @@ - + The extract process within the facility which produced this file. From fc8e43c89abdc99e410c1a986929d096e3f88107 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 20:56:04 +0100 Subject: [PATCH 018/166] Change function to avoid advanced string functions --- docs_build/stylesheet.xsl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 7a71d7f..51e555a 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -256,7 +256,11 @@ + + From d654d172cb646e593a8c24362f93cbee252bd6a6 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 21:08:26 +0100 Subject: [PATCH 019/166] . --- docs_build/stylesheet.xsl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 51e555a..399bb7a 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -269,7 +269,13 @@ - + + + + + From e83c33e983a1dc56e8cad0c6831e03b7be0bae90 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 21:20:54 +0100 Subject: [PATCH 020/166] .2 --- docs_build/stylesheet.xsl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 399bb7a..4cb9c14 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -256,7 +256,9 @@ + + + --> From 723a6415b5a77f0b3b28cdcf0c8672385c46eaac Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 21:37:44 +0100 Subject: [PATCH 022/166] . --- docs_build/stylesheet.xsl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 94cf52e..cb82dce 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -256,7 +256,10 @@ - + + - + - + - + @@ -281,12 +281,6 @@ - From b1e1dbec102161a8fcc5d07a45c7590300b0623c Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 18 Jun 2023 23:44:16 +0100 Subject: [PATCH 027/166] Add print statements --- docs_build/stylesheet.xsl | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index e890628..9fe4514 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -248,21 +248,42 @@ + ZZZ + XXX - + BBB + + + YYY + + + + + + + AAA + + + + + + + + + + From 63e152558516689b05987ab51fcd92c52a9ac0e0 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Mon, 19 Jun 2023 00:00:20 +0100 Subject: [PATCH 028/166] Remove URL attempts for now --- docs_build/stylesheet.xsl | 91 ++++++++++++++++++++++----------------- 1 file changed, 51 insertions(+), 40 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 9fe4514..efb7f7d 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -248,65 +248,76 @@ - ZZZ - XXX - BBB + + + + + This assumes LabOrders/LabOrder.xsd - AAA - + This assumes Types/Whatever.xsd - - - - - - - - - + + + + + + + + + + + --> From c7c639bebedc495f83505329cf8907d472a155bf Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Mon, 19 Jun 2023 00:09:09 +0100 Subject: [PATCH 029/166] . --- docs_build/stylesheet.xsl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index efb7f7d..2b9e7b4 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -255,9 +255,7 @@ - - From d5198289b6c445b6dd3ef6091cb6199fafd01757 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Mon, 19 Jun 2023 00:19:44 +0100 Subject: [PATCH 030/166] . --- schema/ukrdc/UKRDC.xsd | 31 +++++++++++++++++++++++++------ 1 file changed, 25 insertions(+), 6 deletions(-) diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index ed18fe6..7525e14 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -31,23 +31,42 @@ - + + + + ALL + + + The value of this element is the Site or System responsible for the data being sent. + + + - The extract process within the facility which produced this file. + + ALL + + + The type of data feed. This is used to enable different behaviour when the original source of data was something other than a UKRDC feed (i.e. when "PV XML" is converted to "RDA XML" it is given a SendingExtract of "PV"). Unless told otherwise the value should be set to "UKRDC". + - Patient Demographics + + + ALL + + Patient Demographics + - Lab Orders. These are measurements taken about a patient that have been processed by a Laboratory. Our EHR structure requires that all test results are associated with a lab order. If the details of the lab order are not received by the sending system then a generic lab order should be created to contain all results with a common sample time. + Lab Orders - Other Health Related Behaviours. This element should not be submitted without prior discussion with the UKRR + Other Health Related Behaviours @@ -57,7 +76,7 @@ - This is used to record information about conditions diagnosed in the Patient's relatives. This element should not be submitted without prior discussion with the UKRR + Family Histories From 1cc1b9af0d8eeb0121e7c2c17f4db9088508f1b8 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Mon, 19 Jun 2023 00:38:57 +0100 Subject: [PATCH 031/166] . --- docs_build/stylesheet.xsl | 3 +- schema/ukrdc/UKRDC.xsd | 88 ++++++++++++++++++++++++++++++++++++--- 2 files changed, 84 insertions(+), 7 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 2b9e7b4..b7c8f4c 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -255,7 +255,8 @@ - + Type: +
- Clinician Coding Death - - diff --git a/schema/ukrdc/Types/Address.xsd b/schema/ukrdc/Types/Address.xsd index 4d3d3d5..a4b2864 100644 --- a/schema/ukrdc/Types/Address.xsd +++ b/schema/ukrdc/Types/Address.xsd @@ -52,14 +52,14 @@ - + - + diff --git a/schema/ukrdc/Types/CF_RR7_Discharge.xsd b/schema/ukrdc/Types/CF_RR7_Discharge.xsd index f7f12d5..7efef3b 100644 --- a/schema/ukrdc/Types/CF_RR7_Discharge.xsd +++ b/schema/ukrdc/Types/CF_RR7_Discharge.xsd @@ -63,7 +63,7 @@ - + From ca16819155a5b2fff8eaae7cb49c0b51c7dc48bd Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 20 Jun 2023 23:34:47 +0100 Subject: [PATCH 033/166] Fix typo --- docs_build/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index bc67948..db90e63 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -78,7 +78,7 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): namespace = "http://www.w3.org/2001/XMLSchema" xpath_expr = "/xs:complexType/@name|/xs:simpleType/@name" - xsd_types = dom.xpath(xpath_expr, namespaces={"ns": namespace}) + xsd_types = dom.xpath(xpath_expr, namespaces={"xs": namespace}) for xsd_type in xsd_types: type_paths[xsd_type] = in_file[:-4] + ".html" From df9a43a4783d663bd9b67d4c0ca30e6a649b087e Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 20 Jun 2023 23:37:29 +0100 Subject: [PATCH 034/166] . --- docs_build/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index db90e63..af278a2 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -77,7 +77,7 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): dom = ET.parse(in_file.as_posix()) namespace = "http://www.w3.org/2001/XMLSchema" - xpath_expr = "/xs:complexType/@name|/xs:simpleType/@name" + xpath_expr = "//xs:complexType/@name|//xs:simpleType/@name" xsd_types = dom.xpath(xpath_expr, namespaces={"xs": namespace}) for xsd_type in xsd_types: From e90b2836ceef1a9e36f84b6dfd137894dff13b3b Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 20 Jun 2023 23:39:14 +0100 Subject: [PATCH 035/166] . --- docs_build/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index af278a2..ce87c7f 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -81,7 +81,7 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): xsd_types = dom.xpath(xpath_expr, namespaces={"xs": namespace}) for xsd_type in xsd_types: - type_paths[xsd_type] = in_file[:-4] + ".html" + type_paths[xsd_type] = str(in_file)[:-4] + ".html" for xsd_file in [f for f in files if f.endswith(".xsd")]: From 49225288547dab85f55ab250e59a53b84867ab22 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 20 Jun 2023 23:48:18 +0100 Subject: [PATCH 036/166] . --- docs_build/main.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs_build/main.py b/docs_build/main.py index ce87c7f..2ec56bf 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -18,6 +18,9 @@ def replace_strings(html_document, lookup_dict): pattern = r'XXX(\w+)YYY' # Regular expression pattern to match XXXValueYYY + + if isinstance(html_document, bytes): + html_document = html_document.decode() def replace(match): value = match.group(1) From 1ebe06de520aad527565257b4db46b818c780a9d Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 20 Jun 2023 23:50:15 +0100 Subject: [PATCH 037/166] Fix typo --- docs_build/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index 2ec56bf..1180db1 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -25,7 +25,7 @@ def replace_strings(html_document, lookup_dict): def replace(match): value = match.group(1) - type_path = lookup_dict.get(Value, None) + type_path = lookup_dict.get(value, None) if type_path: replacement = f"Type: {value}" From 292616f0ca55f8037baae7abee7ec6d28c036a72 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 20 Jun 2023 23:52:40 +0100 Subject: [PATCH 038/166] . --- docs_build/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index 1180db1..bb2afb4 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -107,7 +107,7 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): html_string = replace_strings(html_string, type_paths) - with open(out_file, "wb") as html_file: + with open(out_file, "w") as html_file: html_file.write(html_string) index_path = out_path.joinpath(path_relative_to_base, "index.html") From 410e6526e010951a35fa1500262839df77df54e9 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 00:02:57 +0100 Subject: [PATCH 039/166] . --- docs_build/main.py | 19 ++++++++++++------- docs_build/stylesheet.xsl | 3 +++ 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/docs_build/main.py b/docs_build/main.py index bb2afb4..9f0db2a 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -15,6 +15,8 @@ xslt = ET.parse(xsl_path.as_posix()) transform = ET.XSLT(xslt) +type_paths = {} + def replace_strings(html_document, lookup_dict): pattern = r'XXX(\w+)YYY' # Regular expression pattern to match XXXValueYYY @@ -26,7 +28,7 @@ def replace(match): value = match.group(1) type_path = lookup_dict.get(value, None) - + if type_path: replacement = f"Type: {value}" else: @@ -63,17 +65,12 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): content += "" return content - for path, dirs, files in os.walk(in_path): path_relative_to_base = Path(path).relative_to(in_path) page_dir = out_path.joinpath(path_relative_to_base) page_dir.mkdir(exist_ok=True) - file_links = [] - - type_paths = {} - for xsd_file in [f for f in files if f.endswith(".xsd")]: in_file = Path(path).joinpath(xsd_file) @@ -84,8 +81,16 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): xsd_types = dom.xpath(xpath_expr, namespaces={"xs": namespace}) for xsd_type in xsd_types: - type_paths[xsd_type] = str(in_file)[:-4] + ".html" + type_path = str(in_file).replace('schema/ukrdc/', '') + type_paths[xsd_type] = str(type_path)[:-4] + ".html" +for path, dirs, files in os.walk(in_path): + + path_relative_to_base = Path(path).relative_to(in_path) + page_dir = out_path.joinpath(path_relative_to_base) + page_dir.mkdir(exist_ok=True) + + file_links = [] for xsd_file in [f for f in files if f.endswith(".xsd")]: base_name = xsd_file.split(".xsd")[0] diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index ed02dd9..e3e15e7 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -254,6 +254,9 @@ + + Type: + XXXYYY
From c0345d96328176af56e2e21da7d1c3cd57c6c796 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 01:56:35 +0100 Subject: [PATCH 040/166] . --- docs_build/stylesheet.xsl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index e3e15e7..d6affe2 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -427,6 +427,8 @@ + + From 45986acc1edf70939b3bd9bdf838a49a4aaf8037 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 02:08:49 +0100 Subject: [PATCH 041/166] . --- docs_build/stylesheet.xsl | 5 ++++- schema/ukrdc/Types/SendingFacility.xsd | 18 +++++++++++++++--- 2 files changed, 19 insertions(+), 4 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index d6affe2..ed6e65f 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -173,8 +173,11 @@ + + Type: + - + XXXYYY diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd index 08f2e46..6f7205b 100644 --- a/schema/ukrdc/Types/SendingFacility.xsd +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -7,9 +7,21 @@ - - - + + + This should be a reference for the System / Version which generated the file. The intended purpose is to allow us to identify, or temporarily rectify, issues with what a particular extract is generating. + + + + + This should be the time that the extract was generated. + + + + + This should be the version (from the XSD Schema) that the extract has been written against. This is to allow us to process incoming files accordingly as well as track which Units are submitting which version. Note that the RDA Schema version is unrelated to the UKRR Dataset version. + + \ No newline at end of file From e5dad838c07f65aa1f5a7d729999bfbefb678fd3 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 02:29:13 +0100 Subject: [PATCH 042/166] . --- docs_build/main.py | 7 +++++++ schema/ukrdc/UKRDC.xsd | 1 + 2 files changed, 8 insertions(+) diff --git a/docs_build/main.py b/docs_build/main.py index 9f0db2a..e537199 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -82,6 +82,10 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): for xsd_type in xsd_types: type_path = str(in_file).replace('schema/ukrdc/', '') + + # HACK: This only fixes a specific case. + type_path.replace('Types/Types/', 'Types/') + type_paths[xsd_type] = str(type_path)[:-4] + ".html" for path, dirs, files in os.walk(in_path): @@ -110,6 +114,9 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): html_string = ET.tostring(newdom, pretty_print=True) + # TODO: This doesn't work if the definition is in a different + # file in the same folder as it's being used in. + # The replace function needs to take account of the current path. html_string = replace_strings(html_string, type_paths) with open(out_file, "w") as html_file: diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index c227b5d..fe79e50 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -63,6 +63,7 @@ UKRRv4,UKRRv5,PKB,RADAR + Test Lab Orders From fdea451ddd6b7b6d4993c9f5a2c4690ba43d2823 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 02:32:13 +0100 Subject: [PATCH 043/166] . --- docs_build/stylesheet.xsl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index ed6e65f..9d8866b 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -1,5 +1,5 @@ - + - +
Should be submitted for:
@@ -247,7 +247,7 @@ - + From 2f9915f281e4417b0c8011b05500472e073023a7 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 02:38:58 +0100 Subject: [PATCH 044/166] . --- docs_build/stylesheet.xsl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 9d8866b..04fd854 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -90,7 +90,7 @@ - +
Should be submitted for:
@@ -247,7 +247,7 @@ - + From e8896901c06b9bb47ff4f72c9001d76c5fa8db2f Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 02:48:52 +0100 Subject: [PATCH 045/166] . --- docs_build/stylesheet.xsl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 04fd854..e4575f8 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -90,7 +90,7 @@ - +
Should be submitted for:
@@ -247,7 +247,7 @@ - + From 2ec4fa1d00f783a6196a6423fd51d320b53ca92a Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 02:53:39 +0100 Subject: [PATCH 046/166] . --- docs_build/stylesheet.xsl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index e4575f8..6d54ab4 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -90,7 +90,7 @@ - +
Should be submitted for:
@@ -247,7 +247,7 @@ - + From ec7b066f3b140b230cfe0c6260d074fec709547c Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 03:07:05 +0100 Subject: [PATCH 047/166] . --- schema/ukrdc/LabOrders/LabOrder.xsd | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index aa6507c..b650f44 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -10,8 +10,12 @@ - - + + Lab Orders + + + Lab Orders + From 37b4094d04edc431210efafcda79a1c89d3411d8 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 03:14:51 +0100 Subject: [PATCH 048/166] . --- schema/ukrdc/LabOrders/LabOrder.xsd | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index b650f44..693c497 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -7,15 +7,16 @@ - - - Lab Orders Lab Orders + + + + From a54da84487a6839cb8f102edf4a5c08cace03567 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 03:21:00 +0100 Subject: [PATCH 049/166] . --- docs_build/main.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index e537199..f247054 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -84,7 +84,10 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): type_path = str(in_file).replace('schema/ukrdc/', '') # HACK: This only fixes a specific case. - type_path.replace('Types/Types/', 'Types/') + type_path_list = type_path.split('/') + if type_path_list[0] == type_path_list[1]: + type_path = "/".join(type_path_list[1:] + # type_path.replace('Types/Types/', 'Types/') type_paths[xsd_type] = str(type_path)[:-4] + ".html" From 845c5bec3c5d1592ebcfc6f5f6f9e6bfe272fd8e Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 03:23:09 +0100 Subject: [PATCH 050/166] . --- docs_build/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs_build/main.py b/docs_build/main.py index f247054..a2ea27d 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -86,7 +86,7 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): # HACK: This only fixes a specific case. type_path_list = type_path.split('/') if type_path_list[0] == type_path_list[1]: - type_path = "/".join(type_path_list[1:] + type_path = "/".join(type_path_list[1:]) # type_path.replace('Types/Types/', 'Types/') type_paths[xsd_type] = str(type_path)[:-4] + ".html" From f803899cd0a58864347002d63610db2dace11645 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 21 Jun 2023 15:58:06 +0100 Subject: [PATCH 051/166] . --- docs_build/main.py | 11 +++++----- schema/ukrdc/Assessments/Assessment.xsd | 28 +++++++++++++++++-------- schema/ukrdc/LabOrders/LabOrder.xsd | 25 +++++++++++++++------- 3 files changed, 42 insertions(+), 22 deletions(-) diff --git a/docs_build/main.py b/docs_build/main.py index a2ea27d..d4521be 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -82,12 +82,13 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): for xsd_type in xsd_types: type_path = str(in_file).replace('schema/ukrdc/', '') - - # HACK: This only fixes a specific case. + type_path_list = type_path.split('/') - if type_path_list[0] == type_path_list[1]: - type_path = "/".join(type_path_list[1:]) - # type_path.replace('Types/Types/', 'Types/') + if len(type_path_list) > 1: + if type_path_list[0] == type_path_list[1]: + type_path = "/".join(type_path_list[1:]) + # HACK: This only fixes a specific case. + # type_path.replace('Types/Types/', 'Types/') type_paths[xsd_type] = str(type_path)[:-4] + ".html" diff --git a/schema/ukrdc/Assessments/Assessment.xsd b/schema/ukrdc/Assessments/Assessment.xsd index be85eee..ede3e72 100644 --- a/schema/ukrdc/Assessments/Assessment.xsd +++ b/schema/ukrdc/Assessments/Assessment.xsd @@ -1,25 +1,33 @@ - - + + UKRRv5 + + - + + UKRRv5 + The Date the Assessment Started - + + UKRRv5 + The Date the Assessment Ended - + - + + UKRRv5 + Assessment Type @@ -27,7 +35,7 @@ - + @@ -50,7 +58,9 @@ - + + UKRRv5 + Assessment Outcome @@ -58,7 +68,7 @@ - + diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index 693c497..30d5221 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -8,10 +8,10 @@ - Lab Orders + - Lab Orders + @@ -27,23 +27,27 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + - + + UKRRv4,UKRRv5,PKB,RADAR + Location or Facility receiving/performing the order. - laborder.placerid + UKRRv4,UKRRv5,PKB,RADAR - ORC:2 Placer's Order Id + ORC:2 Placer (Hospital)'s Order Id @@ -53,8 +57,10 @@ - - + + + UKRRv4,UKRRv5,PKB,RADAR + ORC:3 Filler (Lab)'s Order Id @@ -65,6 +71,9 @@ + + UKRRv4,UKRRv5,PKB,RADAR + Requesting Location (as in Hospital, GP, etc.) From 8d42c04869ef095213d76997aa379ec5745bbb2f Mon Sep 17 00:00:00 2001 From: phil Date: Fri, 23 Jun 2023 10:39:32 +0100 Subject: [PATCH 052/166] added setup.py to resources repo --- setup.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 setup.py diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..ffc2d86 --- /dev/null +++ b/setup.py @@ -0,0 +1,17 @@ +from setuptools import setup, find_packages +import pkg_resources +import xml.etree.ElementTree as ET + + +xsd_file_path = pkg_resources.resource_filename('schema.ukrdc', 'UKRDC.xsd') # File path relative to the repo, like /schema/ukrdc/UKRDC.xsd +xsd_schema = ET.parse(xsd_file_path) +root = xsd_schema.getroot() +version = root.attrib.get('version') # Get the version attribute from the root element + +setup( + name='resources', + version=version, # Set the version to correspond with the XSD schema version + packages=find_packages(), + package_data={'schema.ukrdc': ['*.xsd'], 'schema.pv2': ['*.xsd'], 'schema.rrtf': ['*.xsd']}, + include_package_data=True +) \ No newline at end of file From 2265e7e42d106710ed9226223b620eebde05bc7d Mon Sep 17 00:00:00 2001 From: phil Date: Fri, 23 Jun 2023 13:42:50 +0100 Subject: [PATCH 053/166] added manifest.ini --- manifest.ini | 1 + 1 file changed, 1 insertion(+) create mode 100644 manifest.ini diff --git a/manifest.ini b/manifest.ini new file mode 100644 index 0000000..e2824a5 --- /dev/null +++ b/manifest.ini @@ -0,0 +1 @@ +recursive-include schema *.xsd \ No newline at end of file From 5a0e43712036e2fffba7c39c5ba70f6c31025c56 Mon Sep 17 00:00:00 2001 From: Philip Main Date: Tue, 27 Jun 2023 11:02:51 +0100 Subject: [PATCH 054/166] Revert "added setup.py to resources repo" --- manifest.ini | 1 - setup.py | 17 ----------------- 2 files changed, 18 deletions(-) delete mode 100644 manifest.ini delete mode 100644 setup.py diff --git a/manifest.ini b/manifest.ini deleted file mode 100644 index e2824a5..0000000 --- a/manifest.ini +++ /dev/null @@ -1 +0,0 @@ -recursive-include schema *.xsd \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index ffc2d86..0000000 --- a/setup.py +++ /dev/null @@ -1,17 +0,0 @@ -from setuptools import setup, find_packages -import pkg_resources -import xml.etree.ElementTree as ET - - -xsd_file_path = pkg_resources.resource_filename('schema.ukrdc', 'UKRDC.xsd') # File path relative to the repo, like /schema/ukrdc/UKRDC.xsd -xsd_schema = ET.parse(xsd_file_path) -root = xsd_schema.getroot() -version = root.attrib.get('version') # Get the version attribute from the root element - -setup( - name='resources', - version=version, # Set the version to correspond with the XSD schema version - packages=find_packages(), - package_data={'schema.ukrdc': ['*.xsd'], 'schema.pv2': ['*.xsd'], 'schema.rrtf': ['*.xsd']}, - include_package_data=True -) \ No newline at end of file From 1104603f519be6519e6cc1f1f0643883d125416c Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Thu, 29 Jun 2023 16:50:03 +0100 Subject: [PATCH 055/166] Fix Schema syntax errors --- schema/ukrdc/LabOrders/LabOrder.xsd | 52 ++++++++++++++++++-------- schema/ukrdc/Types/RRTypes.xsd | 2 +- schema/ukrdc/Types/SendingFacility.xsd | 21 ++++++++--- 3 files changed, 53 insertions(+), 22 deletions(-) diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index 30d5221..c6d6ce3 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -7,16 +7,13 @@ + + + - - - - - - @@ -79,7 +76,9 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + OBR:4 Service Id - the identity of the test ordered. @@ -87,14 +86,18 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + OBR:22 - + + UKRRv4,UKRRv5,PKB,RADAR + OBR:14 @@ -162,7 +165,9 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + @@ -185,7 +190,10 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + + Was the sample taken PRE or POST dialysis @@ -215,6 +223,9 @@ + + UKRRv4,UKRRv5,PKB,RADAR + Test Code (OBX:3) @@ -231,7 +242,10 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + + OBX:5 @@ -242,7 +256,10 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + + OBX:6 @@ -253,7 +270,9 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + OBX:7 @@ -264,7 +283,10 @@ - + + UKRRv4,UKRRv5,PKB,RADAR + + Interpretation Codes (OBX:8) diff --git a/schema/ukrdc/Types/RRTypes.xsd b/schema/ukrdc/Types/RRTypes.xsd index 21fb5f0..2b6cb89 100644 --- a/schema/ukrdc/Types/RRTypes.xsd +++ b/schema/ukrdc/Types/RRTypes.xsd @@ -1,6 +1,6 @@ - + UKRDC Schema Version in 0.0.0 Format diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd index 6f7205b..6fbd1b5 100644 --- a/schema/ukrdc/Types/SendingFacility.xsd +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -2,11 +2,18 @@ - - - - - + + + + + + + + + + + + This should be a reference for the System / Version which generated the file. The intended purpose is to allow us to identify, or temporarily rectify, issues with what a particular extract is generating. @@ -22,6 +29,8 @@ This should be the version (from the XSD Schema) that the extract has been written against. This is to allow us to process incoming files accordingly as well as track which Units are submitting which version. Note that the RDA Schema version is unrelated to the UKRR Dataset version. - + + + \ No newline at end of file From 046b25021c52ebeaff1d878a01aa8ec56c4667ed Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 12 Jul 2023 14:06:58 +0100 Subject: [PATCH 056/166] Reference Assessments in UKRDC.xsd --- schema/ukrdc/UKRDC.xsd | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index fe79e50..1bc1b7e 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -1,6 +1,7 @@ + @@ -315,6 +316,19 @@ + + + + NONE + + Assessments + + + + + + + From d1ac4b1750240debd56442c3bf77ff95120b93a3 Mon Sep 17 00:00:00 2001 From: phil Date: Tue, 15 Aug 2023 10:51:42 +0100 Subject: [PATCH 057/166] updated the xsd schema to version 4.0.0 --- sample_files/ukrdc/fullDemographics.xml | 2 +- sample_files/ukrdc/fullFile.xml | 2 +- sample_files/ukrdc/minimalDemographics.xml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/sample_files/ukrdc/fullDemographics.xml b/sample_files/ukrdc/fullDemographics.xml index 5df0871..32b78ea 100644 --- a/sample_files/ukrdc/fullDemographics.xml +++ b/sample_files/ukrdc/fullDemographics.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC diff --git a/sample_files/ukrdc/fullFile.xml b/sample_files/ukrdc/fullFile.xml index 48792e0..152a856 100644 --- a/sample_files/ukrdc/fullFile.xml +++ b/sample_files/ukrdc/fullFile.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC diff --git a/sample_files/ukrdc/minimalDemographics.xml b/sample_files/ukrdc/minimalDemographics.xml index a10fe3d..3295fb1 100644 --- a/sample_files/ukrdc/minimalDemographics.xml +++ b/sample_files/ukrdc/minimalDemographics.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC From 64d7e27b5005e443516bd5ee0dbf41cb837b4e10 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 16 Aug 2023 09:08:08 +0100 Subject: [PATCH 058/166] Initial 4.1.0 changes - see Changelog for details --- codes/code_lists/edta2.csv | 505 ++++++++++++------------ schema/ukrdc/CHANGELOG.md | 6 + schema/ukrdc/Types/CF_EDTA_PRD.xsd | 47 ++- schema/ukrdc/Types/CF_RR7_Treatment.xsd | 29 +- 4 files changed, 329 insertions(+), 258 deletions(-) diff --git a/codes/code_lists/edta2.csv b/codes/code_lists/edta2.csv index 71ce7c1..d820aea 100644 --- a/codes/code_lists/edta2.csv +++ b/codes/code_lists/edta2.csv @@ -1,188 +1,186 @@ -EDTA2,2513,AA amyloid secondary to chronic inflammation -EDTA2,1768,Acquired obstructive nephropathy due to neurogenic bladder -EDTA2,1752,Acquired obstructive uropathy / nephropathy -EDTA2,3442,Acute cortical necrosis -EDTA2,3380,Acute kidney injury -EDTA2,3403,Acute kidney injury due to circulatory failure -EDTA2,3398,Acute kidney injury due to hypovolaemia -EDTA2,3435,Acute kidney injury due to nephrotoxicity -EDTA2,3426,Acute kidney injury due to rhabdomyolysis -EDTA2,3419,Acute kidney injury due to sepsis -EDTA2,3457,Acute pyelonephritis -EDTA2,2196,Acute urate nephropathy - histologically proven -EDTA2,2183,Acute urate nephropathy - no histology -EDTA2,1003,Adult nephrotic syndrome - no histology -EDTA2,2392,Ageing kidney - no histology -EDTA2,2521,AL amyloid secondary to plasma cell dyscrasia -EDTA2,3071,Alagille syndrome -EDTA2,2760,Alport syndrome - histologically proven -EDTA2,2756,Alport syndrome - no histology -EDTA2,1472,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - histologically proven -EDTA2,1464,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - no histology -EDTA2,3118,Apparent mineralocorticoid excess -EDTA2,1995,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - histologically proven -EDTA2,1982,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - no histology -EDTA2,2448,Atheroembolic renal disease - histologically proven -EDTA2,2430,Atheroembolic renal disease - no histology -EDTA2,2623,Atypical haemolytic uraemic syndrome (HUS) - diarrhoea negative -EDTA2,2718,Autosomal dominant (AD) polycystic kidney disease -EDTA2,2725,Autosomal dominant (AD) polycystic kidney disease type I -EDTA2,2739,Autosomal dominant (AD) polycystic kidney disease type II -EDTA2,2741,Autosomal recessive (AR) polycystic kidney disease -EDTA2,3085,Bartter syndrome -EDTA2,2773,Benign familial haematuria -EDTA2,1710,Bladder exstrophy -EDTA2,3322,Branchio-oto-renal syndrome -EDTA2,1845,Calcium oxalate urolithiasis -EDTA2,1832,Calculus nephropathy / urolithiasis -EDTA2,2482,Cardiorenal syndrome -EDTA2,2363,Chronic hypertensive nephropathy - histologically proven -EDTA2,2359,Chronic hypertensive nephropathy - no histology -EDTA2,3564,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - histologically proven -EDTA2,3555,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - no histology -EDTA2,3529,Chronic kidney disease (CKD) / chronic renal failure (CRF) caused by tumour nephrectomy -EDTA2,3540,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to donor nephrectomy -EDTA2,3538,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to traumatic loss of kidney -EDTA2,3708,Chronic renal failure -EDTA2,3643,Chronic renal failure due to systemic infection -EDTA2,2203,Chronic urate nephropathy - histologically proven -EDTA2,3636,Chronic urate nephropathy - no histology -EDTA2,1440,Churg-Strauss syndrome - histologically proven -EDTA2,1438,Churg-Strauss syndrome - no histology -EDTA2,1625,Congenital dysplasia / hypoplasia -EDTA2,2652,Congenital haemolytic uraemic syndrome (HUS) -EDTA2,1088,Congenital nephrotic syndrome (CNS) - congenital infection -EDTA2,1057,Congenital nephrotic syndrome (CNS) - diffuse mesangial sclerosis -EDTA2,1042,Congenital nephrotic syndrome (CNS) - Finnish type - histologically proven +EDTA2,1003,Adult nephrotic syndrome - no histology +EDTA2,1019,Nephrotic syndrome of childhood - steroid sensitive - no histology +EDTA2,1026,Congenital nephrotic syndrome (CNS) - no histology EDTA2,1035,Congenital nephrotic syndrome (CNS) - Finnish type - no histology +EDTA2,1042,Congenital nephrotic syndrome (CNS) - Finnish type - histologically proven +EDTA2,1057,Congenital nephrotic syndrome (CNS) - diffuse mesangial sclerosis EDTA2,1061,Congenital nephrotic syndrome (CNS) - focal segmental glomerulosclerosis (FSGS) -EDTA2,1026,Congenital nephrotic syndrome (CNS) - no histology -EDTA2,1706,Congenital neurogenic bladder -EDTA2,1660,Congenital pelvi-ureteric junction obstruction -EDTA2,1673,Congenital vesico-ureteric junction obstruction -EDTA2,1570,Cryoglobulinaemia secondary to hepatitis C - histologically proven -EDTA2,1562,Cryoglobulinaemia secondary to hepatitis C - no histology -EDTA2,1591,Cryoglobulinaemia secondary to systemic disease - histologically proven -EDTA2,1589,Cryoglobulinaemia secondary to systemic disease - no histology -EDTA2,2794,Cystic kidney disease -EDTA2,2964,Cystinosis -EDTA2,2955,Cystinuria -EDTA2,2929,Dent disease EDTA2,1074,Denys-Drash syndrome -EDTA2,2328,Diabetic nephropathy in type I diabetes - histologically proven -EDTA2,2316,Diabetic nephropathy in type I diabetes - no histology -EDTA2,2344,Diabetic nephropathy in type II diabetes - histologically proven -EDTA2,2337,Diabetic nephropathy in type II diabetes - no histology -EDTA2,1331,Diffuse endocapillary glomerulonephritis -EDTA2,3028,Distal renal tubular acidosis (RTA) - type I -EDTA2,3037,Distal renal tubular acidosis with sensorineural deafness - gene mutations -EDTA2,2005,Drug-induced tubulointerstitial nephritis - no histology -EDTA2,2014,Drug-induced tubulointerstitial nephritis - histologically proven -EDTA2,2005,Drug-induced tubulointerstitial nephritis - no histology -EDTA2,1641,Dysplasia due to fetal ACE-inhibitor exposure -EDTA2,1850,Enteric hyperoxaluria -EDTA2,1558,Essential mixed cryoglobulinaemia - histologically proven -EDTA2,1543,Essential mixed cryoglobulinaemia - no histology -EDTA2,3230,Fabry disease - histologically proven -EDTA2,3224,Fabry disease - no histology -EDTA2,2566,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - histologically proven -EDTA2,2550,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - no histology -EDTA2,2545,Familial amyloid secondary to protein mutations - histologically proven -EDTA2,2532,Familial amyloid secondary to protein mutations - no histology -EDTA2,1308,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - histologically proven -EDTA2,1298,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - no histology -EDTA2,1280,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - histologically proven -EDTA2,1279,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - no histology -EDTA2,2668,Familial haemolytic uraemic syndrome (HUS) -EDTA2,3173,Familial hypercalciuric hypocalcaemia -EDTA2,3160,Familial hypocalciuric hypercalcaemia -EDTA2,3187,Familial hypomagnesaemia -EDTA2,1144,Familial IgA nephropathy - histologically proven -EDTA2,1137,Familial IgA nephropathy - no histology -EDTA2,1911,Familial interstitial nephropathy - histologically proven -EDTA2,1907,Familial interstitial nephropathy - no histology -EDTA2,3379,Familial nephropathy -EDTA2,1618,Familial reflux nephropathy -EDTA2,2675,Familial thrombotic thrombocytopenic purpura (TTP) -EDTA2,2453,Fibromuscular dysplasia of renal artery -EDTA2,1354,Focal and segmental proliferative glomerulonephritis -EDTA2,3754,Focal segmental glomerulosclerosis (FSGS) secondary to HIV -EDTA2,3765,Focal segmental glomerulosclerosis (FSGS) secondary to lithium -EDTA2,1320,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - histologically proven -EDTA2,1312,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - no histology -EDTA2,3777,Focal segmental glomerulosclerosis (FSGS) secondary to sickle cell -EDTA2,3314,Frasier syndrome -EDTA2,3092,Gitelman syndrome -EDTA2,1656,Glomerulocystic disease -EDTA2,1377,Glomerulonephritis - histologically indeterminate -EDTA2,3749,Glomerulonephritis - no histology -EDTA2,1365,Glomerulonephritis - secondary to other systemic disease -EDTA2,1365,Glomerulonephritis - secondary to systemic disease -EDTA2,3125,Glucocorticoid suppressible hyperaldosteronism -EDTA2,1417,Granulomatosis with polyangiitis - histologically proven -EDTA2,1401,Granulomatosis with polyangiitis - no histology -EDTA2,3572,Haematuria and proteinuria - no histology -EDTA2,2610,Haemolytic uraemic syndrome (HUS) - diarrhoea associated -EDTA2,2647,Haemolytic uraemic syndrome (HUS) secondary to systemic disease -EDTA2,2257,Hantavirus nephropathy -EDTA2,1515,Henoch-Schönlein purpura / nephritis - histologically proven -EDTA2,1504,Henoch-Schönlein purpura / nephritis - no histology -EDTA2,2495,Hepatorenal syndrome -EDTA2,3305,Horse-shoe kidney -EDTA2,3662,Hypercalcaemic nephropathy -EDTA2,2993,Hypophosphataemic rickets autosomal recessive (AR) -EDTA2,2986,Hypophosphataemic rickets X-linked (XL) -EDTA2,1251,Idiopathic rapidly progressive (crescentic) glomerulonephritis -EDTA2,1813,Idiopathic retroperitoneal fibrosis -EDTA2,1128,IgA nephropathy - histologically proven +EDTA2,1088,Congenital nephrotic syndrome (CNS) - congenital infection +EDTA2,1090,Minimal change nephropathy - no histology +EDTA2,1100,Minimal change nephropathy - histologically proven EDTA2,1116,IgA nephropathy - no histology -EDTA2,1163,IgA nephropathy secondary to liver cirrhosis - histologically proven +EDTA2,1128,IgA nephropathy - histologically proven +EDTA2,1137,Familial IgA nephropathy - no histology +EDTA2,1144,Familial IgA nephropathy - histologically proven EDTA2,1159,IgA nephropathy secondary to liver cirrhosis - no histology +EDTA2,1163,IgA nephropathy secondary to liver cirrhosis - histologically proven EDTA2,1171,IgM - associated nephropathy -EDTA2,2606,Immunotactoid / fibrillary nephropathy -EDTA2,3823,Infiltration by lymphoma - histologically proven -EDTA2,3139,Inherited / genetic diabetes mellitus type II -EDTA2,2940,Inherited aminoaciduria -EDTA2,2972,Inherited renal glycosuria -EDTA2,2407,Ischaemic nephropathy - no histology -EDTA2,2411,Ischaemic nephropathy / microvascular disease - histologically proven -EDTA2,3712,Isolated haematuria - no histology -EDTA2,3720,Isolated proteinuria - no histology -EDTA2,3810,Kidney stones due to ARPT deficiency -EDTA2,3461,Kidney tumour -EDTA2,3351,Lawrence-Moon-Biedl / Bardet-Biedl syndrome -EDTA2,2177,Lead induced nephropathy - histologically proven -EDTA2,2165,Lead induced nephropathy - no histology -EDTA2,2242,Leptospirosis -EDTA2,3059,Lesch Nyhan syndrome - hypoxanthine guanine phosphoribosyl transferase deficiency -EDTA2,3102,Liddle syndrome -EDTA2,2597,Light chain deposition disease -EDTA2,2938,Lowe syndrome (oculocerebrorenal syndrome) -EDTA2,1866,Magnesium ammonium phosphate (struvite) urolithiasis -EDTA2,2385,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - histologically proven -EDTA2,2371,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - no histology -EDTA2,2804,Medullary cystic kidney disease type I -EDTA2,2815,Medullary cystic kidney disease type II -EDTA2,3295,Medullary sponge kidneys -EDTA2,1723,Megacystis-megaureter -EDTA2,1205,Membranous nephropathy - drug induced EDTA2,1185,Membranous nephropathy - idiopathic -EDTA2,1214,Membranous nephropathy - infection associated EDTA2,1192,Membranous nephropathy - malignancy associated -EDTA2,1349,Mesangial proliferative glomerulonephritis +EDTA2,1205,Membranous nephropathy - drug induced +EDTA2,1214,Membranous nephropathy - infection associated EDTA2,1222,Mesangiocapillary glomerulonephritis type 1 EDTA2,1233,Mesangiocapillary glomerulonephritis type 2 (dense deposit disease) EDTA2,1246,Mesangiocapillary glomerulonephritis type 3 -EDTA2,3501,Mesoblastic nephroma - histologically proven +EDTA2,1251,Idiopathic rapidly progressive (crescentic) glomerulonephritis +EDTA2,1267,Primary focal segmental glomerulosclerosis (FSGS) +EDTA2,1279,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - no histology +EDTA2,1280,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - histologically proven +EDTA2,1298,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - no histology +EDTA2,1308,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - histologically proven +EDTA2,1312,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - no histology +EDTA2,1320,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - histologically proven +EDTA2,1331,Diffuse endocapillary glomerulonephritis +EDTA2,1349,Mesangial proliferative glomerulonephritis +EDTA2,1354,Focal and segmental proliferative glomerulonephritis +EDTA2,1365,Glomerulonephritis - secondary to other systemic disease +EDTA2,1377,Glomerulonephritis - histologically indeterminate +EDTA2,1383,Systemic vasculitis - ANCA negative - histologically proven +EDTA2,1396,Systemic vasculitis - ANCA positive - no histology +EDTA2,1401,Granulomatosis with polyangiitis - no histology +EDTA2,1417,Granulomatosis with polyangiitis - histologically proven EDTA2,1429,Microscopic polyangiitis - histologically proven -EDTA2,1100,Minimal change nephropathy - histologically proven -EDTA2,1090,Minimal change nephropathy - no histology -EDTA2,3367,Mitochondrial cytopathy +EDTA2,1438,Churg-Strauss syndrome - no histology +EDTA2,1440,Churg-Strauss syndrome - histologically proven +EDTA2,1455,Polyarteritis nodosa +EDTA2,1464,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - no histology +EDTA2,1472,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - histologically proven +EDTA2,1486,Systemic lupus erythematosus / nephritis - no histology +EDTA2,1493,Systemic lupus erythematosus / nephritis - histologically proven +EDTA2,1504,Henoch-Schönlein purpura / nephritis - no histology +EDTA2,1515,Henoch-Schönlein purpura / nephritis - histologically proven +EDTA2,1527,Renal scleroderma / systemic sclerosis - no histology +EDTA2,1536,Renal scleroderma / systemic sclerosis - histologically proven +EDTA2,1543,Essential mixed cryoglobulinaemia - no histology +EDTA2,1558,Essential mixed cryoglobulinaemia - histologically proven +EDTA2,1562,Cryoglobulinaemia secondary to hepatitis C - no histology +EDTA2,1570,Cryoglobulinaemia secondary to hepatitis C - histologically proven +EDTA2,1589,Cryoglobulinaemia secondary to systemic disease - no histology +EDTA2,1591,Cryoglobulinaemia secondary to systemic disease - histologically proven +EDTA2,1602,Primary reflux nephropathy - sporadic +EDTA2,1618,Familial reflux nephropathy +EDTA2,1625,Congenital dysplasia / hypoplasia EDTA2,1639,Multicystic dysplastic kidneys -EDTA2,2584,Myeloma cast nephropathy - histologically proven +EDTA2,1641,Dysplasia due to fetal ACE-inhibitor exposure +EDTA2,1656,Glomerulocystic disease +EDTA2,1660,Congenital pelvi-ureteric junction obstruction +EDTA2,1673,Congenital vesico-ureteric junction obstruction +EDTA2,1687,Posterior urethral valves +EDTA2,1694,Syndrome of agenesis of abdominal muscles - prune belly syndrome +EDTA2,1706,Congenital neurogenic bladder +EDTA2,1710,Bladder exstrophy +EDTA2,1723,Megacystis-megaureter +EDTA2,1734,Oligomeganephronia +EDTA2,1747,Renal papillary necrosis +EDTA2,1752,Acquired obstructive uropathy / nephropathy +EDTA2,1768,Acquired obstructive nephropathy due to neurogenic bladder +EDTA2,1775,Obstructive nephropathy due to prostatic hypertrophy +EDTA2,1781,Obstructive nephropathy due to prostate cancer +EDTA2,1799,Obstructive nephropathy due to bladder cancer +EDTA2,1809,Obstructive nephropathy due to other malignancies +EDTA2,1813,Idiopathic retroperitoneal fibrosis +EDTA2,1821,Retroperitoneal fibrosis secondary to malignancies +EDTA2,1832,Calculus nephropathy / urolithiasis +EDTA2,1845,Calcium oxalate urolithiasis +EDTA2,1850,Enteric hyperoxaluria +EDTA2,1866,Magnesium ammonium phosphate (struvite) urolithiasis +EDTA2,1878,Uric acid urolithiasis +EDTA2,1884,Tubulointerstitial nephritis - no histology +EDTA2,1897,Tubulointerstitial nephritis - histologically proven +EDTA2,1907,Familial interstitial nephropathy - no histology +EDTA2,1911,Familial interstitial nephropathy - histologically proven +EDTA2,1924,Tubulointerstitial nephritis associated with autoimmune disease - no histology +EDTA2,1930,Tubulointerstitial nephritis associated with autoimmune disease - histologically proven +EDTA2,1948,Tubulointerstitial nephritis with uveitis (TINU) - no histology +EDTA2,1953,Tubulointerstitial nephritis with uveitis (TINU) - histologically proven +EDTA2,1969,Renal sarcoidosis - no histology +EDTA2,1976,Renal sarcoidosis - histologically proven +EDTA2,1982,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - no histology +EDTA2,1995,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - histologically proven +EDTA2,2005,Drug-induced tubulointerstitial nephritis - no histology +EDTA2,2014,Drug-induced tubulointerstitial nephritis - histologically proven +EDTA2,2022,Nephropathy due to analgesic drugs - no histology +EDTA2,2033,Nephropathy due to analgesic drugs - histologically proven +EDTA2,2046,Nephropathy due to ciclosporin - no histology +EDTA2,2051,Nephropathy due to ciclosporin - histologically proven +EDTA2,2067,Nephropathy due to tacrolimus - no histology +EDTA2,2079,Nephropathy due to tacrolimus - histologically proven +EDTA2,2080,Nephropathy due to aminoglycosides - no histology +EDTA2,2098,Nephropathy due to aminoglycosides - histologically proven +EDTA2,2108,Nephropathy due to amphotericin - no histology +EDTA2,2112,Nephropathy due to amphotericin - histologically proven +EDTA2,2120,Nephropathy due to cisplatin - no histology +EDTA2,2131,Nephropathy due to cisplatin - histologically proven +EDTA2,2149,Nephropathy due to lithium - no histology +EDTA2,2154,Nephropathy due to lithium - histologically proven +EDTA2,2165,Lead induced nephropathy - no histology +EDTA2,2177,Lead induced nephropathy - histologically proven +EDTA2,2183,Acute urate nephropathy - no histology +EDTA2,2196,Acute urate nephropathy - histologically proven +EDTA2,2203,Chronic urate nephropathy - histologically proven +EDTA2,2219,Radiation nephritis +EDTA2,2226,Renal / perinephric abscess +EDTA2,2235,Renal tuberculosis +EDTA2,2242,Leptospirosis +EDTA2,2257,Hantavirus nephropathy +EDTA2,2261,Xanthogranulomatous pyelonephritis +EDTA2,2274,Nephropathy related to HIV - no histology +EDTA2,2288,Nephropathy related to HIV - histologically proven +EDTA2,2290,Schistosomiasis +EDTA2,2300,Other specific infection +EDTA2,2316,Diabetic nephropathy in type I diabetes - no histology +EDTA2,2328,Diabetic nephropathy in type I diabetes - histologically proven +EDTA2,2337,Diabetic nephropathy in type II diabetes - no histology +EDTA2,2344,Diabetic nephropathy in type II diabetes - histologically proven +EDTA2,2359,Chronic hypertensive nephropathy - no histology +EDTA2,2363,Chronic hypertensive nephropathy - histologically proven +EDTA2,2371,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - no histology +EDTA2,2385,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - histologically proven +EDTA2,2392,Ageing kidney - no histology +EDTA2,2407,Ischaemic nephropathy - no histology +EDTA2,2411,Ischaemic nephropathy / microvascular disease - histologically proven +EDTA2,2424,Renal artery stenosis +EDTA2,2430,Atheroembolic renal disease - no histology +EDTA2,2448,Atheroembolic renal disease - histologically proven +EDTA2,2453,Fibromuscular dysplasia of renal artery +EDTA2,2469,Renal arterial thrombosis / occlusion +EDTA2,2476,Renal vein thrombosis +EDTA2,2482,Cardiorenal syndrome +EDTA2,2495,Hepatorenal syndrome +EDTA2,2509,Renal amyloidosis +EDTA2,2513,AA amyloid secondary to chronic inflammation +EDTA2,2521,AL amyloid secondary to plasma cell dyscrasia +EDTA2,2532,Familial amyloid secondary to protein mutations - no histology +EDTA2,2545,Familial amyloid secondary to protein mutations - histologically proven +EDTA2,2550,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - no histology +EDTA2,2566,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - histologically proven EDTA2,2578,Myeloma kidney - no histology -EDTA2,3253,Nail-patella syndrome -EDTA2,3044,Nephrogenic diabetes insipidus +EDTA2,2584,Myeloma cast nephropathy - histologically proven +EDTA2,2597,Light chain deposition disease +EDTA2,2606,Immunotactoid / fibrillary nephropathy +EDTA2,2610,Haemolytic uraemic syndrome (HUS) - diarrhoea associated +EDTA2,2623,Atypical haemolytic uraemic syndrome (HUS) - diarrhoea negative +EDTA2,2634,Thrombotic thrombocytopenic purpura (TTP) +EDTA2,2647,Haemolytic uraemic syndrome (HUS) secondary to systemic disease +EDTA2,2652,Congenital haemolytic uraemic syndrome (HUS) +EDTA2,2668,Familial haemolytic uraemic syndrome (HUS) +EDTA2,2675,Familial thrombotic thrombocytopenic purpura (TTP) +EDTA2,2681,Nephropathy due to eclampsia +EDTA2,2699,Sickle cell nephropathy - no histology +EDTA2,2702,Sickle cell nephropathy - histologically proven +EDTA2,2718,Autosomal dominant (AD) polycystic kidney disease +EDTA2,2725,Autosomal dominant (AD) polycystic kidney disease type I +EDTA2,2739,Autosomal dominant (AD) polycystic kidney disease type II +EDTA2,2741,Autosomal recessive (AR) polycystic kidney disease +EDTA2,2756,Alport syndrome - no histology +EDTA2,2760,Alport syndrome - histologically proven +EDTA2,2773,Benign familial haematuria +EDTA2,2787,Thin basement membrane disease +EDTA2,2794,Cystic kidney disease +EDTA2,2804,Medullary cystic kidney disease type I +EDTA2,2815,Medullary cystic kidney disease type II +EDTA2,2827,Uromodulin-associated nephropathy (familial juvenile hyperuricaemic nephropathy) EDTA2,2836,Nephronophthisis EDTA2,2843,Nephronophthisis - type 1 (juvenile type) EDTA2,2858,Nephronophthisis - type 2 (infantile type) @@ -190,98 +188,97 @@ EDTA2,2862,Nephronophthisis - type 3 (adolescent type) EDTA2,2870,Nephronophthisis - type 4 (juvenile type) EDTA2,2889,Nephronophthisis - type 5 EDTA2,2891,Nephronophthisis - type 6 -EDTA2,2098,Nephropathy due to aminoglycosides - histologically proven -EDTA2,2080,Nephropathy due to aminoglycosides - no histology -EDTA2,2112,Nephropathy due to amphotericin - histologically proven -EDTA2,2108,Nephropathy due to amphotericin - no histology -EDTA2,2033,Nephropathy due to analgesic drugs - histologically proven -EDTA2,2022,Nephropathy due to analgesic drugs - no histology -EDTA2,2051,Nephropathy due to ciclosporin - histologically proven -EDTA2,2046,Nephropathy due to ciclosporin - no histology -EDTA2,2131,Nephropathy due to cisplatin - histologically proven -EDTA2,2120,Nephropathy due to cisplatin - no histology -EDTA2,2154,Nephropathy due to lithium - histologically proven -EDTA2,2149,Nephropathy due to lithium - no histology -EDTA2,2681,Nephropathy due to eclampsia -EDTA2,3834,Nephropathy due to pre- eclampsia -EDTA2,2079,Nephropathy due to tacrolimus - histologically proven -EDTA2,2067,Nephropathy due to tacrolimus - no histology -EDTA2,2288,Nephropathy related to HIV - histologically proven -EDTA2,2274,Nephropathy related to HIV - no histology -EDTA2,3615,Nephrotic syndrome of childhood - no trial of steroids - no histology -EDTA2,3604,Nephrotic syndrome of childhood - steroid resistant - no histology -EDTA2,1019,Nephrotic syndrome of childhood - steroid sensitive - no histology -EDTA2,1799,Obstructive nephropathy due to bladder cancer -EDTA2,1809,Obstructive nephropathy due to other malignancies -EDTA2,1781,Obstructive nephropathy due to prostate cancer -EDTA2,1775,Obstructive nephropathy due to prostatic hypertrophy -EDTA2,1734,Oligomeganephronia -EDTA2,2300,Other specific infection -EDTA2,3063,Phosphoribosyl pyrophosphate synthetase (PRPPS) superactivity -EDTA2,1455,Polyarteritis nodosa -EDTA2,1687,Posterior urethral valves EDTA2,2901,Primary Fanconi syndrome -EDTA2,1267,Primary focal segmental glomerulosclerosis (FSGS) -EDTA2,3194,Primary hyperoxaluria -EDTA2,3207,Primary hyperoxaluria type I -EDTA2,3211,Primary hyperoxaluria type II -EDTA2,3731,Primary hyperoxaluria type III -EDTA2,1602,Primary reflux nephropathy - sporadic +EDTA2,2917,Tubular disorder as part of inherited metabolic diseases +EDTA2,2929,Dent disease +EDTA2,2938,Lowe syndrome (oculocerebrorenal syndrome) +EDTA2,2940,Inherited aminoaciduria +EDTA2,2955,Cystinuria +EDTA2,2964,Cystinosis +EDTA2,2972,Inherited renal glycosuria +EDTA2,2986,Hypophosphataemic rickets X-linked (XL) +EDTA2,2993,Hypophosphataemic rickets autosomal recessive (AR) EDTA2,3000,Primary renal tubular acidosis (RTA) EDTA2,3016,Proximal renal tubular acidosis (RTA) - type II +EDTA2,3028,Distal renal tubular acidosis (RTA) - type I +EDTA2,3037,Distal renal tubular acidosis with sensorineural deafness - gene mutations +EDTA2,3044,Nephrogenic diabetes insipidus +EDTA2,3059,Lesch Nyhan syndrome - hypoxanthine guanine phosphoribosyl transferase deficiency +EDTA2,3063,Phosphoribosyl pyrophosphate synthetase (PRPPS) superactivity +EDTA2,3071,Alagille syndrome +EDTA2,3085,Bartter syndrome +EDTA2,3092,Gitelman syndrome +EDTA2,3102,Liddle syndrome +EDTA2,3118,Apparent mineralocorticoid excess +EDTA2,3125,Glucocorticoid suppressible hyperaldosteronism +EDTA2,3139,Inherited / genetic diabetes mellitus type II EDTA2,3141,Pseudohypoaldosteronism type 1 EDTA2,3156,Pseudohypoaldosteronism type 2 (Gordon syndrome) -EDTA2,2219,Radiation nephritis -EDTA2,2226,Renal / perinephric abscess -EDTA2,2509,Renal amyloidosis -EDTA2,2469,Renal arterial thrombosis / occlusion -EDTA2,2424,Renal artery stenosis +EDTA2,3160,Familial hypocalciuric hypercalcaemia +EDTA2,3173,Familial hypercalciuric hypocalcaemia +EDTA2,3187,Familial hypomagnesaemia +EDTA2,3194,Primary hyperoxaluria +EDTA2,3207,Primary hyperoxaluria type I +EDTA2,3211,Primary hyperoxaluria type II +EDTA2,3224,Fabry disease - no histology +EDTA2,3230,Fabry disease - histologically proven +EDTA2,3248,Xanthinuria +EDTA2,3253,Nail-patella syndrome +EDTA2,3269,Rubinstein-Taybi syndrome +EDTA2,3276,Tuberous sclerosis +EDTA2,3282,Von Hippel-Lindau disease +EDTA2,3295,Medullary sponge kidneys +EDTA2,3305,Horse-shoe kidney +EDTA2,3314,Frasier syndrome +EDTA2,3322,Branchio-oto-renal syndrome +EDTA2,3333,Williams syndrome +EDTA2,3346,Townes-Brocks syndrome +EDTA2,3351,Lawrence-Moon-Biedl / Bardet-Biedl syndrome +EDTA2,3367,Mitochondrial cytopathy +EDTA2,3379,Familial nephropathy +EDTA2,3380,Acute kidney injury +EDTA2,3398,Acute kidney injury due to hypovolaemia +EDTA2,3403,Acute kidney injury due to circulatory failure +EDTA2,3419,Acute kidney injury due to sepsis +EDTA2,3426,Acute kidney injury due to rhabdomyolysis +EDTA2,3435,Acute kidney injury due to nephrotoxicity +EDTA2,3442,Acute cortical necrosis +EDTA2,3457,Acute pyelonephritis +EDTA2,3461,Kidney tumour EDTA2,3474,Renal cell carcinoma - histologically proven -EDTA2,3658,Renal coloboma syndrome +EDTA2,3488,Transitional cell carcinoma - histologically proven +EDTA2,3490,Wilms tumour - histologically proven +EDTA2,3501,Mesoblastic nephroma - histologically proven +EDTA2,3517,Single kidney identified in adulthood +EDTA2,3529,Chronic kidney disease (CKD) / chronic renal failure (CRF) caused by tumour nephrectomy +EDTA2,3538,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to traumatic loss of kidney +EDTA2,3540,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to donor nephrectomy +EDTA2,3555,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - no histology +EDTA2,3564,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - histologically proven +EDTA2,3572,Haematuria and proteinuria - no histology +EDTA2,3604,Nephrotic syndrome of childhood - steroid resistant - no histology +EDTA2,3615,Nephrotic syndrome of childhood - no trial of steroids - no histology EDTA2,3627,Renal cysts and diabetes syndrome -EDTA2,1641,Renal dysplasia due to fetal ACE-inhibitor exposure +EDTA2,3636,Chronic urate nephropathy - no histology +EDTA2,3643,Chronic renal failure due to systemic infection +EDTA2,3658,Renal coloboma syndrome +EDTA2,3662,Hypercalcaemic nephropathy +EDTA2,3670,Retroperitoneal fibrosis secondary to peri-aortitis +EDTA2,3689,Retroperitoneal fibrosis secondary to drugs EDTA2,3691,Renal failure -EDTA2,1747,Renal papillary necrosis -EDTA2,3796,Renal papillary necrosis caused by analgesics +EDTA2,3708,Chronic renal failure +EDTA2,3712,Isolated haematuria - no histology +EDTA2,3720,Isolated proteinuria - no histology +EDTA2,3731,Primary hyperoxaluria type III +EDTA2,3749,Glomerulonephritis - no histology +EDTA2,3754,Focal segmental glomerulosclerosis (FSGS) secondary to HIV +EDTA2,3765,Focal segmental glomerulosclerosis (FSGS) secondary to lithium +EDTA2,3777,Focal segmental glomerulosclerosis (FSGS) secondary to sickle cell EDTA2,3783,Renal papillary necrosis caused by diabetes +EDTA2,3796,Renal papillary necrosis caused by analgesics EDTA2,3806,Renal papillary necrosis caused by sickle cell -EDTA2,1976,Renal sarcoidosis - histologically proven -EDTA2,1969,Renal sarcoidosis - no histology -EDTA2,1536,Renal scleroderma / systemic sclerosis - histologically proven -EDTA2,1527,Renal scleroderma / systemic sclerosis - no histology -EDTA2,2235,Renal tuberculosis -EDTA2,2476,Renal vein thrombosis -EDTA2,3689,Retroperitoneal fibrosis secondary to drugs -EDTA2,1821,Retroperitoneal fibrosis secondary to malignancies -EDTA2,3670,Retroperitoneal fibrosis secondary to peri-aortitis -EDTA2,3269,Rubinstein-Taybi syndrome -EDTA2,2290,Schistosomiasis -EDTA2,2702,Sickle cell nephropathy - histologically proven -EDTA2,2699,Sickle cell nephropathy - no histology -EDTA2,3517,Single kidney identified in adulthood -EDTA2,1694,Syndrome of agenesis of abdominal muscles - prune belly syndrome -EDTA2,1493,Systemic lupus erythematosus / nephritis - histologically proven -EDTA2,1486,Systemic lupus erythematosus / nephritis - no histology -EDTA2,1383,Systemic vasculitis - ANCA negative - histologically proven +EDTA2,3810,Kidney stones due to ARPT deficiency +EDTA2,3823,Infiltration by lymphoma - histologically proven +EDTA2,3834,Nephropathy due to pre- eclampsia EDTA2,3847,Systemic vasculitis - ANCA negative - no histology EDTA2,3852,Systemic vasculitis - ANCA positive - histologically proven -EDTA2,1396,Systemic vasculitis - ANCA positive - no histology -EDTA2,2787,Thin basement membrane disease -EDTA2,2634,Thrombotic thrombocytopenic purpura (TTP) -EDTA2,3346,Townes-Brocks syndrome -EDTA2,3488,Transitional cell carcinoma - histologically proven -EDTA2,3276,Tuberous sclerosis -EDTA2,2917,Tubular disorder as part of inherited metabolic diseases -EDTA2,1897,Tubulointerstitial nephritis - histologically proven -EDTA2,1884,Tubulointerstitial nephritis - no histology -EDTA2,1930,Tubulointerstitial nephritis associated with autoimmune disease - histologically proven -EDTA2,1924,Tubulointerstitial nephritis associated with autoimmune disease - no histology -EDTA2,1953,Tubulointerstitial nephritis with uveitis (TINU) - histologically proven -EDTA2,1948,Tubulointerstitial nephritis with uveitis (TINU) - no histology -EDTA2,1878,Uric acid urolithiasis -EDTA2,2827,Uromodulin-associated nephropathy (familial juvenile hyperuricaemic nephropathy) -EDTA2,3282,Von Hippel-Lindau disease -EDTA2,3333,Williams syndrome -EDTA2,3490,Wilms tumour - histologically proven -EDTA2,3248,Xanthinuria -EDTA2,2261,Xanthogranulomatous pyelonephritis diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index c552a14..d96f7b5 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## 4.1.0 - 2023-08-13 +### Changed +- Added Missing EDTA2 PRD Codes +- Added Missing Admisssion Reason Codes +- Reduced Admission Reason Description to 100 characters to match database. + ## 4.0.0 - 2023-06-13 ### Added - Assessment Element Type diff --git a/schema/ukrdc/Types/CF_EDTA_PRD.xsd b/schema/ukrdc/Types/CF_EDTA_PRD.xsd index 3132814..5e504d6 100644 --- a/schema/ukrdc/Types/CF_EDTA_PRD.xsd +++ b/schema/ukrdc/Types/CF_EDTA_PRD.xsd @@ -1705,6 +1705,51 @@ Glomerulonephritis - No Histology + + + Focal segmental glomerulosclerosis (FSGS) secondary to HIV + + + + + Focal segmental glomerulosclerosis (FSGS) secondary to lithium + + + + + Focal segmental glomerulosclerosis (FSGS) secondary to sickle cell + + + + + Renal papillary necrosis caused by diabetes + + + + + Renal papillary necrosis caused by analgesics + + + + + Renal papillary necrosis caused by sickle cell + + + + + Kidney stones due to ARPT deficiency + + + + + Infiltration by lymphoma - histologically proven + + + + + Nephropathy due to pre-eclampsia + + Systemic vasculitis - ANCA negative - no histology @@ -2857,7 +2902,7 @@ -  Chronic kidney disease following excision of renal neoplasm (disorder) + Chronic kidney disease following excision of renal neoplasm (disorder) diff --git a/schema/ukrdc/Types/CF_RR7_Treatment.xsd b/schema/ukrdc/Types/CF_RR7_Treatment.xsd index bdc3980..5969154 100644 --- a/schema/ukrdc/Types/CF_RR7_Treatment.xsd +++ b/schema/ukrdc/Types/CF_RR7_Treatment.xsd @@ -111,13 +111,16 @@ Acute Kidney Injury - RRT not provided by renal service - + + + Acute Kidney Injury receiving RRT not by renal service + + First Assessment by Renal Service - Conservative Management - Mutual decision not to offer RRT @@ -163,6 +166,26 @@ CKD (Not on RRT) + + + Patient - ESKD with no RRT + + + + + Patient - CKD-advanced MDT clinic + + + + + Patient - CKD-clinic follow-up + + + + + Patient - CKD-remote monitoring + + @@ -255,7 +278,7 @@ - + From 92899a82fa09e5e736f1218449cc6b060fd46051 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 22 Aug 2023 11:07:47 +0100 Subject: [PATCH 059/166] Add batchNo, Change mandatory DialysisPrescription fields --- .../DialysisPrescription.xsd | 10 +-- schema/ukrdc/Types/SendingFacility.xsd | 65 ++++++++++--------- 2 files changed, 38 insertions(+), 37 deletions(-) diff --git a/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd b/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd index 687d662..eefda60 100644 --- a/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd +++ b/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd @@ -13,7 +13,7 @@ The date the Dialysis Prescription was created. - + Time the Period the Dialysis Prescription Applies To Starts @@ -25,25 +25,25 @@ Time the Period the Dialysis Prescription Applies To Ends - + Session Type (Same as QHD41) - + Number of Dialysis Sessions per Week - + Time Dialysed (Minutes) - + Vascular Access to Use (QHD20) diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd index 6fbd1b5..c04bb1c 100644 --- a/schema/ukrdc/Types/SendingFacility.xsd +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -1,36 +1,37 @@ + - - - - - - - - - - - - - - - - - This should be a reference for the System / Version which generated the file. The intended purpose is to allow us to identify, or temporarily rectify, issues with what a particular extract is generating. - - - - - This should be the time that the extract was generated. - - - - - This should be the version (from the XSD Schema) that the extract has been written against. This is to allow us to process incoming files accordingly as well as track which Units are submitting which version. Note that the RDA Schema version is unrelated to the UKRR Dataset version. - - - - - + + + + + + + + + + + + This should be a reference for the System / Version which generated the file. The intended purpose is to allow us to identify, or temporarily rectify, issues with what a particular extract is generating. + + + + + This should be the time that the extract was generated. + + + + + This should be the version (from the XSD Schema) that the extract has been written against. This is to allow us to process incoming files accordingly as well as track which Units are submitting which version. Note that the RDA Schema version is unrelated to the UKRR Dataset version. + + + + + The batch number as used in the filenames. This should be incremented each time the extract is run, not per-patient + + + + + \ No newline at end of file From 7e0d09fe70e2e5fa26489ac2929064f617bb3569 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 23 Aug 2023 13:23:45 +0100 Subject: [PATCH 060/166] Update Changelog --- schema/ukrdc/CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index d96f7b5..de0f69e 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -5,6 +5,8 @@ - Added Missing EDTA2 PRD Codes - Added Missing Admisssion Reason Codes - Reduced Admission Reason Description to 100 characters to match database. +- Changed Mandatory fields in DialysisPrescription + ## 4.0.0 - 2023-06-13 ### Added From 132a6da02e9e4b83b4b6e335f1be4f3af35b3b13 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Fri, 15 Sep 2023 11:23:03 +0100 Subject: [PATCH 061/166] . --- dataset/UKRR/v4/RR-Dataset-v4.2.xls | Bin 729088 -> 729088 bytes .../v5/~$DataSet_v5_0_For Renal units.xlsx | Bin 0 -> 165 bytes 2 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 dataset/UKRR/v5/~$DataSet_v5_0_For Renal units.xlsx diff --git a/dataset/UKRR/v4/RR-Dataset-v4.2.xls b/dataset/UKRR/v4/RR-Dataset-v4.2.xls index 04074aeb57d4fb2e9e784e46d8644485500f5776..3cc6daed793d2b231404eb32c91bc3f910a11bfd 100644 GIT binary patch delta 65 zcmZoTpwn8ftUk`If0mKdl3tF GpELlwrV~s6 delta 65 zcmZoTpwn+Qy>NiGPpCOGUPK9F{A@&1%_aTa)wNXJRnR3ij@Fm J@_?e$f&hyw7Q+Al literal 0 HcmV?d00001 From 30bcfb9f64dbac7107106626323018ff19f8f0a3 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 20 Sep 2023 14:16:07 +0100 Subject: [PATCH 062/166] Modify Diagnosis Types --- schema/ukrdc/CHANGELOG.md | 1 + schema/ukrdc/Diagnoses/Diagnosis.xsd | 2 +- schema/ukrdc/Types/Diagnosis.xsd | 29 ++++++++++++++++++++++++++++ 3 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 schema/ukrdc/Types/Diagnosis.xsd diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index de0f69e..f2214a5 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -6,6 +6,7 @@ - Added Missing Admisssion Reason Codes - Reduced Admission Reason Description to 100 characters to match database. - Changed Mandatory fields in DialysisPrescription +- Modified Diagnosis to allow LOCAL/ICD-10 CodingStandards ## 4.0.0 - 2023-06-13 diff --git a/schema/ukrdc/Diagnoses/Diagnosis.xsd b/schema/ukrdc/Diagnoses/Diagnosis.xsd index e2f5da1..bcfb95a 100644 --- a/schema/ukrdc/Diagnoses/Diagnosis.xsd +++ b/schema/ukrdc/Diagnoses/Diagnosis.xsd @@ -1,7 +1,7 @@ - + diff --git a/schema/ukrdc/Types/Diagnosis.xsd b/schema/ukrdc/Types/Diagnosis.xsd new file mode 100644 index 0000000..56d0074 --- /dev/null +++ b/schema/ukrdc/Types/Diagnosis.xsd @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ce0f8618a0712c86e895f302d99bfda94a2787c4 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 20 Sep 2023 14:21:36 +0100 Subject: [PATCH 063/166] Fix names --- schema/ukrdc/Diagnoses/Diagnosis.xsd | 4 ++-- schema/ukrdc/Types/{Diagnosis.xsd => DiagnosisCodeType.xsd} | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename schema/ukrdc/Types/{Diagnosis.xsd => DiagnosisCodeType.xsd} (95%) diff --git a/schema/ukrdc/Diagnoses/Diagnosis.xsd b/schema/ukrdc/Diagnoses/Diagnosis.xsd index bcfb95a..9d4b055 100644 --- a/schema/ukrdc/Diagnoses/Diagnosis.xsd +++ b/schema/ukrdc/Diagnoses/Diagnosis.xsd @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ National Clinicial code where possible or other local code if not. - + SNOMED CT coded diagnoses. This should also include any diagnosis that has been submitted elsewhere as a Primary Renal Diagnosis. diff --git a/schema/ukrdc/Types/Diagnosis.xsd b/schema/ukrdc/Types/DiagnosisCodeType.xsd similarity index 95% rename from schema/ukrdc/Types/Diagnosis.xsd rename to schema/ukrdc/Types/DiagnosisCodeType.xsd index 56d0074..41496d4 100644 --- a/schema/ukrdc/Types/Diagnosis.xsd +++ b/schema/ukrdc/Types/DiagnosisCodeType.xsd @@ -1,5 +1,5 @@ - + From 29a0740b81ceea6b59b5bbbf71cad4359db5d598 Mon Sep 17 00:00:00 2001 From: andreoap Date: Tue, 24 Oct 2023 11:33:15 +0100 Subject: [PATCH 064/166] Remove the duplicate entry for code 83 in CF_RR7_Treatment --- schema/ukrdc/Types/CF_RR7_Treatment.xsd | 5 ----- 1 file changed, 5 deletions(-) diff --git a/schema/ukrdc/Types/CF_RR7_Treatment.xsd b/schema/ukrdc/Types/CF_RR7_Treatment.xsd index 5969154..eca1478 100644 --- a/schema/ukrdc/Types/CF_RR7_Treatment.xsd +++ b/schema/ukrdc/Types/CF_RR7_Treatment.xsd @@ -106,11 +106,6 @@ Acute Kidney Injury - Peritoneal Dialysis - - - Acute Kidney Injury - RRT not provided by renal service - - Acute Kidney Injury receiving RRT not by renal service From 612e6aa627363477a80ff5da7ec14c28c69a64f2 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 5 Dec 2023 09:52:11 +0000 Subject: [PATCH 065/166] Initial 4.2.0 Changes --- schema/ukrdc/CHANGELOG.md | 6 ++++++ schema/ukrdc/Encounters/Treatment.xsd | 7 ++++++- schema/ukrdc/LabOrders/LabOrder.xsd | 2 +- schema/ukrdc/Observations/Observation.xsd | 2 +- schema/ukrdc/UKRDC.xsd | 2 +- 5 files changed, 15 insertions(+), 4 deletions(-) diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index f2214a5..6a31d53 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## 4.2.0 - 2023-12-05 +### Changed +- Restricted Treatment/VisitDescription to 255 characters +- Increased ResultItem/ResultValue to 30 characters +- Increased Observation/ObservationValue to 30 characters + ## 4.1.0 - 2023-08-13 ### Changed - Added Missing EDTA2 PRD Codes diff --git a/schema/ukrdc/Encounters/Treatment.xsd b/schema/ukrdc/Encounters/Treatment.xsd index 482ed03..19a5c07 100644 --- a/schema/ukrdc/Encounters/Treatment.xsd +++ b/schema/ukrdc/Encounters/Treatment.xsd @@ -75,12 +75,17 @@ National code for the hospital providing care - e.g. RXF01 - + Free text about the Treatment record. + + + + + diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index c6d6ce3..365fa9d 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -250,7 +250,7 @@ - + diff --git a/schema/ukrdc/Observations/Observation.xsd b/schema/ukrdc/Observations/Observation.xsd index bc44a25..5745660 100644 --- a/schema/ukrdc/Observations/Observation.xsd +++ b/schema/ukrdc/Observations/Observation.xsd @@ -77,7 +77,7 @@ - + diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 1bc1b7e..2aef1e5 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -1,4 +1,4 @@ - + From 227abb9f2aa032944d67de027c444f24a431e9ce Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 6 Dec 2023 08:02:59 +0000 Subject: [PATCH 066/166] Restrict UoM to CF_RR23.xsd type --- schema/ukrdc/Medications/Medication.xsd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/schema/ukrdc/Medications/Medication.xsd b/schema/ukrdc/Medications/Medication.xsd index 135da58..4ace4a8 100644 --- a/schema/ukrdc/Medications/Medication.xsd +++ b/schema/ukrdc/Medications/Medication.xsd @@ -1,4 +1,5 @@ + @@ -107,7 +108,7 @@ Dose - + From a80e0c5ecf6021fd8c71e6220a05e6c4599e520d Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 6 Dec 2023 08:03:23 +0000 Subject: [PATCH 067/166] Update Changelog --- schema/ukrdc/CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index 6a31d53..6a72a7a 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -5,6 +5,7 @@ - Restricted Treatment/VisitDescription to 255 characters - Increased ResultItem/ResultValue to 30 characters - Increased Observation/ObservationValue to 30 characters +- Amended Medication UoM to use CF_RR23 type. ## 4.1.0 - 2023-08-13 ### Changed From 9453427cebbf4b9f072f2f1254380bd5b7c409d2 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Wed, 6 Dec 2023 08:06:02 +0000 Subject: [PATCH 068/166] Update Sample File --- sample_files/ukrdc/fullFile.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/sample_files/ukrdc/fullFile.xml b/sample_files/ukrdc/fullFile.xml index 152a856..37adbea 100644 --- a/sample_files/ukrdc/fullFile.xml +++ b/sample_files/ukrdc/fullFile.xml @@ -251,16 +251,16 @@ CF_RR23 l - Description61 + Litre Frequency0 Comments17 0 - CodingStandard62 - Code62 - Description62 + CF_RR23 + other + Other Indication0 EncounterNumber2 From 16e2c55568428b6648c2b84ada9bd0d48392d598 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Fri, 8 Dec 2023 13:39:01 +0000 Subject: [PATCH 069/166] Update schema version in UKRDC.xsd --- schema/ukrdc/UKRDC.xsd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 1bc1b7e..44613da 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -1,4 +1,4 @@ - + From 68a6193ecca61020165209f5bbbd8f52dd3a5511 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 10 Dec 2023 19:48:21 +0000 Subject: [PATCH 070/166] Move codes from services to resources --- .../dose_units_snomed_to_radar.csv | 17 + .../pv_facilities_to_rr1plus.csv | 9 + .../code_conv_lists/pv_testcodes_to_loinc.csv | 82 ++++ .../pv_testcodes_to_snomed.csv | 7 + .../code_conv_lists/pvmig_testcodes_to_pv.csv | 83 ++++ .../code_conv_lists/pvmig_testunits_to_pv.csv | 53 +++ .../code_conv_lists/pvraw_testcodes_to_pv.csv | 3 + .../radar_facilities_to_rr1plus.csv | 26 ++ .../rawpvrrtstatus_to_pvrrtstatus.csv | 101 +++++ .../rr1plus_facilities_to_pv.csv | 7 + .../rr1plus_facilities_to_radar.csv | 3 + .../snomed_testcodes_to_pv.csv | 1 + .../snomed_to_survey_types.csv | 5 + .../survey_types_to_snomed.csv | 5 + .../survey_units_to_rr1plus.csv | 72 ++++ .../ukrr_testcodes_to_loinc.csv | 50 +++ .../code_conv_lists/ukrr_testcodes_to_pv.csv | 46 ++ codes/code_exclusions/pv_observations.csv | 3 + codes/code_importer.py | 236 +++++++++++ codes/code_lists/RR22.csv | 7 + codes/code_lists/RR23.csv | 11 + codes/code_lists/cf_rr7_discharge.csv | 9 + codes/code_lists/cf_rr7_treatment.csv | 51 +++ codes/code_lists/dose_units.csv | 18 + codes/code_lists/edta_cod.csv | 65 +++ codes/code_lists/edta_prd.csv | 339 +++++++++++++++ codes/code_lists/loinc_observations.csv | 86 ++++ .../nhs_data_dictionary_employment_status.csv | 9 + .../nhs_data_dictionary_ethnicity.csv | 17 + .../nhs_data_dictionary_language_code.csv | 184 ++++++++ codes/code_lists/pv_admit_reason.csv | 2 + codes/code_lists/pv_groups.csv | 175 ++++++++ codes/code_lists/pv_observations.csv | 92 ++++ codes/code_lists/pv_rrtstatus.csv | 5 + codes/code_lists/pv_tpstatus.csv | 7 + codes/code_lists/radar_facilities.csv | 1 + codes/code_lists/rawpvrrtstatus.csv | 101 +++++ codes/code_lists/rr1plus_facilities.csv | 400 ++++++++++++++++++ codes/code_lists/snomed_codes.csv | 7 + codes/code_lists/survey_questions.csv | 28 ++ codes/code_lists/survey_types.csv | 4 + codes/code_lists/ukrr_observations.csv | 61 +++ codes/code_writer.py | 67 +++ codes/redis_code_importer.py | 148 +++++++ codes/satellite_map/satellite_map.csv | 221 ++++++++++ 45 files changed, 2924 insertions(+) create mode 100644 codes/code_conv_lists/dose_units_snomed_to_radar.csv create mode 100644 codes/code_conv_lists/pv_facilities_to_rr1plus.csv create mode 100644 codes/code_conv_lists/pv_testcodes_to_loinc.csv create mode 100644 codes/code_conv_lists/pv_testcodes_to_snomed.csv create mode 100644 codes/code_conv_lists/pvmig_testcodes_to_pv.csv create mode 100644 codes/code_conv_lists/pvmig_testunits_to_pv.csv create mode 100644 codes/code_conv_lists/pvraw_testcodes_to_pv.csv create mode 100644 codes/code_conv_lists/radar_facilities_to_rr1plus.csv create mode 100644 codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv create mode 100644 codes/code_conv_lists/rr1plus_facilities_to_pv.csv create mode 100644 codes/code_conv_lists/rr1plus_facilities_to_radar.csv create mode 100644 codes/code_conv_lists/snomed_testcodes_to_pv.csv create mode 100644 codes/code_conv_lists/snomed_to_survey_types.csv create mode 100644 codes/code_conv_lists/survey_types_to_snomed.csv create mode 100644 codes/code_conv_lists/survey_units_to_rr1plus.csv create mode 100644 codes/code_conv_lists/ukrr_testcodes_to_loinc.csv create mode 100644 codes/code_conv_lists/ukrr_testcodes_to_pv.csv create mode 100644 codes/code_exclusions/pv_observations.csv create mode 100644 codes/code_importer.py create mode 100644 codes/code_lists/RR22.csv create mode 100644 codes/code_lists/RR23.csv create mode 100644 codes/code_lists/cf_rr7_discharge.csv create mode 100644 codes/code_lists/cf_rr7_treatment.csv create mode 100644 codes/code_lists/dose_units.csv create mode 100644 codes/code_lists/edta_cod.csv create mode 100644 codes/code_lists/edta_prd.csv create mode 100644 codes/code_lists/loinc_observations.csv create mode 100644 codes/code_lists/nhs_data_dictionary_employment_status.csv create mode 100644 codes/code_lists/nhs_data_dictionary_ethnicity.csv create mode 100644 codes/code_lists/nhs_data_dictionary_language_code.csv create mode 100644 codes/code_lists/pv_admit_reason.csv create mode 100644 codes/code_lists/pv_groups.csv create mode 100644 codes/code_lists/pv_observations.csv create mode 100644 codes/code_lists/pv_rrtstatus.csv create mode 100644 codes/code_lists/pv_tpstatus.csv create mode 100644 codes/code_lists/radar_facilities.csv create mode 100644 codes/code_lists/rawpvrrtstatus.csv create mode 100644 codes/code_lists/rr1plus_facilities.csv create mode 100644 codes/code_lists/snomed_codes.csv create mode 100644 codes/code_lists/survey_questions.csv create mode 100644 codes/code_lists/survey_types.csv create mode 100644 codes/code_lists/ukrr_observations.csv create mode 100644 codes/code_writer.py create mode 100644 codes/redis_code_importer.py create mode 100644 codes/satellite_map/satellite_map.csv diff --git a/codes/code_conv_lists/dose_units_snomed_to_radar.csv b/codes/code_conv_lists/dose_units_snomed_to_radar.csv new file mode 100644 index 0000000..a88d2c6 --- /dev/null +++ b/codes/code_conv_lists/dose_units_snomed_to_radar.csv @@ -0,0 +1,17 @@ +SNOMED,258770004,RADAR,l +SNOMED,258771000,RADAR,dl +SNOMED,258773002,RADAR,ml +SNOMED,258682000,RADAR,g +SNOMED,258684004,RADAR,mg +SNOMED,258685003,RADAR,µg +SNOMED,258686002,RADAR,ng +SNOMED,428673006,RADAR,tab +SNOMED,258997004,RADAR,iu +SNOMED,258718000,RADAR,mmol +SNOMED,415215001,RADAR,puff +SNOMED,767525000,RADAR,unit +SNOMED,413516001,RADAR,ampoule +SNOMED,404218003,RADAR,drop +SNOMED,428641000,RADAR,capsule +SNOMED,419702001,RADAR,patch +SNOMED,733013000,RADAR,sachet diff --git a/codes/code_conv_lists/pv_facilities_to_rr1plus.csv b/codes/code_conv_lists/pv_facilities_to_rr1plus.csv new file mode 100644 index 0000000..bc1623b --- /dev/null +++ b/codes/code_conv_lists/pv_facilities_to_rr1plus.csv @@ -0,0 +1,9 @@ +PV,RSC02,RR1+,SSC02 +PV,RX1CC,RR1+,RCSLB +PV,R1H00,RR1+,RNJ00 +PV,RJ100,RR1+,RJ121 +PV,RQR00,RR1+,RQR13 +PV,SYC01,RR1+,SYC02 +PV,SGC05,RR1+,SGC04 +PV,RCD37,RR1+,RD1 +PV,99RHM01,RR1+,RHM02 \ No newline at end of file diff --git a/codes/code_conv_lists/pv_testcodes_to_loinc.csv b/codes/code_conv_lists/pv_testcodes_to_loinc.csv new file mode 100644 index 0000000..f4b272c --- /dev/null +++ b/codes/code_conv_lists/pv_testcodes_to_loinc.csv @@ -0,0 +1,82 @@ +PV,acr,LOINC,32294-1 +PV,adjustedcalcium,LOINC,19072-8 +PV,albumin,LOINC,1751-7 +PV,albumin_post,LOINC,1751-7 +PV,alp,LOINC,6768-6 +PV,alt,LOINC,1742-6 +PV,amy,LOINC,1798-8 +PV,ast,LOINC,1920-8 +PV,bili,LOINC,14631-6 +PV,calcium,LOINC,1996-8 +PV,calcium_post,LOINC,59148-7 +PV,cholesterol,LOINC,14647-2 +PV,covid19antibody,LOINC,95542-7 +PV,covid19lflow,LOINC,95209-3 +PV,covid19pcr,LOINC,94500-6 +PV,creatinine,LOINC,14682-9 +PV,creatinine_post,LOINC,51620-3 +PV,crp,LOINC,1988-5 +PV,egfr,LOINC,69405-9 +PV,FaecalCalprotectin,LOINC,38445-3 +PV,ferritin,LOINC,2276-4 +PV,folate,LOINC,2284-8 +PV,ft3,LOINC,14928-6 +PV,ft4,LOINC,14920-3 +PV,ggt,LOINC,2324-2 +PV,glucose,LOINC,14749-6 +PV,hb,LOINC,718-7 +PV,hba1c,LOINC,59261-8 +PV,hbv,LOINC,13952-7 +PV,hco3,LOINC,1959-6 +PV,hco3_post,LOINC,48631-6 +PV,hct,LOINC,4544-3 +PV,hcv,LOINC,16128-1 +PV,hdl,LOINC,14646-4 +PV,inr,LOINC,6301-6 +PV,iron,LOINC,14798-3 +PV,ironsat,LOINC,2502-3 +PV,ktv,LOINC,70961-8 +PV,ktv_post,LOINC,70961-8 +PV,ldh,LOINC,2532-0 +PV,ldl,LOINC,39469-2 +PV,lhratio,LOINC,44915-7 +PV,lipase,LOINC,3040-3 +PV,lithium,LOINC,14334-7 +PV,magnesium,LOINC,2601-3 +PV,mmp,LOINC,90294-0 +PV,neutrophils,LOINC,751-8 +PV,pcr,LOINC,34366-5 +PV,phepku,LOINC, +PV,phosphate,LOINC,14879-1 +PV,phosphate_post,LOINC,55972-4 +PV,platelets,LOINC,777-3 +PV,potassium,LOINC,2823-3 +PV,potassium_post,LOINC,29349-8 +PV,psa,LOINC,2857-1 +PV,pth,LOINC,14866-8 +PV,ret-he,LOINC,42810-2 +PV,sirolimus,LOINC,29247-4 +PV,sodium,LOINC,2951-2 +PV,sodium_post,LOINC,74688-3 +PV,t4,LOINC,3024-7 +PV,tacrolimus,LOINC,11253-2 +PV,testosterone,LOINC,2986-8 +PV,tg,LOINC,2571-8 +PV,tgn,LOINC,34381-4 +PV,tpmt,LOINC,91141-2 +PV,transferrin,LOINC,3034-6 +PV,trop,LOINC,6598-7 +PV,tsh,LOINC,3016-3 +PV,ualbumin,LOINC,6942-7 +PV,ucreatinine,LOINC,14683-7 +PV,updipstick,LOINC,20454-5 +PV,uprotein,LOINC,2888-6 +PV,urate,LOINC,14933-6 +PV,urea,LOINC,14937-7 +PV,urea_post,LOINC,39776-0 +PV,urr,LOINC,54456-9 +PV,urr_post,LOINC,54456-9 +PV,vitb12,LOINC,2132-9 +PV,vitd,LOINC,46269-7 +PV,wbc,LOINC,6690-2 +PV,ciclosporin,LOINC,3520-4 diff --git a/codes/code_conv_lists/pv_testcodes_to_snomed.csv b/codes/code_conv_lists/pv_testcodes_to_snomed.csv new file mode 100644 index 0000000..ddcb161 --- /dev/null +++ b/codes/code_conv_lists/pv_testcodes_to_snomed.csv @@ -0,0 +1,7 @@ +PV,weight,SNOMED,27113001 +PV,height,SNOMED,162755006 +PV,bmi,SNOMED,301331008 +PV,pulse,SNOMED,162986007 +PV,bpsys,SNOMED,163030003 +PV,bpdia,SNOMED,163031004 +PV,bp_header,SNOMED,75367002 \ No newline at end of file diff --git a/codes/code_conv_lists/pvmig_testcodes_to_pv.csv b/codes/code_conv_lists/pvmig_testcodes_to_pv.csv new file mode 100644 index 0000000..ef902a0 --- /dev/null +++ b/codes/code_conv_lists/pvmig_testcodes_to_pv.csv @@ -0,0 +1,83 @@ +PVMIGRATE,acr,PV,acr +PVMIGRATE,Adjusted Calcium,PV,adjustedcalcium +PVMIGRATE,adjustedca,PV,adjustedcalcium +PVMIGRATE,adjustedcalcium,PV,adjustedcalcium +PVMIGRATE,albumin,PV,albumin +PVMIGRATE,Alkaline Phosphatase,PV,alp +PVMIGRATE,alp,PV,alp +PVMIGRATE,alt,PV,alt +PVMIGRATE,amy,PV,amy +PVMIGRATE,ast,PV,ast +PVMIGRATE,bili,PV,bili +PVMIGRATE,bmi,PV,bmi +PVMIGRATE,BodyTemperature,PV,BodyTemperature +PVMIGRATE,BP dia,PV,bpdia +PVMIGRATE,BP sys,PV,bpsys +PVMIGRATE,bpdia,PV,bpdia +PVMIGRATE,bpsys,PV,bpsys +PVMIGRATE,calcium,PV,calcium +PVMIGRATE,cholestero,PV,cholesterol +PVMIGRATE,cholesterol,PV,cholesterol +PVMIGRATE,ciclospori,PV,ciclosporin +PVMIGRATE,ciclosporin,PV,ciclosporin +PVMIGRATE,creatinine,PV,creatinine +PVMIGRATE,crp,PV,crp +PVMIGRATE,egfr,PV,egfr +PVMIGRATE,FaecalCalprotectin,PV,FaecalCalprotectin +PVMIGRATE,ferr,PV,ferritin +PVMIGRATE,ferritin,PV,ferritin +PVMIGRATE,folate,PV,folate +PVMIGRATE,ft3,PV,ft3 +PVMIGRATE,ft4,PV,ft4 +PVMIGRATE,ggt,PV,ggt +PVMIGRATE,glucose,PV,glucose +PVMIGRATE,hb,PV,hb +PVMIGRATE,hba1c,PV,hba1c +PVMIGRATE,HbA1c (IFCC),PV,hba1c +PVMIGRATE,hco3,PV,hco3 +PVMIGRATE,hct,PV,hct +PVMIGRATE,hdl,PV,hdl +PVMIGRATE,height,PV,height +PVMIGRATE,hypotension,PV,hypotension +PVMIGRATE,inr,PV,inr +PVMIGRATE,iron,PV,iron +PVMIGRATE,ironsat,PV,ironsat +PVMIGRATE,KT/V,PV,ktv +PVMIGRATE,ktv,PV,ktv +PVMIGRATE,ldh,PV,ldh +PVMIGRATE,ldl,PV,ldl +PVMIGRATE,lhratio,PV,lhratio +PVMIGRATE,lipase,PV,lipase +PVMIGRATE,lithium,PV,lithium +PVMIGRATE,magnesium,PV,magnesium +PVMIGRATE,neutrophils,PV,neutrophils +PVMIGRATE,pcr,PV,pcr +PVMIGRATE,phepku,PV,phepku +PVMIGRATE,phosphate,PV,phosphate +PVMIGRATE,platelets,PV,platelets +PVMIGRATE,potassium,PV,potassium +PVMIGRATE,psa,PV,psa +PVMIGRATE,pth,PV,pth +PVMIGRATE,pulse,PV,pulse +PVMIGRATE,Random plasma glucose:,PV,glucose +PVMIGRATE,Serum Creatinine,PV,creatinine +PVMIGRATE,Serum Urea,PV,urea +PVMIGRATE,sirolimus,PV,sirolimus +PVMIGRATE,sirolimus (rapamycin),PV,sirolimus +PVMIGRATE,sodium,PV,sodium +PVMIGRATE,t4,PV,t4 +PVMIGRATE,tacrolimus,PV,tacrolimus +PVMIGRATE,testosterone,PV,testosterone +PVMIGRATE,tg,PV,tg +PVMIGRATE,tpmt,PV,tpmt +PVMIGRATE,transferri,PV,transferrin +PVMIGRATE,transferrin,PV,transferrin +PVMIGRATE,tsh,PV,tsh +PVMIGRATE,ualbumin,PV,ualbumin +PVMIGRATE,urate,PV,urate +PVMIGRATE,urea,PV,urea +PVMIGRATE,urr,PV,urr +PVMIGRATE,vitb12,PV,vitb12 +PVMIGRATE,vitd,PV,vitd +PVMIGRATE,wbc,PV,wbc +PVMIGRATE,weight,PV,weight diff --git a/codes/code_conv_lists/pvmig_testunits_to_pv.csv b/codes/code_conv_lists/pvmig_testunits_to_pv.csv new file mode 100644 index 0000000..da3dcae --- /dev/null +++ b/codes/code_conv_lists/pvmig_testunits_to_pv.csv @@ -0,0 +1,53 @@ +PVMIGRATION,#G ( )/L,PV,ml/min/1.73m2 +PVMIGRATION,*10^9/cumm,PV,x10^9/L +PVMIGRATION,/mL,PV,ml/min/1.73m2 +PVMIGRATION,10**9/L,PV,x10^9/L +PVMIGRATION,10*9 cells/L,PV,x10^9/L +PVMIGRATION,10*9/L,PV,x10^9/L +PVMIGRATION,10^9/l,PV,x10^9/L +PVMIGRATION,IU/L,PV,IU/L +PVMIGRATION,IU/l,PV,IU/L +PVMIGRATION,Kg,PV,kg +PVMIGRATION,MCMOL/L,PV,micromol/L +PVMIGRATION,MMOL/L,PV,mmol/L +PVMIGRATION,None,PV,ml/min/1.73m2 +PVMIGRATION,U/L,PV,IU/L +PVMIGRATION,Ug/L,PV,microg/L +PVMIGRATION,Ug/L,PV,ng/mL +PVMIGRATION,bpm,PV,bpm +PVMIGRATION,cm,PV,cm +PVMIGRATION,g/L,PV,g/L +PVMIGRATION,g/l,PV,g/L +PVMIGRATION,g/mol,PV,mg/mmol +PVMIGRATION,gm/l,PV,g/L +PVMIGRATION,kg,PV,kg +PVMIGRATION,mL/24h/1.73m*2,PV,ml/min/1.73m2 +PVMIGRATION,mL/min,PV,ml/min/1.73m2 +PVMIGRATION,mL/min/1.73m*2,PV,ml/min/1.73m2 +PVMIGRATION,mL/min/1.73m2,PV,ml/min/1.73m2 +PVMIGRATION,mL/min/1.73m^2,PV,ml/min/1.73m2 +PVMIGRATION,mU/L,PV,mIU/L +PVMIGRATION,mg/L,PV,mg/L +PVMIGRATION,mg/mmol,PV,mg/mmol +PVMIGRATION,mg/mmol(creat),PV,mg/mmol +PVMIGRATION,micmol/l,PV,micromol/L +PVMIGRATION,micromol/l,PV,micromol/L +PVMIGRATION,ml/min/1.73m,PV,ml/min/1.73m2 +PVMIGRATION,ml/min/1.73m*2,PV,ml/min/1.73m2 +PVMIGRATION,ml/min/1.73m2,PV,ml/min/1.73m2 +PVMIGRATION,mm Hg,PV,mmHg +PVMIGRATION,mmHg,PV,mmHg +PVMIGRATION,mm[Hg],PV,mmHg +PVMIGRATION,mmo/L,PV,mmol/L +PVMIGRATION,mmol/L,PV,mmol/L +PVMIGRATION,mmol/l,PV,mmol/L +PVMIGRATION,mmol/mol,PV,mmol/mol +PVMIGRATION,mu/L,PV,mIU/L +PVMIGRATION,ng/L,PV,ng/L +PVMIGRATION,ng/mL,PV,ng/mL +PVMIGRATION,pmol/L,PV,pmol/L +PVMIGRATION,u/L,PV,IU/L +PVMIGRATION,ug/l,PV,microg/L +PVMIGRATION,umol/L,PV,micromol/L +PVMIGRATION,x10^9/L,PV,x10^9/L +PVMIGRATION,x10^9/l,PV,x10^9/L diff --git a/codes/code_conv_lists/pvraw_testcodes_to_pv.csv b/codes/code_conv_lists/pvraw_testcodes_to_pv.csv new file mode 100644 index 0000000..c16e23e --- /dev/null +++ b/codes/code_conv_lists/pvraw_testcodes_to_pv.csv @@ -0,0 +1,3 @@ +PV_RAW,mg,PV,magnesium +PV_RAW,faecalcalprotectin,PV,FaecalCalprotectin +PV_RAW,targetweight,PV,TargetWeight \ No newline at end of file diff --git a/codes/code_conv_lists/radar_facilities_to_rr1plus.csv b/codes/code_conv_lists/radar_facilities_to_rr1plus.csv new file mode 100644 index 0000000..e4d832e --- /dev/null +++ b/codes/code_conv_lists/radar_facilities_to_rr1plus.csv @@ -0,0 +1,26 @@ +RADAR,RCF22,RR1+,RQR13 +RADAR,RWY01,RR1+,RQR13 +RADAR,88RAZ,RR1+,RAZ +RADAR,RNXWC,RR1+,RNX02 +RADAR,RNU93,RR1+,RNX02 +RADAR,99RHM01,RR1+,RHM02 +RADAR,RWJ01,RR1+,RM574 +RADAR,RM327,RR1+,RM574 +RADAR,D1,RR1+,RJZ +RADAR,RM114,RR1+,RGT01 +RADAR,RH878,RR1+,RH8 +RADAR,RA901,RR1+,RH8 +RADAR,SGC05,RR1+,SGC04 +RADAR,NVH,RR1+,SGC04 +RADAR,RTD05,RR1+,RTD01 +RADAR,RJE55,RR1+,RFPFG +RADAR,RTG02,RR1+,RFPFG +RADAR,RR111,RR1+,RRK02 +RADAR,RLQ01,RR1+,RRK02 +RADAR,RLU01,RR1+,RRK02 +RADAR,RJ100,RR1+,RJ121 +RADAR,RSC02,RR1+,SSC02 +RADAR,RX1CC,RR1+,RCSLB +RADAR,RXP,RR1+,RCJAT +RADAR,RWP50,RR1+,RRK02 +RADAR,RWDDA,RR1+,RKZDA diff --git a/codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv b/codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv new file mode 100644 index 0000000..87e772e --- /dev/null +++ b/codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv @@ -0,0 +1,101 @@ +PV_RAW_RRTSTATUS,AAPD,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,ACUTE ITU,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,ACUTE,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,ALD,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,APD,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,CAPD,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,CK,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,CKD/TX,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,CLINIC,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,HD (HOME),PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,HD (HOSP),PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,HOME APD,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,HOME CAPD,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,HOME HD NOCTURNAL,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,HOME HD,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,HOSPITAL HD,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,IN-CENTRE HD,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,LOST,PV_RRTSTATUS,XFER +PV_RAW_RRTSTATUS,LRD,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,MOVED OUT,PV_RRTSTATUS,XFER +PV_RAW_RRTSTATUS,PR,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,PRE,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,REC,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,T/P RENAL(C),PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,T/P RENAL(L),PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,TRANSPLANT,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,TX (KL),PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,TX (PAK),PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,TX (PAT),PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,TX (SPK),PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,0,PV_RRTSTATUS,GEN +PV_RAW_RRTSTATUS,1,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,2,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,3,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,4,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,5,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,9,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,10,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,11,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,12,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,13,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,14,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,15,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,16,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,17,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,19,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,20,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,21,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,22,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,23,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,24,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,25,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,26,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,27,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,28,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,29,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,41,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,42,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,43,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,44,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,45,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,49,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,50,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,51,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,52,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,53,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,54,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,55,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,56,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,57,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,59,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,60,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,61,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,62,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,63,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,64,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,65,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,66,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,68,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,69,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,74,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,75,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,77,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,81,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,82,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,83,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,111,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,114,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,115,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,117,PV_RRTSTATUS,TP +PV_RAW_RRTSTATUS,121,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,162,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,181,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,182,PV_RRTSTATUS,HD +PV_RAW_RRTSTATUS,183,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,201,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,202,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,203,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,241,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,242,PV_RRTSTATUS,PD +PV_RAW_RRTSTATUS,243,PV_RRTSTATUS,PD \ No newline at end of file diff --git a/codes/code_conv_lists/rr1plus_facilities_to_pv.csv b/codes/code_conv_lists/rr1plus_facilities_to_pv.csv new file mode 100644 index 0000000..8bfadc3 --- /dev/null +++ b/codes/code_conv_lists/rr1plus_facilities_to_pv.csv @@ -0,0 +1,7 @@ +RR1+,SSC02,PV,RSC02 +RR1+,RCSLB,PV,RX1CC +RR1+,RNJ00,PV,R1H00 +RR1+,RJ121,PV,RJ100 +RR1+,RQR13,PV,RQR00 +RR1+,SYC02,PV,SYC01 +RR1+,SGC04,PV,SGC05 \ No newline at end of file diff --git a/codes/code_conv_lists/rr1plus_facilities_to_radar.csv b/codes/code_conv_lists/rr1plus_facilities_to_radar.csv new file mode 100644 index 0000000..b940cbb --- /dev/null +++ b/codes/code_conv_lists/rr1plus_facilities_to_radar.csv @@ -0,0 +1,3 @@ +RR1+,RJ121,RADAR,RJ100 +RR1+,SSC02,RADAR,RSC02 +RR1+,RCSLB,RADAR,RX1CC diff --git a/codes/code_conv_lists/snomed_testcodes_to_pv.csv b/codes/code_conv_lists/snomed_testcodes_to_pv.csv new file mode 100644 index 0000000..dea599d --- /dev/null +++ b/codes/code_conv_lists/snomed_testcodes_to_pv.csv @@ -0,0 +1 @@ +SNOMED,75367002,PV,bp_header \ No newline at end of file diff --git a/codes/code_conv_lists/snomed_to_survey_types.csv b/codes/code_conv_lists/snomed_to_survey_types.csv new file mode 100644 index 0000000..dafa9c7 --- /dev/null +++ b/codes/code_conv_lists/snomed_to_survey_types.csv @@ -0,0 +1,5 @@ +SNOMED,821531000000101,SURVEY,EQ5D +SNOMED,925401000000103,SURVEY,PAM +SNOMED,761865002,SURVEY,PROM +SNOMED,925431000000109,SURVEY,PAM13_SCORE +SNOMED,962851000000103,SURVEY,PAM13_LEVEL diff --git a/codes/code_conv_lists/survey_types_to_snomed.csv b/codes/code_conv_lists/survey_types_to_snomed.csv new file mode 100644 index 0000000..2e8e857 --- /dev/null +++ b/codes/code_conv_lists/survey_types_to_snomed.csv @@ -0,0 +1,5 @@ +SURVEY,EQ5D,SNOMED,821531000000101 +SURVEY,PAM,SNOMED,925401000000103 +SURVEY,PROM,SNOMED,761865002 +SURVEY,PAM13_SCORE,SNOMED,925431000000109 +SURVEY,PAM13_LEVEL,SNOMED,962851000000103 diff --git a/codes/code_conv_lists/survey_units_to_rr1plus.csv b/codes/code_conv_lists/survey_units_to_rr1plus.csv new file mode 100644 index 0000000..bc93256 --- /dev/null +++ b/codes/code_conv_lists/survey_units_to_rr1plus.csv @@ -0,0 +1,72 @@ +"source_coding_standard","source_code","destination_coding_standard","destination_code" +"YOURHEALTH_UNITNAME","ALTRINCHAM - SHARED CARE","RR1+","RM403" +"YOURHEALTH_UNITNAME","ALTRINCHAM DIALYSIS UNIT","RR1+","RM403" +"YOURHEALTH_UNITNAME","ALTRINCHAM","RR1+","RM403" +"YOURHEALTH_UNITNAME","BATH","RR1+","RD1" +"YOURHEALTH_UNITNAME","BEDFORD","RR1+","9RFU" +"YOURHEALTH_UNITNAME","BELFAST CITY HOSPITAL","RR1+","2020" +"YOURHEALTH_UNITNAME","BIRMINGHAM HEARTLANDS HOSPITAL","RR1+","RL7" +"YOURHEALTH_UNITNAME","CANNOCK","RR1+","RRE14" +"YOURHEALTH_UNITNAME","CASTLE VALE","RR1+","9RJH01" +"YOURHEALTH_UNITNAME","CENTENARY WING","RR1+","9RCSLB" +"YOURHEALTH_UNITNAME","CITY HOSPITAL","RR1+","RCSLB" +"YOURHEALTH_UNITNAME","COSSHAM","RR1+","9RVJ21" +"YOURHEALTH_UNITNAME","COVENTRY","RR1+","RKB01" +"YOURHEALTH_UNITNAME","DERBY","RR1+","RFPFG" +"YOURHEALTH_UNITNAME","DERRIFORD HOSPITAL","RR1+","RK950" +"YOURHEALTH_UNITNAME","DEWSBURY","RR1+","RMW10" +"YOURHEALTH_UNITNAME","DURHAM DRYBURN","RR1+","RR9" +"YOURHEALTH_UNITNAME","EASINGWOLD","RR1+","RCB23" +"YOURHEALTH_UNITNAME","FREEMAN HOSPITAL","RR1+","RTD01" +"YOURHEALTH_UNITNAME","GUY'S AND ST THOMAS'S HOSPITAL","RR1+","RJ121" +"YOURHEALTH_UNITNAME","HAMMERSMITH HOSPITAL","RR1+","RQN02" +"YOURHEALTH_UNITNAME","HARLOW","RR1+","RQW" +"YOURHEALTH_UNITNAME","HARROGATE","RR1+","RCD35" +"YOURHEALTH_UNITNAME","HEARTLANDS HOSPITAL (SOLIHULL DISTRICT GENERAL)","RR1+","RL301" +"YOURHEALTH_UNITNAME","HEELEY","RR1+","9RK7CC" +"YOURHEALTH_UNITNAME","HUDDERSFIELD","RR1+","RGB04" +"YOURHEALTH_UNITNAME","ILKESTON","RR1+","RXM56" +"YOURHEALTH_UNITNAME","JAMES COOK UNIVERSITY HOSPITAL","RR1+","RCJAT" +"YOURHEALTH_UNITNAME","KING'S COLLEGE HOSPITAL","RR1+","RJZ" +"YOURHEALTH_UNITNAME","KING'S LONDON","RR1+","RJZ" +"YOURHEALTH_UNITNAME","KINGS MILL","RR1+","RFJBC" +"YOURHEALTH_UNITNAME","LEEDS GENERAL INFIRMARY","RR1+","RQS01" +"YOURHEALTH_UNITNAME","LICHFIELD - HEARTLANDS","RR1+","RNG10" +"YOURHEALTH_UNITNAME","LISTER HOSPITAL","RR1+","RAQ01" +"YOURHEALTH_UNITNAME","LUTON & DUNSTABLE","RR1+","RC971" +"YOURHEALTH_UNITNAME","MANCHESTER ROYAL INFIRMARY","RR1+","RM574" +"YOURHEALTH_UNITNAME","NEW CROSS GATE","RR1+","8RJ121" +"YOURHEALTH_UNITNAME","NEW CROSS HOSPITAL","RR1+","RL403" +"YOURHEALTH_UNITNAME","NORTHERN GENERAL HOSPITAL","RR1+","RK7CC" +"YOURHEALTH_UNITNAME","NORTHERN TRUST - ANTRIM AREA HOSPITAL","RR1+","24027" +"YOURHEALTH_UNITNAME","NOTTINGHAM CITY HOSPITAL","RR1+","RCSLB" +"YOURHEALTH_UNITNAME","PONTEFRACT","RR1+","RXF03" +"YOURHEALTH_UNITNAME","QUEEN ELIZABETH HOSPITAL - BIRMINGHAM","RR1+","RRK02" +"YOURHEALTH_UNITNAME","QUEEN ELIZABETH HOSPITAL BIRMINGHAM","RR1+","RRK02" +"YOURHEALTH_UNITNAME","ROTHERHAM","RR1+","RFRPA" +"YOURHEALTH_UNITNAME","ROYAL DERBY HOSPITAL","RR1+","RFPFG" +"YOURHEALTH_UNITNAME","ROYAL LIVERPOOL HOSPITAL","RR1+","RQ617" +"YOURHEALTH_UNITNAME","ROYAL LIVERPOOL UNIVERSITY HOSPITAL","RR1+","RQ617" +"YOURHEALTH_UNITNAME","ROYAL PRESTON HOSPITAL","RR1+","RMF01" +"YOURHEALTH_UNITNAME","ROYAL SUSSEX COUNTY HOSPITAL","RR1+","RGU01" +"YOURHEALTH_UNITNAME","SALFORD ROYAL HOSPITAL","RR1+","RM301" +"YOURHEALTH_UNITNAME","SEACROFT - R & S","RR1+","9RQR14" +"YOURHEALTH_UNITNAME","SOLIHULL DISTRICT GENERAL","RR1+","RL301" +"YOURHEALTH_UNITNAME","SOUTHMEAD HOSPITAL","RR1+","REE01" +"YOURHEALTH_UNITNAME","ST HELIER HOSPITAL","RR1+","RAZ" +"YOURHEALTH_UNITNAME","ST JAMES HOSPITAL","RR1+","RQR13" +"YOURHEALTH_UNITNAME","ST JAMES'S HOSPITAL","RR1+","RQR13" +"YOURHEALTH_UNITNAME","ST JAMES'S UNIVERSITY HOSPITAL","RR1+","RQR13" +"YOURHEALTH_UNITNAME","ST LUKE'S HOSPITAL","RR1+","RAE05" +"YOURHEALTH_UNITNAME","ST LUKES HOSPITAL","RR1+","RAE05" +"YOURHEALTH_UNITNAME","STOCKPORT","RR1+","9RWJ" +"YOURHEALTH_UNITNAME","SUNDERLAND ROYAL HOSPITAL","RR1+","RLNGH" +"YOURHEALTH_UNITNAME","TAMESIDE","RR1+","RMP01" +"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL COVENTRY AND WARWICKSHIRE","RR1+","RKB01" +"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL CROSSHOUSE","RR1+","SAC02" +"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL OF NORTH MIDLANDS","RR1+","RJE01" +"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL OF NORTH STAFFORDSHIRE","RR1+","RJE01" +"YOURHEALTH_UNITNAME","WASHINGTON","RR1+","9RLNGH" +"YOURHEALTH_UNITNAME","WESTERN TRUST - ALTNAGELVIN HOSPITAL","RR1+","45020" +"YOURHEALTH_UNITNAME","WOLVERHAMPTON","RR1+","RL403" +"YOURHEALTH_UNITNAME","YORK HOSPITAL","RR1+","RCB55" \ No newline at end of file diff --git a/codes/code_conv_lists/ukrr_testcodes_to_loinc.csv b/codes/code_conv_lists/ukrr_testcodes_to_loinc.csv new file mode 100644 index 0000000..0fdfa33 --- /dev/null +++ b/codes/code_conv_lists/ukrr_testcodes_to_loinc.csv @@ -0,0 +1,50 @@ +UKRR,QBLA1,LOINC,14682-9 +UKRR,QBLA3,LOINC,14937-7 +UKRR,QBLA4,LOINC,1959-6 +UKRR,QBLA6,LOINC,2951-2 +UKRR,QBLA9,LOINC,2823-3 +UKRR,QBLAB,LOINC,69405-9 +UKRR,QBLAC,LOINC,14933-6 +UKRR,QBLAL,LOINC,33914-3 +UKRR,QBLB1,LOINC,14879-1 +UKRR,QBLB3,LOINC,1996-8 +UKRR,QBLB4,LOINC,29265-6 +UKRR,QBLB5,LOINC,6768-6 +UKRR,QBLB7,LOINC,1751-7 +UKRR,QBLB9,LOINC,14866-8 +UKRR,QBLC1,LOINC,34366-5 +UKRR,QBLC3,LOINC,32294-1 +UKRR,QBLD1,LOINC,14647-2 +UKRR,QBLD3,LOINC,14646-4 +UKRR,QBLD4,LOINC,39469-2 +UKRR,QBLD5,LOINC,2571-8 +UKRR,QBLD6,LOINC,1988-5 +UKRR,QBLD8,LOINC,4548-4 +UKRR,QBLDA,LOINC,59261-8 +UKRR,QBLE1,LOINC,718-7 +UKRR,QBLE3,LOINC,59467-1 +UKRR,QBLE4,LOINC,777-3 +UKRR,QBLE5,LOINC,6690-2 +UKRR,QBLEB,LOINC,718-7 +UKRR,QBLF1,LOINC,2276-4 +UKRR,QBLF3,LOINC,3034-6 +UKRR,QBLF5,LOINC,76069-4 +UKRR,QBLF7,LOINC,2132-9 +UKRR,QBLF9,LOINC,2284-8 +UKRR,QBLFB,LOINC,2283-0 +UKRR,QBLFD,LOINC,14593-8 +UKRR,QBLFF,LOINC,11253-2 +UKRR,QBLFH,LOINC,29247-4 +UKRR,QBLG9,LOINC,54456-9 +UKRR,QBLGG,LOINC,70961-8 +UKRR,QBLHA,LOINC,13952-7 +UKRR,QBLHC,LOINC,13952-7 +UKRR,QBLHE,LOINC,16128-1 +UKRR,QBLHK,LOINC,30247-1 +UKRR,QBLHM,LOINC,56888-1 +UKRR,QBLHN,LOINC,21594-7 +UKRR,QBLHR,LOINC,69949-6 +UKRR,QBLHX,LOINC,14683-7 +UKRR,QBLPC,LOINC,1742-6 +UKRR,QBLPD,LOINC,751-8 +UKRR,QBLPE,LOINC,732-8 diff --git a/codes/code_conv_lists/ukrr_testcodes_to_pv.csv b/codes/code_conv_lists/ukrr_testcodes_to_pv.csv new file mode 100644 index 0000000..a49b14e --- /dev/null +++ b/codes/code_conv_lists/ukrr_testcodes_to_pv.csv @@ -0,0 +1,46 @@ +UKRR,QBLA1,PV,creatinine +UKRR,QBLA3,PV,urea +UKRR,QBLA4,PV,hco3 +UKRR,QBLA6,PV,sodium +UKRR,QBLA9,PV,potassium +UKRR,QBLAB,PV,egfr +UKRR,QBLAC,PV,urate +UKRR,QBLAL,PV,egfr +UKRR,QBLB1,PV,phosphate +UKRR,QBLB3,PV,calcium +UKRR,QBLB4,PV,adjustedcalcium +UKRR,QBLB5,PV,alp +UKRR,QBLB7,PV,albumin +UKRR,QBLB9,PV,pth +UKRR,QBLC1,PV,pcr +UKRR,QBLC3,PV,acr +UKRR,QBLD1,PV,cholesterol +UKRR,QBLD3,PV,hdl +UKRR,QBLD4,PV,ldl +UKRR,QBLD5,PV,tg +UKRR,QBLD6,PV,crp +UKRR,QBLD8,PV,hba1c +UKRR,QBLE1,PV,hb +UKRR,QBLE4,PV,platelets +UKRR,QBLE5,PV,wbc +UKRR,QBLEB,PV,hb +UKRR,QBLF1,PV,ferritin +UKRR,QBLF3,PV,transferrin +UKRR,QBLF7,PV,vitb12 +UKRR,QBLF9,PV,folate +UKRR,QBLFB,PV,folate +UKRR,QBLFF,PV,tacrolimus +UKRR,QBLFH,PV,sirolimus +UKRR,QBLFK,PV,ciclosporin +UKRR,QBLG1,PV,weight +UKRR,QBLG3,PV,bpsys +UKRR,QBLG4,PV,bpdia +UKRR,QBLG9,PV,urr +UKRR,QBLGG,PV,ktv +UKRR,QBLGB,PV,height +UKRR,QBLHA,PV,hbv +UKRR,QBLHC,PV,hbv +UKRR,QBLHE,PV,hcv +UKRR,QBLHX,PV,ucreatinine +UKRR,QBLPC,PV,alt +UKRR,QBLPD,PV,neutrophils diff --git a/codes/code_exclusions/pv_observations.csv b/codes/code_exclusions/pv_observations.csv new file mode 100644 index 0000000..4f3f41b --- /dev/null +++ b/codes/code_exclusions/pv_observations.csv @@ -0,0 +1,3 @@ +PV,covid19pcr,RADAR +PV,covid19antibody,RADAR +PV,covid19lflow,RADAR diff --git a/codes/code_importer.py b/codes/code_importer.py new file mode 100644 index 0000000..850e2e6 --- /dev/null +++ b/codes/code_importer.py @@ -0,0 +1,236 @@ +import csv +import argparse +import sys +import os + +import psycopg2 + +from ukrdc.database import Connection + + +class CodeUpdater(object): + def upload(self): + for row in self.rows: + self.add_row(row) + self.connection.commit() + + @property + def connection(self): + return self._connection + + @connection.setter + def connection(self, connection): + self._connection = connection + self.cursor = connection.cursor() + + def insert(self, sql, row): + try: + self.cursor.execute(sql, (row)) + except psycopg2.IntegrityError as e: + self.connection.rollback() + print("Problem with integrity " + str(e)) + except Exception: + print(sql) + print(row) + raise + + def select(self, sql, row): + try: + self.cursor.execute(sql, (row)) + return list(self.cursor.fetchall()) + except psycopg2.Error as e: + print(e) + + +class CodeList(CodeUpdater): + def __init__(self): + self.rows = [] + + def truncate(self): + sqlstring = """ + TRUNCATE TABLE CODE_LIST + """ + self.cursor.execute(sqlstring) + self.connection.commit() + + def get_row(self, *args): + sql = """ + select + coding_standard, code, description, object_type + from + extract.code_list + where + coding_standard = %s and + code = %s and + description = %s and + object_type = %s + """ + return self.insert(sql, args) + + def update(self): + for row in self.rows: + results = self.get_row(row) + if results: + print("Yes we have that row") + else: + self.update_row(row[0], row[1], row) + + def add_row(self, row): + sqlstring = """ + INSERT INTO CODE_LIST + ( + CODING_STANDARD, + CODE, + DESCRIPTION, + OBJECT_TYPE, + UNITS + ) + VALUES (%s, %s, %s, %s, %s) + """ + self.insert(sqlstring, row) + + def read_csv(self): + base_folder = "conf/pv2_codes/code_lists/" + + for filename in os.listdir(base_folder): + print(f"Reading {filename}") + fp = os.path.join(base_folder, filename) + csvreader = csv.reader(open(fp, "r", encoding="utf-8")) + + for row in csvreader: + # Get Row to expected length + row = list(row)[:5] + diff_len = 5 - len(row) + if diff_len > 0: + row = row + [None] * diff_len + if row[0] == "": + print("Empty Row, continue") + continue + self.rows.append(row) + + +class CodeMap(CodeUpdater): + def __init__(self): + self.rows = [] + + def truncate(self): + + sqlstring = """ + TRUNCATE TABLE CODE_MAP + """ + self.cursor.execute(sqlstring) + self.connection.commit() + + def add_row(self, row): + sqlstring = """ + INSERT INTO CODE_MAP + ( + SOURCE_CODING_STANDARD, + SOURCE_CODE, + DESTINATION_CODING_STANDARD, + DESTINATION_CODE + ) + VALUES(%s, %s, %s, %s)""" + self.insert(sqlstring, row) + + def read_csv(self): + # Code Conv List + + base_folder = "conf/pv2_codes/code_conv_lists/" + + for filename in os.listdir(base_folder): + fp = os.path.join(base_folder, filename) + print(fp) + csvreader = csv.reader(open(fp, "r", encoding="utf-8")) + for row in csvreader: + self.rows.append(row) + + +class SatelliteMap(CodeUpdater): + def __init__(self): + self.rows = [] + + def truncate(self): + + sqlstring = """ + TRUNCATE TABLE SATELLITE_MAP + """ + self.cursor.execute(sqlstring) + self.connection.commit() + + def add_row(self, row): + sqlstring = """ + INSERT INTO SATELLITE_MAP + ( + SATELLITE_CODE, + MAIN_UNIT_CODE + ) + VALUES(%s, %s)""" + self.insert(sqlstring, row) + + def read_csv(self): + # Satellite Mapping List + + base_folder = "conf/pv2_codes/satellite_map/" + + for filename in os.listdir(base_folder): + + fp = os.path.join(base_folder, filename) + print(fp) + csvreader = csv.reader(open(fp, "r", encoding="utf-8")) + for row in csvreader: + self.rows.append(row) + + +def main(): + + servers = ["ukrdc_dev", "ukrdc_staging", "ukrdc_live"] + + parser = argparse.ArgumentParser(description="Update codes") + parser.add_argument("--server", nargs="+", default=servers) + parser.add_argument("--upload-codelist", action="store_true") + parser.add_argument("--upload-codemap", action="store_true") + parser.add_argument("--upload-satellitemap", action="store_true") + + if not len(sys.argv) > 1: + parser.print_help() + return + args = parser.parse_args() + if args.upload_codelist: + codelist = CodeList() + codelist.read_csv() + if args.upload_codemap: + codemap = CodeMap() + codemap.read_csv() + if args.upload_satellitemap: + satellitemap = SatelliteMap() + satellitemap.read_csv() + + for server in args.server: + print(f"server: {server}") + engine = Connection.get_engine_from_file(None, server) + connection = engine.raw_connection() + print("Connected") + if args.upload_codelist: + codelist.connection = connection + print("Truncating Code List") + codelist.truncate() + print("Populating Code List") + codelist.upload() + if args.upload_codemap: + codemap.connection = connection + print("Truncating Code Map") + codemap.truncate() + print("Populating Code Map") + codemap.upload() + if args.upload_satellitemap: + satellitemap.connection = connection + print("Truncating Satellite Map") + satellitemap.truncate() + print("Uploading Satellite Map") + satellitemap.upload() + connection.close() + + +if __name__ == "__main__": + main() diff --git a/codes/code_lists/RR22.csv b/codes/code_lists/RR22.csv new file mode 100644 index 0000000..badf8f4 --- /dev/null +++ b/codes/code_lists/RR22.csv @@ -0,0 +1,7 @@ +RR22,1,Oral +RR22,2,Topical +RR22,3,Inhalation +RR22,4,Injection +RR22,5,Intra peritoneal +RR22,6,Rectal +RR22,9,Other - please specify in comments diff --git a/codes/code_lists/RR23.csv b/codes/code_lists/RR23.csv new file mode 100644 index 0000000..849e859 --- /dev/null +++ b/codes/code_lists/RR23.csv @@ -0,0 +1,11 @@ +CF_RR23,l,Litres +CF_RR23,dl,Decilitres +CF_RR23,ml,Mililitres +CF_RR23,g,Grams +CF_RR23,mg,Miligrams +CF_RR23,μg,Micrograms +CF_RR23,ng,Nanograms +CF_RR23,tab,Tablets +CF_RR23,units,Units (i.e. for Epoetins) +CF_RR23,mmol,Minimols +CF_RR23,other,Other \ No newline at end of file diff --git a/codes/code_lists/cf_rr7_discharge.csv b/codes/code_lists/cf_rr7_discharge.csv new file mode 100644 index 0000000..6b9730b --- /dev/null +++ b/codes/code_lists/cf_rr7_discharge.csv @@ -0,0 +1,9 @@ +CF_RR7_DISCHARGE,30,Kidney Transplant Failure +CF_RR7_DISCHARGE,38,Patient Transferred Out +CF_RR7_DISCHARGE,84,ARF - Recovered +CF_RR7_DISCHARGE,85,ARF - Stopped Dialysis (without recovery of function) +CF_RR7_DISCHARGE,86,ARF - Transferred Out +CF_RR7_DISCHARGE,90,Treatment Stopped (Renal Function Recovered) +CF_RR7_DISCHARGE,91,Treatment Stopped (Without Recovery of Function) +CF_RR7_DISCHARGE,92,Conservative Management - Treatment stopped without recovery +CF_RR7_DISCHARGE,95,Patient - Lost to follow-up diff --git a/codes/code_lists/cf_rr7_treatment.csv b/codes/code_lists/cf_rr7_treatment.csv new file mode 100644 index 0000000..8e51611 --- /dev/null +++ b/codes/code_lists/cf_rr7_treatment.csv @@ -0,0 +1,51 @@ +CF_RR7_TREATMENT,1,Haemodialysis +CF_RR7_TREATMENT,2,Haemofiltration +CF_RR7_TREATMENT,3,Haemodiafiltration +CF_RR7_TREATMENT,4,Haemodialysis > 4 days per week / daily +CF_RR7_TREATMENT,5,Ultrafiltration +CF_RR7_TREATMENT,9,Haemodialysis - Type Unknown +CF_RR7_TREATMENT,10,CAPD Connect +CF_RR7_TREATMENT,11,CAPD Disconnect +CF_RR7_TREATMENT,12,Cycling PD >= 6 Nights/Week Dry +CF_RR7_TREATMENT,13,Cycling PD < 6 Nights/Week Dry +CF_RR7_TREATMENT,14,Cycling PD >= 6 Nights/Week Wet (Day Dwell) +CF_RR7_TREATMENT,15,Cycling PD < 6 Nights/Week Wet (Day Dwell) +CF_RR7_TREATMENT,16,Assisted Cycling PD >= 6 nights/Week Dry +CF_RR7_TREATMENT,17,Assisted Cycling PD >= 6 nights/Week Wet (Day Dwell) +CF_RR7_TREATMENT,19,Peritoneal Dialysis - Type Unknown +CF_RR7_TREATMENT,20,Transplant; Cadaver Donor +CF_RR7_TREATMENT,21,Transplant; Live Related - Sibling +CF_RR7_TREATMENT,22,Transplant; Live Related - Parent or Child +CF_RR7_TREATMENT,23,Transplant; Live Related - Other +CF_RR7_TREATMENT,24,Transplant; Live Genetically Unrelated +CF_RR7_TREATMENT,25,Transplant; Cadaver + Transp Other Organ +CF_RR7_TREATMENT,26,Transplant; Live Donor + Transp Other Organ +CF_RR7_TREATMENT,27,Transplant; Live Donor Non-UK Transplant +CF_RR7_TREATMENT,28,Transplant; Non-Heart Beating Donor +CF_RR7_TREATMENT,29,Transplant; Type Unknown +CF_RR7_TREATMENT,31,Graft Acute Rejection Episode - Biopsy Proven +CF_RR7_TREATMENT,32,Graft Acute Rejection Episode - No Biopsy +CF_RR7_TREATMENT,74,Transplant; Live Related - Father +CF_RR7_TREATMENT,75,Transplant; Live Related - Mother +CF_RR7_TREATMENT,77,Transplant; Live Related - Child +CF_RR7_TREATMENT,78,Transplant; Live Donor +CF_RR7_TREATMENT,80,Acute Renal Failure Not Dialysed +CF_RR7_TREATMENT,81,Acute Kidney Injury - Haemodialysis +CF_RR7_TREATMENT,82,Acute Kidney Injury - Haemofiltration +CF_RR7_TREATMENT,83,Acute Kidney Injury - Peritoneal Dialysis +CF_RR7_TREATMENT,88,Acute Kidney Injury receiving RRT not by renal service +CF_RR7_TREATMENT,93,Conservative Management - Mutual Decision not to offer RRT +CF_RR7_TREATMENT,94,Conservative Management - Clinical Decision not to offer RRT +CF_RR7_TREATMENT,101,First Assessment by Renal Service +CF_RR7_TREATMENT,110,Plasmapharesis / Plasma Exchange +CF_RR7_TREATMENT,111,Assisted CAPD +CF_RR7_TREATMENT,120,Transplant Clinic Followup +CF_RR7_TREATMENT,121,Assisted APD +CF_RR7_TREATMENT,201,Hybrid CAPD with HD +CF_RR7_TREATMENT,202,Hybrid APD with HD +CF_RR7_TREATMENT,203,Hybrid APD with CAPD +CF_RR7_TREATMENT,900,CKD (Not on RRT) +CF_RR7_TREATMENT,901,Patient - ESKD with no RRT +CF_RR7_TREATMENT,902,Patient - CKD-advanced MDT clinic +CF_RR7_TREATMENT,903,Patient - CKD-clinic follow-up +CF_RR7_TREATMENT,904,Patient - CKD-remote monitoring diff --git a/codes/code_lists/dose_units.csv b/codes/code_lists/dose_units.csv new file mode 100644 index 0000000..22f8564 --- /dev/null +++ b/codes/code_lists/dose_units.csv @@ -0,0 +1,18 @@ +RADAR,l,litre,dose_unit +RADAR,dl,decilitre,dose_unit +RADAR,ml,millilitre,dose_unit +RADAR,g,gram,dose_unit +RADAR,mg,milligram,dose_unit +RADAR,ng,nanogram,dose_unit +RADAR,tab,tablet,dose_unit +RADAR,iu,international unit,dose_unit +RADAR,mmol,millimole,dose_unit +RADAR,puff,puff,dose_unit +RADAR,unit,unit,dose_unit +RADAR,ampoule,ampoule,dose_unit +RADAR,drop,drop,dose_unit +RADAR,capsule,capsule,dose_unit +RADAR,patch,patch,dose_unit +RADAR,sachet,sachet,dose_unit +RADAR,µg,microgram,dose_unit +RADAR,tbsp,table_spoon,dose_unit diff --git a/codes/code_lists/edta_cod.csv b/codes/code_lists/edta_cod.csv new file mode 100644 index 0000000..2ad9ab3 --- /dev/null +++ b/codes/code_lists/edta_cod.csv @@ -0,0 +1,65 @@ +EDTA_COD,0,cause of death uncertain/not determined +EDTA_COD,11,myocardial ischaemia and infraction +EDTA_COD,12,hyperkalaemia +EDTA_COD,13,haemorrhagic pericarditis +EDTA_COD,14,other causes of cardiac failure +EDTA_COD,15,cardiac arrest/sudden death; other cause or unknown +EDTA_COD,16,hypertensive cardiac failure +EDTA_COD,17,hypokalaemia +EDTA_COD,18,fluid overload/pulmonary oedema +EDTA_COD,19,elevated pvr/pulmonary hypertension +EDTA_COD,21,pulmonary embolus +EDTA_COD,22,"cerebro-vascular accident, other cause or unspecified" +EDTA_COD,23,gastro-intestinal haemorrhage (digestive) +EDTA_COD,24,haemorrhage from graft site +EDTA_COD,25,haemorrhage from vascular access or dialysis circuit +EDTA_COD,26,cerebral haemorrhage from ruptured vascular aneurysm +EDTA_COD,27,haemorrhage from surgery (except digestive haemorrhage) +EDTA_COD,28,"other haemorrhage, other site and/or other cause" +EDTA_COD,29,mesenteric infarction +EDTA_COD,31,pulmonary infection (bacterial) +EDTA_COD,32,pulmonary infection (viral) +EDTA_COD,33,pulmonary infection (fungal or protozoal; parasitic) +EDTA_COD,34,infections elsewhere (except viral hepatitis) +EDTA_COD,35,septicaemia +EDTA_COD,36,tuberculosis (lung) +EDTA_COD,37,tuberculosis (elsewhere) +EDTA_COD,38,generalized viral infection +EDTA_COD,39,peritonitis (all causes except for peritoneal dialysis) +EDTA_COD,41,liver disease due to hepatitis b virus +EDTA_COD,42,liver disease due to other viral hepatitis +EDTA_COD,43,liver disease due to drug toxicity +EDTA_COD,44,cirrhosis - not viral (alcoholic or other cause) +EDTA_COD,45,cystic liver disease +EDTA_COD,46,liver failure - cause unknown +EDTA_COD,51,patient refused further treatment for erf +EDTA_COD,52,suicide +EDTA_COD,53,erf treatment ceased for any other reason +EDTA_COD,54,erf treatment withdrawn for medical reasons +EDTA_COD,61,ureamia caused by graft failure +EDTA_COD,62,pancreatitis +EDTA_COD,63,bone marrow depression (aplosia) +EDTA_COD,64,cachexia +EDTA_COD,66,malignant disease in patient treated by immunosuppressive therapy +EDTA_COD,67,malignant disease: solid tumors except those of 66 +EDTA_COD,68,malignant disease: lymphoproliferative disorders (except 66) +EDTA_COD,69,dementia +EDTA_COD,70,"peritonitis (sclerosing, with peritoneal dialysis)" +EDTA_COD,71,perforation of peptic ulcer +EDTA_COD,72,perforation of colon +EDTA_COD,73,chronic obstructive pulmonary disease +EDTA_COD,79,multi-system failure +EDTA_COD,81,accident related to erf treatment +EDTA_COD,82,accident unrelated to erf treatment +EDTA_COD,99,other identified cause of death +EDTA_COD,100,"peritonitis (bacterial, with peritoneal dialysis)" +EDTA_COD,101,"peritonitis (fungal, with peritoneal dialysis)" +EDTA_COD,102,"peritonitis (due to other cause, with peritoneal dialysis)" +EDTA_COD,103,peripheral vascular disease +EDTA_COD,104,calciphylaxis +EDTA_COD,105,ischaemic bowel +EDTA_COD,106,ruptured aaa +EDTA_COD,107,advanced ckd not on dialysis(conservative management) +EDTA_COD,108,acute kidney injury +EDTA_COD,109,c diff colitis +EDTA_COD,110,line related sepsis diff --git a/codes/code_lists/edta_prd.csv b/codes/code_lists/edta_prd.csv new file mode 100644 index 0000000..5363173 --- /dev/null +++ b/codes/code_lists/edta_prd.csv @@ -0,0 +1,339 @@ +EDTA,0,"CHRONIC RENAL FAILURE, AETIOLOGY UNCERTAIN" +EDTA,10,"GLOMERULONEPHRITIS, HISTOLOGICALLY NOT EXAMINED" +EDTA,11,SEVERE NEPHROTIC SYNDROME WITH FOCAL SCLEROSIS (PAEDIATRIC) +EDTA,12,IGA NEPHROPATHY PROVEN BY IMMUNOFLUORESCENCE +EDTA,13,"DENSE DEPOSIT DISEASE, MEMBRANO-PROLIF. GN TYPE II" +EDTA,14,MEMBRANOUS NEPHROPATHY +EDTA,15,MEMBRANO-PROLIFERATIVE GN TYPE I +EDTA,16,RAPIDLY PROGRESSIVE GN WITHOUT SYSTEMIC DISEASE (CRESCENTIC +EDTA,17,FOCAL SEGMENTAL GLOMERULOSCEROSIS WITH NEPHROTIC SYNDROME IN ADULTS +EDTA,19,"GLOMERULONEPHRITIS, HISTOLOGICALLY EXAMINED" +EDTA,199,UNAVAILABLE +EDTA,20,PYELO/INTERSTITIAL NEPHRITIS - CAUSE NOT SPECIFIED +EDTA,21,PYELO/INTERSTITIAL NEPHRITIS - WITH NEUROGENIC BLADDER +EDTA,22,PYELO/INTERSTITIAL NEPHRITIS - CONGEN. OBST. UROPATHY +/- REFLUX +EDTA,23,PYELO/INTERSTITIAL NEPHRITIS - ACQUIRED OBST. UROPATHY +EDTA,24,PYELO/INTERSTITIAL NEPHRITIS - VESICO-URETERIC REFLUX NO OBSTRUCTION +EDTA,25,PYELO/INTERSTITIAL NEPHRITIS - DUE TO UROLITHIASIS +EDTA,29,PYELO/INTERSTITIAL NEPHRITIS DUE TO OTHER CAUSE (PLEASE SPECIFY) +EDTA,30,TUBULO INTERSTITIAL NEPHRITIS (NOT PYELONEPHRITIS) +EDTA,31,NEPHROPATHY DUE TO ANALGESIC DRUGS +EDTA,32,NEPHROPATHY DUE TO CIS-PLATINUM +EDTA,33,NEPHROPATHY DUE TO CYCLOSPORIN A +EDTA,34,LEAD INDUCED NEPHROPATHY (INTERSTITIAL) +EDTA,39,NEPHROPATHY CAUSED BY OTHER SPECIFIC DRUG +EDTA,40,CYSTIC KIDNEY DISEASE - TYPE UNSPECIFIED +EDTA,41,POLYCYSTIC KIDNEYS - ADULT TYPE (DOMINANT) +EDTA,42,POLYCYSTIC KIDNEYS - INFANTILE (RECESSIVE) +EDTA,43,MEDULLARY CYSTIC DISEASE - INCLUDING NEPHRONOPHTHISIS +EDTA,49,CYSTIC KIDNEY DISEASE - OTHER SPECIFIED TYPE +EDTA,50,HEREDITARY/FAMILIAL NEPHROPATHY - TYPE UNSPECIFIED +EDTA,51,HEREDITARY NEPHRITIS WITH NERVE DEAFNESS (ALPORT'S) +EDTA,52,CYSTINOSIS +EDTA,53,PRIMARY OXALOSIS +EDTA,54,FABRY'S DISEASE +EDTA,59,HEREDITARY NEPHROPATHY - OTHER +EDTA,60,CONGENITAL RENAL HYPOPLASIA - TYPE UNSPECIFIED +EDTA,61,OLIGOMEGANEPHRONIC HYPOPLASIA +EDTA,63,CONGENITAL RENAL DYSPLASIA +/- URINARY TRACT MALFORMATION +EDTA,66,SYNDROME OF AGENESIS OF ABDO. MUSCLES - PRUNE BELLY SYNDROME +EDTA,70,RENAL VASCULAR DISEASE - TYPE UNSPECIFIED +EDTA,71,RENAL VASCULAR DISEASE DUE TO MALIGNANT HYPERTENSION +EDTA,72,RENAL VASCULAR DISEASE DUE TO HYPERTENSION +EDTA,73,RENAL VASCULAR DISEASE DUE TO POLYARTERITIS +EDTA,74,WEGENER'S GRANULOMATOSIS +EDTA,75,ISCHAEMIC RENAL DISEASE/CHOLESTEROL EMBOLISM +EDTA,76,GLOMERULONEPHRITIS RELATED TO LIVER CIRRHOSIS +EDTA,78,CRYOGLOBULINAEMIC GLOMERULONEPHRITIS +EDTA,79,RENAL VASCULAR DISEASE - CLASSIFIED (PLEASE SPECIFY) +EDTA,80,DIABETES TYPE 1 (INSULIN DEPENDENT) +EDTA,81,DIABETES TYPE 2 (NON-INSULIN DEPENDENT) +EDTA,82,MYELOMATOSIS +EDTA,83,AMYLOID +EDTA,84,SYSTEMIC LUPUS ERYTHEMATOSUS +EDTA,85,HENOCH-SCHONLEIN PURPURA +EDTA,86,GOODPASTURES SYNDROME +EDTA,87,SCLERODERMA +EDTA,88,HAEMOLYTIC URAEMIC SYNDROME +EDTA,89,MULTI-SYSTEM DISEASE - TYPE UNSPECIFIED +EDTA,90,CORTICAL OR TUBULAR NECROSIS +EDTA,91,TUBERCULOSIS +EDTA,92,GOUT +EDTA,93,NEPHROCALCINOSIS / HYPERCALCAEMIC NEPHROPATHY +EDTA,94,BALKAN NEPHROPATHY +EDTA,95,KIDNEY TUMOUR +EDTA,96,TRAUMATIC OR SURGICAL LOSS OF KIDNEY +EDTA,99,OTHER IDENTIFIED RENAL DISORDERS - PLEASE SPECIFY +EDTA2,1003,ADULT NEPHROTIC SYNDROME - NO HISTOLOGY +EDTA2,1019,NEPHROTIC SYNDROME OF CHILDHOOD - STEROID SENSITIVE - NO HISTOLOGY +EDTA2,1026,CONGENITAL NEPHROTIC SYNDROME (CNS) - NO HISTOLOGY +EDTA2,1035,CONGENITAL NEPHROTIC SYNDROME (CNS) - FINNISH TYPE - NO HISTOLOGY +EDTA2,1042,CONGENITAL NEPHROTIC SYNDROME (CNS) - FINNISH TYPE - HISTOLOGICALLY PROVEN +EDTA2,1057,CONGENITAL NEPHROTIC SYNDROME (CNS) - DIFFUSE MESANGIAL SCLEROSIS +EDTA2,1061,CONGENITAL NEPHROTIC SYNDROME (CNS) - FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) +EDTA2,1074,DENYS-DRASH SYNDROME +EDTA2,1088,CONGENITAL NEPHROTIC SYNDROME (CNS) - CONGENITAL INFECTION +EDTA2,1090,MINIMAL CHANGE NEPHROPATHY - NO HISTOLOGY +EDTA2,1100,MINIMAL CHANGE NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,1116,IGA NEPHROPATHY - NO HISTOLOGY +EDTA2,1128,IGA NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,1137,FAMILIAL IGA NEPHROPATHY - NO HISTOLOGY +EDTA2,1144,FAMILIAL IGA NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,1159,IGA NEPHROPATHY SECONDARY TO LIVER CIRRHOSIS - NO HISTOLOGY +EDTA2,1163,IGA NEPHROPATHY SECONDARY TO LIVER CIRRHOSIS - HISTOLOGICALLY PROVEN +EDTA2,1171,IGM - ASSOCIATED NEPHROPATHY +EDTA2,1185,MEMBRANOUS NEPHROPATHY - IDIOPATHIC +EDTA2,1192,MEMBRANOUS NEPHROPATHY - MALIGNANCY ASSOCIATED +EDTA2,1205,MEMBRANOUS NEPHROPATHY - DRUG INDUCED +EDTA2,1214,MEMBRANOUS NEPHROPATHY - INFECTION ASSOCIATED +EDTA2,1222,MESANGIOCAPILLARY GLOMERULONEPHRITIS TYPE 1 +EDTA2,1233,MESANGIOCAPILLARY GLOMERULONEPHRITIS TYPE 2 (DENSE DEPOSIT DISEASE) +EDTA2,1246,MESANGIOCAPILLARY GLOMERULONEPHRITIS TYPE 3 +EDTA2,1251,IDIOPATHIC RAPIDLY PROGRESSIVE (CRESCENTIC) GLOMERULONEPHRITIS +EDTA2,1267,PRIMARY FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) +EDTA2,1279,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL RECESSIVE - NO HISTOLOGY +EDTA2,1280,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL RECESSIVE - HISTOLOGICALLY PROVEN +EDTA2,1298,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL DOMINANT - NO HISTOLOGY +EDTA2,1308,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL DOMINANT - HISTOLOGICALLY PROVEN +EDTA2,1312,FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) SECONDARY TO OBESITY - NO HISTOLOGY +EDTA2,1320,FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) SECONDARY TO OBESITY - HISTOLOGICALLY PROVEN +EDTA2,1331,DIFFUSE ENDOCAPILLARY GLOMERULONEPHRITIS +EDTA2,1349,MESANGIAL PROLIFERATIVE GLOMERULONEPHRITIS +EDTA2,1354,FOCAL AND SEGMENTAL PROLIFERATIVE GLOMERULONEPHRITIS +EDTA2,1365,GLOMERULONEPHRITIS - SECONDARY TO OTHER SYSTEMIC DISEASE +EDTA2,1377,GLOMERULONEPHRITIS - HISTOLOGICALLY INDETERMINATE +EDTA2,1383,SYSTEMIC VASCULITIS - ANCA NEGATIVE - HISTOLOGICALLY PROVEN +EDTA2,1396,SYSTEMIC VASCULITIS - ANCA POSITIVE - NO HISTOLOGY +EDTA2,1401,GRANULOMATOSIS WITH POLYANGIITIS - NO HISTOLOGY +EDTA2,1417,GRANULOMATOSIS WITH POLYANGIITIS - HISTOLOGICALLY PROVEN +EDTA2,1429,MICROSCOPIC POLYANGIITIS - HISTOLOGICALLY PROVEN +EDTA2,1438,CHURG-STRAUSS SYNDROME - NO HISTOLOGY +EDTA2,1440,CHURG-STRAUSS SYNDROME - HISTOLOGICALLY PROVEN +EDTA2,1455,POLYARTERITIS NODOSA +EDTA2,1464,ANTI-GLOMERULAR BASEMENT MEMBRANE (GBM) DISEASE / GOODPASTURE'S SYNDROME - NO HISTOLOGY +EDTA2,1472,ANTI-GLOMERULAR BASEMENT MEMBRANE (GBM) DISEASE / GOODPASTURE'S SYNDROME - HISTOLOGICALLY PROVEN +EDTA2,1486,SYSTEMIC LUPUS ERYTHEMATOSUS / NEPHRITIS - NO HISTOLOGY +EDTA2,1493,SYSTEMIC LUPUS ERYTHEMATOSUS / NEPHRITIS - HISTOLOGICALLY PROVEN +EDTA2,1504,HENOCH-SCHONLEIN PURPURA / NEPHRITIS - NO HISTOLOGY +EDTA2,1515,HENOCH-SCHONLEIN PURPURA / NEPHRITIS - HISTOLOGICALLY PROVEN +EDTA2,1527,RENAL SCLERODERMA / SYSTEMIC SCLEROSIS - NO HISTOLOGY +EDTA2,1536,RENAL SCLERODERMA / SYSTEMIC SCLEROSIS - HISTOLOGICALLY PROVEN +EDTA2,1543,ESSENTIAL MIXED CRYOGLOBULINAEMIA - NO HISTOLOGY +EDTA2,1558,ESSENTIAL MIXED CRYOGLOBULINAEMIA - HISTOLOGICALLY PROVEN +EDTA2,1562,CRYOGLOBULINAEMIA SECONDARY TO HEPATITIS C - NO HISTOLOGY +EDTA2,1570,CRYOGLOBULINAEMIA SECONDARY TO HEPATITIS C - HISTOLOGICALLY PROVEN +EDTA2,1589,CRYOGLOBULINAEMIA SECONDARY TO SYSTEMIC DISEASE - NO HISTOLOGY +EDTA2,1591,CRYOGLOBULINAEMIA SECONDARY TO SYSTEMIC DISEASE - HISTOLOGICALLY PROVEN +EDTA2,1602,PRIMARY REFLUX NEPHROPATHY - SPORADIC +EDTA2,1618,FAMILIAL REFLUX NEPHROPATHY +EDTA2,1625,CONGENITAL DYSPLASIA / HYPOPLASIA +EDTA2,1639,MULTICYSTIC DYSPLASTIC KIDNEYS +EDTA2,1641,DYSPLASIA DUE TO FETAL ACE-INHIBITOR EXPOSURE +EDTA2,1656,GLOMERULOCYSTIC DISEASE +EDTA2,1660,CONGENITAL PELVI-URETERIC JUNCTION OBSTRUCTION +EDTA2,1673,CONGENITAL VESICO-URETERIC JUNCTION OBSTRUCTION +EDTA2,1687,POSTERIOR URETHRAL VALVES +EDTA2,1694,SYNDROME OF AGENESIS OF ABDOMINAL MUSCLES - PRUNE BELLY SYNDROME +EDTA2,1706,CONGENITAL NEUROGENIC BLADDER +EDTA2,1710,BLADDER EXSTROPHY +EDTA2,1723,MEGACYSTIS-MEGAURETER +EDTA2,1734,OLIGOMEGANEPHRONIA +EDTA2,1747,RENAL PAPILLARY NECROSIS - CAUSE UNKNOWN +EDTA2,1752,ACQUIRED OBSTRUCTIVE UROPATHY / NEPHROPATHY +EDTA2,1768,ACQUIRED OBSTRUCTIVE NEPHROPATHY DUE TO NEUROGENIC BLADDER +EDTA2,1775,OBSTRUCTIVE NEPHROPATHY DUE TO PROSTATIC HYPERTROPHY +EDTA2,1781,OBSTRUCTIVE NEPHROPATHY DUE TO PROSTATE CANCER +EDTA2,1799,OBSTRUCTIVE NEPHROPATHY DUE TO BLADDER CANCER +EDTA2,1809,OBSTRUCTIVE NEPHROPATHY DUE TO OTHER MALIGNANCIES +EDTA2,1813,IDIOPATHIC RETROPERITONEAL FIBROSIS +EDTA2,1821,RETROPERITONEAL FIBROSIS SECONDARY TO MALIGNANCIES +EDTA2,1832,CALCULUS NEPHROPATHY / UROLITHIASIS +EDTA2,1845,CALCIUM OXALATE UROLITHIASIS +EDTA2,1850,ENTERIC HYPEROXALURIA +EDTA2,1866,MAGNESIUM AMMONIUM PHOSPHATE (STRUVITE) UROLITHIASIS +EDTA2,1878,URIC ACID UROLITHIASIS +EDTA2,1884,TUBULOINTERSTITIAL NEPHRITIS - NO HISTOLOGY +EDTA2,1897,TUBULOINTERSTITIAL NEPHRITIS - HISTOLOGICALLY PROVEN +EDTA2,1907,FAMILIAL INTERSTITIAL NEPHROPATHY - NO HISTOLOGY +EDTA2,1911,FAMILIAL INTERSTITIAL NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,1924,TUBULOINTERSTITIAL NEPHRITIS ASSOCIATED WITH AUTOIMMUNE DISEASE - NO HISTOLOGY +EDTA2,1930,TUBULOINTERSTITIAL NEPHRITIS ASSOCIATED WITH AUTOIMMUNE DISEASE - HISTOLOGICALLY PROVEN +EDTA2,1948,TUBULOINTERSTITIAL NEPHRITIS WITH UVEITIS (TINU) - NO HISTOLOGY +EDTA2,1953,TUBULOINTERSTITIAL NEPHRITIS WITH UVEITIS (TINU) - HISTOLOGICALLY PROVEN +EDTA2,1969,RENAL SARCOIDOSIS - NO HISTOLOGY +EDTA2,1976,RENAL SARCOIDOSIS - HISTOLOGICALLY PROVEN +EDTA2,1982,ARISTOLOCHIC ACID NEPHROPATHY (BALKAN / CHINESE HERB / ENDEMIC NEPHROPATHY) - NO HISTOLOGY +EDTA2,1995,ARISTOLOCHIC ACID NEPHROPATHY (BALKAN / CHINESE HERB / ENDEMIC NEPHROPATHY) - HISTOLOGICALLY PROVEN +EDTA2,2005,DRUG-INDUCED TUBULOINTERSTITIAL NEPHRITIS - NO HISTOLOGY +EDTA2,2014,DRUG-INDUCED TUBULOINTERSTITIAL NEPHRITIS - HISTOLOGICALLY PROVEN +EDTA2,2022,NEPHROPATHY DUE TO ANALGESIC DRUGS - NO HISTOLOGY +EDTA2,2033,NEPHROPATHY DUE TO ANALGESIC DRUGS - HISTOLOGICALLY PROVEN +EDTA2,2046,NEPHROPATHY DUE TO CICLOSPORIN - NO HISTOLOGY +EDTA2,2051,NEPHROPATHY DUE TO CICLOSPORIN - HISTOLOGICALLY PROVEN +EDTA2,2067,NEPHROPATHY DUE TO TACROLIMUS - NO HISTOLOGY +EDTA2,2079,NEPHROPATHY DUE TO TACROLIMUS - HISTOLOGICALLY PROVEN +EDTA2,2080,NEPHROPATHY DUE TO AMINOGLYCOSIDES - NO HISTOLOGY +EDTA2,2098,NEPHROPATHY DUE TO AMINOGLYCOSIDES - HISTOLOGICALLY PROVEN +EDTA2,2108,NEPHROPATHY DUE TO AMPHOTERICIN - NO HISTOLOGY +EDTA2,2112,NEPHROPATHY DUE TO AMPHOTERICIN - HISTOLOGICALLY PROVEN +EDTA2,2120,NEPHROPATHY DUE TO CISPLATIN - NO HISTOLOGY +EDTA2,2131,NEPHROPATHY DUE TO CISPLATIN - HISTOLOGICALLY PROVEN +EDTA2,2149,NEPHROPATHY DUE TO LITHIUM - NO HISTOLOGY +EDTA2,2154,NEPHROPATHY DUE TO LITHIUM - HISTOLOGICALLY PROVEN +EDTA2,2165,LEAD INDUCED NEPHROPATHY - NO HISTOLOGY +EDTA2,2177,LEAD INDUCED NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2183,ACUTE URATE NEPHROPATHY - NO HISTOLOGY +EDTA2,2196,ACUTE URATE NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2203,CHRONIC URATE NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2219,RADIATION NEPHRITIS +EDTA2,2226,RENAL / PERINEPHRIC ABSCESS +EDTA2,2235,RENAL TUBERCULOSIS +EDTA2,2242,LEPTOSPIROSIS +EDTA2,2257,HANTAVIRUS NEPHROPATHY +EDTA2,2261,XANTHOGRANULOMATOUS PYELONEPHRITIS +EDTA2,2274,NEPHROPATHY RELATED TO HIV - NO HISTOLOGY +EDTA2,2288,NEPHROPATHY RELATED TO HIV - HISTOLOGICALLY PROVEN +EDTA2,2290,SCHISTOSOMIASIS +EDTA2,2300,OTHER SPECIFIC INFECTION +EDTA2,2316,DIABETIC NEPHROPATHY IN TYPE I DIABETES - NO HISTOLOGY +EDTA2,2328,DIABETIC NEPHROPATHY IN TYPE I DIABETES - HISTOLOGICALLY PROVEN +EDTA2,2337,DIABETIC NEPHROPATHY IN TYPE II DIABETES - NO HISTOLOGY +EDTA2,2344,DIABETIC NEPHROPATHY IN TYPE II DIABETES - HISTOLOGICALLY PROVEN +EDTA2,2359,CHRONIC HYPERTENSIVE NEPHROPATHY - NO HISTOLOGY +EDTA2,2363,CHRONIC HYPERTENSIVE NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2371,MALIGNANT HYPERTENSIVE NEPHROPATHY / ACCELERATED HYPERTENSIVE NEPHROPATHY - NO HISTOLOGY +EDTA2,2385,MALIGNANT HYPERTENSIVE NEPHROPATHY / ACCELERATED HYPERTENSIVE NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2392,AGEING KIDNEY - NO HISTOLOGY +EDTA2,2407,ISCHAEMIC NEPHROPATHY - NO HISTOLOGY +EDTA2,2411,ISCHAEMIC NEPHROPATHY / MICROVASCULAR DISEASE - HISTOLOGICALLY PROVEN +EDTA2,2424,RENAL ARTERY STENOSIS +EDTA2,2430,ATHEROEMBOLIC RENAL DISEASE - NO HISTOLOGY +EDTA2,2448,ATHEROEMBOLIC RENAL DISEASE - HISTOLOGICALLY PROVEN +EDTA2,2453,FIBROMUSCULAR DYSPLASIA OF RENAL ARTERY +EDTA2,2469,RENAL ARTERIAL THROMBOSIS / OCCLUSION +EDTA2,2476,RENAL VEIN THROMBOSIS +EDTA2,2482,CARDIORENAL SYNDROME +EDTA2,2495,HEPATORENAL SYNDROME +EDTA2,2509,RENAL AMYLOIDOSIS +EDTA2,2513,AA AMYLOID SECONDARY TO CHRONIC INFLAMMATION +EDTA2,2521,AL AMYLOID SECONDARY TO PLASMA CELL DYSCRASIA +EDTA2,2532,FAMILIAL AMYLOID SECONDARY TO PROTEIN MUTATIONS - NO HISTOLOGY +EDTA2,2545,FAMILIAL AMYLOID SECONDARY TO PROTEIN MUTATIONS - HISTOLOGICALLY PROVEN +EDTA2,2550,FAMILIAL AA AMYLOID SECONDARY TO FAMILIAL MEDITERRANEAN FEVER / TRAPS (HIBERNIAN FEVER) - NO HISTOLOGY +EDTA2,2566,FAMILIAL AA AMYLOID SECONDARY TO FAMILIAL MEDITERRANEAN FEVER / TRAPS (HIBERNIAN FEVER) - HISTOLOGICALLY PROVEN +EDTA2,2578,MYELOMA KIDNEY - NO HISTOLOGY +EDTA2,2584,MYELOMA CAST NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2597,LIGHT CHAIN DEPOSITION DISEASE +EDTA2,2606,IMMUNOTACTOID / FIBRILLARY NEPHROPATHY +EDTA2,2610,HAEMOLYTIC URAEMIC SYNDROME (HUS) - DIARRHOEA ASSOCIATED +EDTA2,2623,ATYPICAL HAEMOLYTIC URAEMIC SYNDROME (HUS) - DIARRHOEA NEGATIVE +EDTA2,2634,THROMBOTIC THROMBOCYTOPENIC PURPURA (TTP) +EDTA2,2647,HAEMOLYTIC URAEMIC SYNDROME (HUS) SECONDARY TO SYSTEMIC DISEASE +EDTA2,2652,CONGENITAL HAEMOLYTIC URAEMIC SYNDROME (HUS) +EDTA2,2668,FAMILIAL HAEMOLYTIC URAEMIC SYNDROME (HUS) +EDTA2,2675,FAMILIAL THROMBOTIC THROMBOCYTOPENIC PURPURA (TTP) +EDTA2,2681,NEPHROPATHY DUE TO PRE-ECLAMPSIA / ECLAMPSIA +EDTA2,2699,SICKLE CELL NEPHROPATHY - NO HISTOLOGY +EDTA2,2702,SICKLE CELL NEPHROPATHY - HISTOLOGICALLY PROVEN +EDTA2,2718,AUTOSOMAL DOMINANT (AD) POLYCYSTIC KIDNEY DISEASE +EDTA2,2725,AUTOSOMAL DOMINANT (AD) POLYCYSTIC KIDNEY DISEASE TYPE I +EDTA2,2739,AUTOSOMAL DOMINANT (AD) POLYCYSTIC KIDNEY DISEASE TYPE II +EDTA2,2741,AUTOSOMAL RECESSIVE (AR) POLYCYSTIC KIDNEY DISEASE +EDTA2,2756,ALPORT SYNDROME - NO HISTOLOGY +EDTA2,2760,ALPORT SYNDROME - HISTOLOGICALLY PROVEN +EDTA2,2773,BENIGN FAMILIAL HAEMATURIA +EDTA2,2787,THIN BASEMENT MEMBRANE DISEASE +EDTA2,2794,CYSTIC KIDNEY DISEASE +EDTA2,2804,MEDULLARY CYSTIC KIDNEY DISEASE TYPE I +EDTA2,2815,MEDULLARY CYSTIC KIDNEY DISEASE TYPE II +EDTA2,2827,UROMODULIN-ASSOCIATED NEPHROPATHY (FAMILIAL JUVENILE HYPERURICAEMIC NEPHROPATHY) +EDTA2,2836,NEPHRONOPHTHISIS +EDTA2,2843,NEPHRONOPHTHISIS - TYPE 1 (JUVENILE TYPE) +EDTA2,2858,NEPHRONOPHTHISIS - TYPE 2 (INFANTILE TYPE) +EDTA2,2862,NEPHRONOPHTHISIS - TYPE 3 (ADOLESCENT TYPE) +EDTA2,2870,NEPHRONOPHTHISIS - TYPE 4 (JUVENILE TYPE) +EDTA2,2889,NEPHRONOPHTHISIS - TYPE 5 +EDTA2,2891,NEPHRONOPHTHISIS - TYPE 6 +EDTA2,2901,PRIMARY FANCONI SYNDROME +EDTA2,2917,TUBULAR DISORDER AS PART OF INHERITED METABOLIC DISEASES +EDTA2,2929,DENT DISEASE +EDTA2,2938,LOWE SYNDROME (OCULOCEREBRORENAL SYNDROME) +EDTA2,2940,INHERITED AMINOACIDURIA +EDTA2,2955,CYSTINURIA +EDTA2,2964,CYSTINOSIS +EDTA2,2972,INHERITED RENAL GLYCOSURIA +EDTA2,2986,HYPOPHOSPHATAEMIC RICKETS X-LINKED (XL) +EDTA2,2993,HYPOPHOSPHATAEMIC RICKETS AUTOSOMAL RECESSIVE (AR) +EDTA2,3000,PRIMARY RENAL TUBULAR ACIDOSIS (RTA) +EDTA2,3016,PROXIMAL RENAL TUBULAR ACIDOSIS (RTA) - TYPE II +EDTA2,3028,DISTAL RENAL TUBULAR ACIDOSIS (RTA) - TYPE I +EDTA2,3037,DISTAL RENAL TUBULAR ACIDOSIS WITH SENSORINEURAL DEAFNESS - GENE MUTATIONS +EDTA2,3044,NEPHROGENIC DIABETES INSIPIDUS +EDTA2,3059,LESCH NYHAN SYNDROME - HYPOXANTHINE GUANINE PHOSPHORIBOSYL TRANSFERASE DEFICIENCY +EDTA2,3063,PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE (PRPPS) SUPERACTIVITY +EDTA2,3071,ALAGILLE SYNDROME +EDTA2,3085,BARTTER SYNDROME +EDTA2,3092,GITELMAN SYNDROME +EDTA2,3102,LIDDLE SYNDROME +EDTA2,3118,APPARENT MINERALOCORTICOID EXCESS +EDTA2,3125,GLUCOCORTICOID SUPPRESSIBLE HYPERALDOSTERONISM +EDTA2,3139,INHERITED / GENETIC DIABETES MELLITUS TYPE II +EDTA2,3141,PSEUDOHYPOALDOSTERONISM TYPE 1 +EDTA2,3156,PSEUDOHYPOALDOSTERONISM TYPE 2 (GORDON SYNDROME) +EDTA2,3160,FAMILIAL HYPOCALCIURIC HYPERCALCAEMIA +EDTA2,3173,FAMILIAL HYPERCALCIURIC HYPOCALCAEMIA +EDTA2,3187,FAMILIAL HYPOMAGNESAEMIA +EDTA2,3194,PRIMARY HYPEROXALURIA +EDTA2,3207,PRIMARY HYPEROXALURIA TYPE I +EDTA2,3211,PRIMARY HYPEROXALURIA TYPE II +EDTA2,3224,FABRY DISEASE - NO HISTOLOGY +EDTA2,3230,FABRY DISEASE - HISTOLOGICALLY PROVEN +EDTA2,3248,XANTHINURIA +EDTA2,3253,NAIL-PATELLA SYNDROME +EDTA2,3269,RUBINSTEIN-TAYBI SYNDROME +EDTA2,3276,TUBEROUS SCLEROSIS +EDTA2,3282,VON HIPPEL-LINDAU DISEASE +EDTA2,3295,MEDULLARY SPONGE KIDNEYS +EDTA2,3305,HORSE-SHOE KIDNEY +EDTA2,3314,FRASIER SYNDROME +EDTA2,3322,BRANCHIO-OTO-RENAL SYNDROME +EDTA2,3333,WILLIAMS SYNDROME +EDTA2,3346,TOWNES-BROCKS SYNDROME +EDTA2,3351,LAWRENCE-MOON-BIEDL / BARDET-BIEDL SYNDROME +EDTA2,3367,MITOCHONDRIAL CYTOPATHY +EDTA2,3379,FAMILIAL NEPHROPATHY +EDTA2,3380,ACUTE KIDNEY INJURY +EDTA2,3398,ACUTE KIDNEY INJURY DUE TO HYPOVOLAEMIA +EDTA2,3403,ACUTE KIDNEY INJURY DUE TO CIRCULATORY FAILURE +EDTA2,3419,ACUTE KIDNEY INJURY DUE TO SEPSIS +EDTA2,3426,ACUTE KIDNEY INJURY DUE TO RHABDOMYOLYSIS +EDTA2,3435,ACUTE KIDNEY INJURY DUE TO NEPHROTOXICITY +EDTA2,3442,ACUTE CORTICAL NECROSIS +EDTA2,3457,ACUTE PYELONEPHRITIS +EDTA2,3461,KIDNEY TUMOUR +EDTA2,3474,RENAL CELL CARCINOMA - HISTOLOGICALLY PROVEN +EDTA2,3488,TRANSITIONAL CELL CARCINOMA - HISTOLOGICALLY PROVEN +EDTA2,3490,WILMS TUMOUR - HISTOLOGICALLY PROVEN +EDTA2,3501,MESOBLASTIC NEPHROMA - HISTOLOGICALLY PROVEN +EDTA2,3517,SINGLE KIDNEY IDENTIFIED IN ADULTHOOD +EDTA2,3529,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) CAUSED BY TUMOUR NEPHRECTOMY +EDTA2,3538,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) DUE TO TRAUMATIC LOSS OF KIDNEY +EDTA2,3540,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) DUE TO DONOR NEPHRECTOMY +EDTA2,3555,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) - AETIOLOGY UNCERTAIN / UNKNOWN - NO HISTOLOGY +EDTA2,3564,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) - AETIOLOGY UNCERTAIN / UNKNOWN - HISTOLOGICALLY PROVEN +EDTA2,3572,HAEMATURIA AND PROTEINURIA - NO HISTOLOGY +EDTA2,3604,NEPHROTIC SYNDROME OF CHILDHOOD - STEROID RESISTANT - NO HISTOLOGY +EDTA2,3615,NEPHROTIC SYNDROME OF CHILDHOOD - NO TRIAL OF STEROIDS - NO HISTOLOGY +EDTA2,3627,RENAL CYSTS AND DIABETES SYNDROME +EDTA2,3636,CHRONIC URATE NEPHROPATHY - NO HISTOLOGY +EDTA2,3643,CHRONIC RENAL FAILURE DUE TO SYSTEMIC INFECTION +EDTA2,3658,RENAL COLOBOMA SYNDROME +EDTA2,3662,HYPERCALCAEMIC NEPHROPATHY +EDTA2,3670,RETROPERITONEAL FIBROSIS SECONDARY TO PERI-AORTITIS +EDTA2,3689,RETROPERITONEAL FIBROSIS SECONDARY TO DRUGS +EDTA2,3691,RENAL FAILURE +EDTA2,3708,CHRONIC RENAL FAILURE +EDTA2,3712,ISOLATED HAEMATURIA - NO HISTOLOGY +EDTA2,3720,ISOLATED PROTEINURIA - NO HISTOLOGY +EDTA2,3731,PRIMARY HYPEROXALURIA TYPE III +EDTA2,3749,GLOMERULONEPHRITIS - NO HISTOLOGY diff --git a/codes/code_lists/loinc_observations.csv b/codes/code_lists/loinc_observations.csv new file mode 100644 index 0000000..57933d3 --- /dev/null +++ b/codes/code_lists/loinc_observations.csv @@ -0,0 +1,86 @@ +LOINC,32294-1,Albumin:creatinine ratio,result,mg/mmol +LOINC,19072-8,Adjusted Calcium,result,mmol/L +LOINC,1751-7,Albumin,result,g/L +LOINC,6768-6,AlkP,result,U/L +LOINC,1742-6,ALT,result,U/L +LOINC,1798-8,Amylase,result,U/L +LOINC,1920-8,AST,result,U/L +LOINC,14631-6,Bilirubin,result,umol/L +LOINC,1996-8,Calcium,result,mmol/L +LOINC,14647-2,Cholesterol,result,mmol/L +LOINC,14682-9,Creatinine,result,umol/L +LOINC,1988-5,C-reactive Protein,result,mg/L +LOINC,69405-9,eGFR,result,mL/min/1.73m2 +LOINC,77147-7,eGFR (MDRD),result,mL/min/1.73m2 +LOINC,2276-4,Ferritin,result,ng/mL or ug/L +LOINC,14928-6,Free T3,result,pmol/L +LOINC,14920-3,Free T4,result,pmol/L +LOINC,2324-2,GGT,result,U/L +LOINC,14749-6,glucose,result,mmol/L +LOINC,718-7,hb,result,g/L +LOINC,59261-8,hba1c,result,mmol/mol +LOINC,13952-7,hbv,result, +LOINC,1959-6,hco3,result,mmol/L +LOINC,4544-3,hct,result,% +LOINC,16128-1,Hepatitis C Antibody,result, +LOINC,14646-4,HDL,result,mmol/L +LOINC,6301-6,INR,result, +LOINC,14798-3,Iron,result,umol/L +LOINC,2502-3,Iron Saturation,result,% +LOINC,70961-8,Kt/V,result, +LOINC,2532-0,LDH,result,U/L +LOINC,39469-2,LDL,result,mmol/L +LOINC,44915-7,LDL:HDL Ratio,result, +LOINC,3040-3,Lipase,result,U/L +LOINC,14334-7,Lithium Level,result,mmol/L +LOINC,2601-3,Magnesium,result,mmol/L +LOINC,751-8,Neutrophils,result,billion/L or 10^9/L +LOINC,34366-5,Protein Creatinine Ratio,result,mg/mmol +LOINC,14879-1,Phosphate,result,mmol/L +LOINC,777-3,Platelets,result,10^9/L +LOINC,2823-3,Potassium,result,mmol/L +LOINC,2857-1,Prostate Specific Antigen,result,ng/mL +LOINC,14866-8,Parathyroid Hormone,result,pmol/L +LOINC,42810-2,Reticulocyte Haemoglobin,result,pg +LOINC,2951-2,Sodium,result,mmol/L +LOINC,3024-7,Total Thyroxine,result,ng/L +LOINC,11253-2,Tacrolimus,result,ng/mL +LOINC,2986-8,Testosterone,result,ng/dL +LOINC,2571-8,Triglycerides,result,mg/dL +LOINC,91141-2,TPMT,result,mU/L +LOINC,3034-6,Transferrin,result,mg/dL +LOINC,6598-7,Troponin-T,result,ng/mL +LOINC,3016-3,Thyroid stimulating hormone,result,mU/L +LOINC,6942-7,Urine Albumin,result,mg/L +LOINC,14683-7,Urine Creatinine,result,mmol/L +LOINC,2888-6,Urine Protein,result,mmol/L +LOINC,14933-6,Urate,result,mmol/L +LOINC,14937-7,Urea,result,mmol/L +LOINC,54456-9,URR,result, +LOINC,2132-9,Vitamin B12,result,ng/L or pg/mL +LOINC,46269-7,Vitamin D,result,nmol/L +LOINC,6690-2,White Blood Cell Count,result,billion/L or 10^9/L +LOINC,29247-4,Sirolimus,result,ng/mL +LOINC,51620-3,Creatinine (Post-Dialysis),result,mmol/L +LOINC,39776-0,Urea (Post-Dialysis),result,mmol/L +LOINC,29349-8,Potassium (Post-Dialysis),result,mmol/L +LOINC,74688-3,Sodium (Post-Dialysis),result,mmol/L +LOINC,48631-6,hco3 (Post-Dialysis),result,mmol/L +LOINC,2284-8,Serum Folate,result,ng/mL +LOINC,34381-4,TGN,result,ng/mL +LOINC,90294-0,MMP,result,U/mL +LOINC,4548-4,hba1c,result,% +LOINC,38445-3,Faecal Calprotectin,result,ug/g +LOINC,95209-3,Covid-19 Lateral Flow Test,result, +LOINC,95542-7,Covid-19 Antibody Test,result, +LOINC,94500-6,Covid-19 PCR Test,result, +LOINC,732-8,ALC,result,10^3/uL +LOINC,76069-4,Hypochromic Red Cells,result,% +LOINC,59467-1,MCH,result,mmol/L +LOINC,2283-0,Red Cell Folate,result,ng/mL +LOINC,29265-6,Corrected Calcium,result,mmol/L +LOINC,69949-6,EBV Status,result, +LOINC,56888-1,HIV Antigen,result, +LOINC,55972-4,Phosphate (Post),result,mmol/L +LOINC,59148-7,Calcium (Post),result,mmol/L +LOINC,3520-4,Ciclosporin,result,ng/mL diff --git a/codes/code_lists/nhs_data_dictionary_employment_status.csv b/codes/code_lists/nhs_data_dictionary_employment_status.csv new file mode 100644 index 0000000..13dd608 --- /dev/null +++ b/codes/code_lists/nhs_data_dictionary_employment_status.csv @@ -0,0 +1,9 @@ +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,01,Employed +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,02,Unemployed and actively seeking work +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,03,Undertaking full (at least 16 hours per week) or part-time (less than 16 hours per week) education or training as a student and not working or actively seeking work +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,04,Long-term sick or disabled, those receiving government sickness and disability benefits +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,05,Looking after the family or home as a homemaker and not working or actively seeking work +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,06,Not receiving government sickness and disability benefits and not working or actively seeking work +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,07,Unpaid voluntary work and not working or actively seeking work +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,08,Retired +NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,ZZ,Not Stated (PERSON asked but declined to provide a response) diff --git a/codes/code_lists/nhs_data_dictionary_ethnicity.csv b/codes/code_lists/nhs_data_dictionary_ethnicity.csv new file mode 100644 index 0000000..aa62e0f --- /dev/null +++ b/codes/code_lists/nhs_data_dictionary_ethnicity.csv @@ -0,0 +1,17 @@ +NHS_DATA_DICTIONARY,A,British, +NHS_DATA_DICTIONARY,B,Irish, +NHS_DATA_DICTIONARY,C,Any other White Background, +NHS_DATA_DICTIONARY,D,White and Black Caribbean, +NHS_DATA_DICTIONARY,E,White and Black African, +NHS_DATA_DICTIONARY,F,White and Asian, +NHS_DATA_DICTIONARY,G,Any other mixed background, +NHS_DATA_DICTIONARY,H,Indian, +NHS_DATA_DICTIONARY,J,Pakistani, +NHS_DATA_DICTIONARY,K,Bangladeshi, +NHS_DATA_DICTIONARY,L,Any other Asian background, +NHS_DATA_DICTIONARY,M,Caribbean, +NHS_DATA_DICTIONARY,N,African, +NHS_DATA_DICTIONARY,P,Any other black background, +NHS_DATA_DICTIONARY,R,Chinese, +NHS_DATA_DICTIONARY,S,Any other ethnic group, +NHS_DATA_DICTIONARY,Z,Not stated, diff --git a/codes/code_lists/nhs_data_dictionary_language_code.csv b/codes/code_lists/nhs_data_dictionary_language_code.csv new file mode 100644 index 0000000..5de20f8 --- /dev/null +++ b/codes/code_lists/nhs_data_dictionary_language_code.csv @@ -0,0 +1,184 @@ +NHS_DATA_DICTIONARY_LANGUAGE_CODE,aa,Afar +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ab,Abkhazian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ae,Avestan +NHS_DATA_DICTIONARY_LANGUAGE_CODE,af,Afrikaans +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ak,Akan +NHS_DATA_DICTIONARY_LANGUAGE_CODE,am,Amharic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,an,Aragonese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ar,Arabic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,as,Assamese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,av,Avaric +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ay,Aymara +NHS_DATA_DICTIONARY_LANGUAGE_CODE,az,Azerbaijani +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ba,Bashkir +NHS_DATA_DICTIONARY_LANGUAGE_CODE,be,Belarusian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bg,Bulgarian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bh,Bihari languages +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bi,Bislama +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bm,Bambara +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bn,Bengali +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bo,Tibetan +NHS_DATA_DICTIONARY_LANGUAGE_CODE,br,Breton +NHS_DATA_DICTIONARY_LANGUAGE_CODE,bs,Bosnian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ca,Catalan; Valencian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ce,Chechen +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ch,Chamorro +NHS_DATA_DICTIONARY_LANGUAGE_CODE,co,Corsican +NHS_DATA_DICTIONARY_LANGUAGE_CODE,cr,Cree +NHS_DATA_DICTIONARY_LANGUAGE_CODE,cs,Czech +NHS_DATA_DICTIONARY_LANGUAGE_CODE,cu,Church Slavic; Old Slavonic; Church Slavonic; Old Bulgarian; Old Church Slavonic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,cv,Chuvash +NHS_DATA_DICTIONARY_LANGUAGE_CODE,cy,Welsh +NHS_DATA_DICTIONARY_LANGUAGE_CODE,da,Danish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,de,German +NHS_DATA_DICTIONARY_LANGUAGE_CODE,dv,Divehi; Dhivehi; Maldivian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,dz,Dzongkha +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ee,Ewe +NHS_DATA_DICTIONARY_LANGUAGE_CODE,el,"Greek, Modern (1453-)" +NHS_DATA_DICTIONARY_LANGUAGE_CODE,en,English +NHS_DATA_DICTIONARY_LANGUAGE_CODE,eo,Esperanto +NHS_DATA_DICTIONARY_LANGUAGE_CODE,es,Spanish; Castilian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,et,Estonian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,eu,Basque +NHS_DATA_DICTIONARY_LANGUAGE_CODE,fa,Persian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ff,Fulah +NHS_DATA_DICTIONARY_LANGUAGE_CODE,fi,Finnish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,fj,Fijian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,fo,Faroese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,fr,French +NHS_DATA_DICTIONARY_LANGUAGE_CODE,fy,Western Frisian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ga,Irish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,gd,Gaelic; Scottish Gaelic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,gl,Galician +NHS_DATA_DICTIONARY_LANGUAGE_CODE,gn,Guarani +NHS_DATA_DICTIONARY_LANGUAGE_CODE,gu,Gujarati +NHS_DATA_DICTIONARY_LANGUAGE_CODE,gv,Manx +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ha,Hausa +NHS_DATA_DICTIONARY_LANGUAGE_CODE,he,Hebrew +NHS_DATA_DICTIONARY_LANGUAGE_CODE,hi,Hindi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ho,Hiri Motu +NHS_DATA_DICTIONARY_LANGUAGE_CODE,hr,Croatian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ht,Haitian; Haitian Creole +NHS_DATA_DICTIONARY_LANGUAGE_CODE,hu,Hungarian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,hy,Armenian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,hz,Herero +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ia,Interlingua (International Auxiliary Language Association) +NHS_DATA_DICTIONARY_LANGUAGE_CODE,id,Indonesian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ie,Interlingue; Occidental +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ig,Igbo +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ii,Sichuan Yi; Nuosu +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ik,Inupiaq +NHS_DATA_DICTIONARY_LANGUAGE_CODE,io,Ido +NHS_DATA_DICTIONARY_LANGUAGE_CODE,is,Icelandic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,it,Italian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,iu,Inuktitut +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ja,Japanese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,jv,Javanese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ka,Georgian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kg,Kongo +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ki,Kikuyu; Gikuyu +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kj,Kuanyama; Kwanyama +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kk,Kazakh +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kl,Kalaallisut; Greenlandic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,km,Central Khmer +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kn,Kannada +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ko,Korean +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kr,Kanuri +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ks,Kashmiri +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ku,Kurdish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kv,Komi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,kw,Cornish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ky,Kirghiz; Kyrgyz +NHS_DATA_DICTIONARY_LANGUAGE_CODE,la,Latin +NHS_DATA_DICTIONARY_LANGUAGE_CODE,lb,Luxembourgish; Letzeburgesch +NHS_DATA_DICTIONARY_LANGUAGE_CODE,lg,Ganda +NHS_DATA_DICTIONARY_LANGUAGE_CODE,li,Limburgan; Limburger; Limburgish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ln,Lingala +NHS_DATA_DICTIONARY_LANGUAGE_CODE,lo,Lao +NHS_DATA_DICTIONARY_LANGUAGE_CODE,lt,Lithuanian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,lu,Luba-Katanga +NHS_DATA_DICTIONARY_LANGUAGE_CODE,lv,Latvian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mg,Malagasy +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mh,Marshallese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mi,Maori +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mk,Macedonian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ml,Malayalam +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mn,Mongolian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mr,Marathi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ms,Malay +NHS_DATA_DICTIONARY_LANGUAGE_CODE,mt,Maltese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,my,Burmese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,na,Nauru +NHS_DATA_DICTIONARY_LANGUAGE_CODE,nb,"Bokmål, Norwegian; Norwegian Bokmål" +NHS_DATA_DICTIONARY_LANGUAGE_CODE,nd,"Ndebele, North; North Ndebele" +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ne,Nepali +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ng,Ndonga +NHS_DATA_DICTIONARY_LANGUAGE_CODE,nl,Dutch; Flemish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,nn,"Norwegian Nynorsk; Nynorsk, Norwegian" +NHS_DATA_DICTIONARY_LANGUAGE_CODE,no,Norwegian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,nr,"Ndebele, South; South Ndebele" +NHS_DATA_DICTIONARY_LANGUAGE_CODE,nv,Navajo; Navaho +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ny,Chichewa; Chewa; Nyanja +NHS_DATA_DICTIONARY_LANGUAGE_CODE,oc,Occitan (post 1500) +NHS_DATA_DICTIONARY_LANGUAGE_CODE,oj,Ojibwa +NHS_DATA_DICTIONARY_LANGUAGE_CODE,om,Oromo +NHS_DATA_DICTIONARY_LANGUAGE_CODE,or,Oriya +NHS_DATA_DICTIONARY_LANGUAGE_CODE,os,Ossetian; Ossetic +NHS_DATA_DICTIONARY_LANGUAGE_CODE,pa,Panjabi; Punjabi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,pi,Pali +NHS_DATA_DICTIONARY_LANGUAGE_CODE,pl,Polish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ps,Pushto; Pashto +NHS_DATA_DICTIONARY_LANGUAGE_CODE,pt,Portuguese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,qu,Quechua +NHS_DATA_DICTIONARY_LANGUAGE_CODE,rm,Romansh +NHS_DATA_DICTIONARY_LANGUAGE_CODE,rn,Rundi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ro,Romanian; Moldavian; Moldovan +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ru,Russian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,rw,Kinyarwanda +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sa,Sanskrit +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sc,Sardinian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sd,Sindhi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,se,Northern Sami +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sg,Sango +NHS_DATA_DICTIONARY_LANGUAGE_CODE,si,Sinhala; Sinhalese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sk,Slovak +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sl,Slovenian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sm,Samoan +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sn,Shona +NHS_DATA_DICTIONARY_LANGUAGE_CODE,so,Somali +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sq,Albanian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sr,Serbian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ss,Swati +NHS_DATA_DICTIONARY_LANGUAGE_CODE,st,"Sotho, Southern" +NHS_DATA_DICTIONARY_LANGUAGE_CODE,su,Sundanese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sv,Swedish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,sw,Swahili +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ta,Tamil +NHS_DATA_DICTIONARY_LANGUAGE_CODE,te,Telugu +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tg,Tajik +NHS_DATA_DICTIONARY_LANGUAGE_CODE,th,Thai +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ti,Tigrinya +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tk,Turkmen +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tl,Tagalog +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tn,Tswana +NHS_DATA_DICTIONARY_LANGUAGE_CODE,to,Tonga (Tonga Islands) +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tr,Turkish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ts,Tsonga +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tt,Tatar +NHS_DATA_DICTIONARY_LANGUAGE_CODE,tw,Twi +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ty,Tahitian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ug,Uighur; Uyghur +NHS_DATA_DICTIONARY_LANGUAGE_CODE,uk,Ukrainian +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ur,Urdu +NHS_DATA_DICTIONARY_LANGUAGE_CODE,uz,Uzbek +NHS_DATA_DICTIONARY_LANGUAGE_CODE,ve,Venda +NHS_DATA_DICTIONARY_LANGUAGE_CODE,vi,Vietnamese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,vo,Volapük +NHS_DATA_DICTIONARY_LANGUAGE_CODE,wa,Walloon +NHS_DATA_DICTIONARY_LANGUAGE_CODE,wo,Wolof +NHS_DATA_DICTIONARY_LANGUAGE_CODE,xh,Xhosa +NHS_DATA_DICTIONARY_LANGUAGE_CODE,yi,Yiddish +NHS_DATA_DICTIONARY_LANGUAGE_CODE,yo,Yoruba +NHS_DATA_DICTIONARY_LANGUAGE_CODE,za,Zhuang; Chuang +NHS_DATA_DICTIONARY_LANGUAGE_CODE,zh,Chinese +NHS_DATA_DICTIONARY_LANGUAGE_CODE,zu,Zulu diff --git a/codes/code_lists/pv_admit_reason.csv b/codes/code_lists/pv_admit_reason.csv new file mode 100644 index 0000000..a053310 --- /dev/null +++ b/codes/code_lists/pv_admit_reason.csv @@ -0,0 +1,2 @@ +PV,INS_HOSPITALISATION +PV,INS_RELAPSE \ No newline at end of file diff --git a/codes/code_lists/pv_groups.csv b/codes/code_lists/pv_groups.csv new file mode 100644 index 0000000..53a3699 --- /dev/null +++ b/codes/code_lists/pv_groups.csv @@ -0,0 +1,175 @@ +PV,AAHF1,A&A Heart,,,,,,,,,,,,,,, +PV,SNC01,Aberdeen Royal,,,,,,,,,,,,,,, +PV,AHUS,AHUS,,,,,,,,,,,,,,, +PV,RW402,Aintree Hospital,,,,,,,,,,,,,,, +PV,9RW402,Aintree-FDU,,,,,,,,,,,,,,, +PV,RW402H,Aintree-HomeD,,,,,,,,,,,,,,, +PV,SLC01,Airdrie,,,,,,,,,,,,,,, +PV,ALPORT,Alport,,,,,,,,,,,,,,, +PV,45020,Altnagelvin,,,,,,,,,,,,,,, +PV,RM403,Altrincham,,,,,,,,,,,,,,, +PV,24027,Antrim,,,,,,,,,,,,,,, +PV,APRT,APRT Def,,,,,,,,,,,,,,, +PV,ARPKD,ARPKD,,,,,,,,,,,,,,, +PV,RQBAU,Bangor,,,,,,,,,,,,,,, +PV,RFRAA,Barnsley,,,,,,,,,,,,,,, +PV,RDDH0,Basildon,,,,,,,,,,,,,,, +PV,RCD37,Bath,,,,,,,,,,,,,,, +PV,RD1,Bath - Royal United,,,,,,,,,,,,,,, +PV,9RFU,Bedford,,,,,,,,,,,,,,, +PV,9RQR13,Beeston,,,,,,,,,,,,,,, +PV,11023,Belfast - Paeds,,,,,,,,,,,,,,, +PV,2020,Belfast City,,,,,,,,,,,,,,, +PV,7021,Belfast-Ulster Hosp,,,,,,,,,,,,,,, +PV,RQ3,B'Ham - Paeds,,,,,,,,,,,,,,, +PV,RL7,B'Ham-Heartlands,,,,,,,,,,,,,,, +PV,RRK02,B'Ham-QEH,,,,,,,,,,,,,,, +PV,RBL14,Birkenhead-Arrowe Pk,,,,,,,,,,,,,,, +PV,RKGA1,Bodlewyddan - Glan C,,,,,,,,,,,,,,, +PV,RMC00,Bolton,,,,,,,,,,,,,,, +PV,RAE05,Bradford,,,,,,,,,,,,,,, +PV,RGU01,Brighton,,,,,,,,,,,,,,, +PV,REE01,Bristol,,,,,,,,,,,,,,, +PV,RA723,Bristol-Childrens,,,,,,,,,,,,,,, +PV,CAIRO,Cairo,,,,,,,,,,,,,,, +PV,RGT01,Cambridge,,,,,,,,,,,,,,, +PV,RRE14,Cannock,,,,,,,,,,,,,,, +PV,RRBBV,Cardiff,,,,,,,,,,,,,,, +PV,RLGAY,Carlisle,,,,,,,,,,,,,,, +PV,RAZ,Carshalton-St Helier,,,,,,,,,,,,,,, +PV,9RJH01,Castle Vale,,,,,,,,,,,,,,, +PV,CCL,CCL,,,,,,,,,,,,,,, +PV,9RCSLB,Centenary Wing Dialy,,,,,,,,,,,,,,, +PV,RQ8L0,Chelmsford,,,,,,,,,,,,,,, +PV,RJR05,Chester,,,,,,,,,,,,,,, +PV,CHI,CHI,,,,,,,,,,,,,,, +PV,RBL20,Clatterbridge-satell,,,,,,,,,,,,,,, +PV,RDEE4,Colchester,,,,,,,,,,,,,,, +PV,9RVJ21,Cossham,,,,,,,,,,,,,,, +PV,RKB01,Coventry,,,,,,,,,,,,,,, +PV,CYSTIN,CYSTIN,,,,,,,,,,,,,,, +PV,CYSURIA,Cysuria,,,,,,,,,,,,,,, +PV,DEMO,Demonstration,,,,,,,,,,,,,,, +PV,DENTLOWE,Dent and Lowe,,,,,,,,,,,,,,, +PV,RFPFG,Derby,,,,,,,,,,,,,,, +PV,RMW10,Dewsbury,,,,,,,,,,,,,,, +PV,Diabetes,Diabetes,,,,,,,,,,,,,,, +PV,RP5,Doncaster,,,,,,,,,,,,,,, +PV,RBD01,Dorchester,,,,,,,,,,,,,,, +PV,RR9,Dryburn,,,,,,,,,,,,,,, +PV,RNA03,Dudley,,,,,,,,,,,,,,, +PV,SYC01,Dumfries,,,,,,,,,,,,,,, +PV,DUMMY,Dummy,,,,,,,,,,,,,,, +PV,STC01,Dundee,,,,,,,,,,,,,,, +PV,RCB23,Easingwold,,,,,,,,,,,,,,, +PV,ECS,ECS,,,,,,,,,,,,,,, +PV,RSC02,Edin,,,,,,,,,,,,,,, +PV,EDINHF1,Edin Heart,,,,,,,,,,,,,,, +PV,RH8,Exeter,,,,,,,,,,,,,,, +PV,SFC01,Fife,,,,,,,,,,,,,,, +PV,FUAN,FUAN,,,,,,,,,,,,,,, +PV,Generic,Generic,,,,,,,,,,,,,,, +PV,GGCHF1,GG&C Heart,,,,,,,,,,,,,,, +PV,SGC02,Glasgow Children's,,,,,,,,,,,,,,, +PV,SGC05,Glasgow QEUH,,,,,,,,,,,,,,, +PV,SGC04,Glasgow Renal,,,,,,,,,,,,,,, +PV,RH641,Gloucester,,,,,,,,,,,,,,, +PV,RBN63,Halton_Satellite,,,,,,,,,,,,,,, +PV,RQW,Harlow,,,,,,,,,,,,,,, +PV,RCD35,Harogate,,,,,,,,,,,,,,, +PV,Cardiol,Heart failure,,,,,,,,,,,,,,, +PV,9RK7CC,Heely,,,,,,,,,,,,,,, +PV,HNF1B,HNF1B,,,,,,,,,,,,,,, +PV,RGB04,Huddersfield,,,,,,,,,,,,,,, +PV,RF201,Hull,,,,,,,,,,,,,,, +PV,HYPERRDG,HY_OXALURIA,,,,,,,,,,,,,,, +PV,IBD,IBD,,,,,,,,,,,,,,, +PV,RXM56,Ilkeston,,,,,,,,,,,,,,, +PV,NEWDEHLI,INDIA New Dehli,,,,,,,,,,,,,,, +PV,BANGALORE,INDIA-Bangalore,,,,,,,,,,,,,,, +PV,VELLORE,INDIA-Vellore,,,,,,,,,,,,,,, +PV,SHC01,Inverness,,,,,,,,,,,,,,, +PV,RGQ02,Ipswich,,,,,,,,,,,,,,, +PV,TEHRAN,IRAN-Tehran,,,,,,,,,,,,,,, +PV,GUNMA,Japan - GUNMA,,,,,,,,,,,,,,, +PV,RVVKC,Kent,,,,,,,,,,,,,,, +PV,SAC02,Kilmarnock,,,,,,,,,,,,,,, +PV,RFJBC,King's Mill,,,,,,,,,,,,,,, +PV,RQS01,Leeds Infirmary,,,,,,,,,,,,,,, +PV,99RQR13,Leeds -Paeds,,,,,,,,,,,,,,, +PV,RQR00,Leeds- St James's,,,,,,,,,,,,,,, +PV,RFBAK,Leicester,,,,,,,,,,,,,,, +PV,RNG10,Lichfield,,,,,,,,,,,,,,, +PV,RBS25,Liverpool-A Hey,,,,,,,,,,,,,,, +PV,RQ601,Liverpool-Broadgreen,,,,,,,,,,,,,,, +PV,RQ617,Liverpool-Royal,,,,,,,,,,,,,,, +PV,RJZ,London - Kings,,,,,,,,,,,,,,, +PV,R1H00,London-Barts,,,,,,,,,,,,,,, +PV,RP4,London-GOSH,,,,,,,,,,,,,,, +PV,RJ100,London-Guys+Tommys,,,,,,,,,,,,,,, +PV,RAL01,London-Royal Free,,,,,,,,,,,,,,, +PV,RJ701,London-St George's,,,,,,,,,,,,,,, +PV,RQN02,London-West,,,,,,,,,,,,,,, +PV,RC971,Luton & Dunstable,,,,,,,,,,,,,,, +PV,RW3RM,Manchester Childrens,,,,,,,,,,,,,,, +PV,RM574,Manchester Royal I,,,,,,,,,,,,,,, +PV,MEMRDG,MEMRDG,,,,,,,,,,,,,,, +PV,RCJAT,Middlesbrough-J-Cook,,,,,,,,,,,,,,, +PV,MPGN,MPGN,,,,,,,,,,,,,,, +PV,8RJ121,New Cross Gate,,,,,,,,,,,,,,, +PV,RTD01,Newcastle,,,,,,,,,,,,,,, +PV,33020,Newry-Daisy Hill,,,,,,,,,,,,,,, +PV,RM102,Norfolk Norwich,,,,,,,,,,,,,,, +PV,RX1CC,Nottingham,,,,,,,,,,,,,,, +PV,99RCSLB,Nottingham -Paeds,,,,,,,,,,,,,,, +PV,48021,Omagh-Tyrone,,,,,,,,,,,,,,, +PV,RNX02,Oxford,,,,,,,,,,,,,,, +PV,PATIENT_ENTERED,Patient Entered,,,,,,,,,,,,,,, +PV,PV_SUP,PatientView Support,,,,,,,,,,,,,,, +PV,RK950,Plymouth,,,,,,,,,,,,,,, +PV,RXF03,Pontefract,,,,,,,,,,,,,,, +PV,RHU02,Portsmouth-Q-Alex,,,,,,,,,,,,,,, +PV,OBS,Pregnancy,,,,,,,,,,,,,,, +PV,RMF01,Preston,,,,,,,,,,,,,,, +PV,PRESR1,PRESTON_RES_GP1,,,,,,,,,,,,,,, +PV,RHW01,Reading,,,,,,,,,,,,,,, +PV,REDCAPLASIA,RedCAplasia,,,,,,,,,,,,,,, +PV,Renal,Renal,,,,,,,,,,,,,,, +PV,RENALREG,Renal Registry,,,,,,,,,,,,,,, +PV,RFRPA,Rotherham,,,,,,,,,,,,,,, +PV,SALIBD,Salford IBD,,,,,,,,,,,,,,, +PV,RM301,Salford Royal,,,,,,,,,,,,,,, +PV,DSF01,Salford_Diabetes,,,,,,,,,,,,,,, +PV,HYPALK,Salt Wasting,,,,,,,,,,,,,,, +PV,9RQR14,Seacroft,,,,,,,,,,,,,,, +PV,RK7CC,Sheffield,,,,,,,,,,,,,,, +PV,RLZ01,Shrewsbury,,,,,,,,,,,,,,, +PV,RL301,Solihull,,,,,,,,,,,,,,, +PV,99RHM01,Southampton-Paed,,,,,,,,,,,,,,, +PV,RAJ01,Southend,,,,,,,,,,,,,,, +PV,RVY01,Southport,,,,,,,,,,,,,,, +PV,SRNS,SRNS,,,,,,,,,,,,,,, +PV,9RBN01,St Helens_Satellite,,,,,,,,,,,,,,, +PV,STAFF_ENTERED,Staff Entered,,,,,,,,,,,,,,, +PV,STECHUS,STECHUS,,,,,,,,,,,,,,, +PV,RAQ01,Stevenage-Lister,,,,,,,,,,,,,,, +PV,9RWJ,Stockport,,,,,,,,,,,,,,, +PV,RJE01,Stoke,,,,,,,,,,,,,,, +PV,RLNGH,Sunderland,,,,,,,,,,,,,,, +PV,RQHC7,Swansea,,,,,,,,,,,,,,, +PV,RMP01,Tameside,,,,,,,,,,,,,,, +PV,REF12,Truro -Treliske,,,,,,,,,,,,,,, +PV,UNKNOWNTESTGROUP,Unknown,,,,,,,,,,,,,,, +PV,VASRDG,VASRDG,,,,,,,,,,,,,,, +PV,9RBK,Walsall Renal Unit,,,,,,,,,,,,,,, +PV,RKC81,Warrington,,,,,,,,,,,,,,, +PV,9RLNGH,Washington,,,,,,,,,,,,,,, +PV,REM26,Waterloo_Satellite,,,,,,,,,,,,,,, +PV,9RM301,Wigan,,,,,,,,,,,,,,, +PV,RL403,Wolverhampton,,,,,,,,,,,,,,, +PV,RKHA4,Wrexham,,,,,,,,,,,,,,, +PV,RCB55,York,,,,,,,,,,,,,,, +PV,PV,PatientView System +PV,INS_WEB,INS Website +PV,INS_APP,INS App +PV,NHSWLS,NHS Wales \ No newline at end of file diff --git a/codes/code_lists/pv_observations.csv b/codes/code_lists/pv_observations.csv new file mode 100644 index 0000000..c39ca10 --- /dev/null +++ b/codes/code_lists/pv_observations.csv @@ -0,0 +1,92 @@ +PV,BodyTemperature,Body Temperature,obs +PV,FaecalCalprotectin,Faecal Calprotectin,result,ug/g +PV,TargetWeight,Target Weight,obs +PV,acr,ACR,result,mg/mmol +PV,adjustedcalcium,Adjusted Calcium,result,mmol/L +PV,albumin,Albumin,result,g/L +PV,albumin_post,Albumin (Post),result,g/L +PV,alp,AlkP,result,U/L +PV,alt,ALT,result,U/L +PV,amy,Amylase,result,U/L +PV,ast,AST,result,U/L +PV,bili,Bili,result,umol/L +PV,bmi,BMI,obs, +PV,bpdia,BP Diastolic,obs,mm Hg +PV,bpsys,BP Systolic,obs,mm Hg +PV,calcium,Calcium,result,mmol/l +PV,calcium_post,Calcium (Post),result +PV,cholesterol,Cholesterol,result,mmol/l +PV,ciclosporin,Ciclosporin,result,ng/ml +PV,covid19antibody,Covid-19 Antibody,result +PV,covid19lflow,Covid-19 Lateral Flow,result +PV,covid19pcr,Covid-19 PCR,result +PV,creatinine,Creatinine,result,umol/l +PV,creatinine_post,Creatinine (Post),result +PV,crp,CRP,result,mg/l +PV,egfr,eGFR,result,mL/min/1.73m^2 +PV,egfr_post,eGFR (Post),result,mL/min/1.73m^2 +PV,ferritin,Ferritin,result,ug/l +PV,folate,Folate,result,ug/l +PV,ft3,Free T3,result,pmol/l +PV,ft4,Free T4,result,pmol/l +PV,ggt,GGT,result,U/l +PV,glucose,Glucose Random,result,mmol/l +PV,hb,Hb,result,g/l +PV,hba1c,HbA1c,result,mmol/mol +PV,hbv,Hep B,result +PV,hco3,Bicarb,result,mmol/l +PV,hco3_post,HCO3 (Post),result +PV,hct,HCT/PCV,result,I/l +PV,hcv,Hep C,result +PV,hdl,HDL,result,mmol/l +PV,height,Height,obs,cm +PV,hypotension,Symptomatic Hypotension,obs +PV,inr,INR,result,ratio +PV,iron,Iron,result,mmol/l +PV,ironsat,Fe Sat,result,% +PV,ktv,Kt/V,result,ratio +PV,ldh,LDH,result,U/l +PV,ldl,LDL,result,mmol/l +PV,lhratio,LDL:LDH Ratio,result,ratio +PV,lipase,Lipase,result,U/l +PV,lithium,Lithium,result,mEq/l +PV,magnesium,Mg,result,mmol/l +PV,mmp,MMP Level,result, +PV,neutrophils,Neutrophils,result,10^9/l +PV,odema,Odema,obs +PV,pcr,PCR,result,mg/mmol +PV,phepku,Phenylalanine,result,mg/dl +PV,phosphate,Phosphate,result,mmol/l +PV,phosphate_post,Phosphate (Post),result,mmol/l +PV,platelets,Platelets,result,10^9/l +PV,potassium,Potassium,result,mmol/l +PV,potassium_post,Potassium (Post),result,mmol/l +PV,psa,PSA,result,ng/ml +PV,pth,PTH,result,pmol/l +PV,pulse,Pulse,obs,bpm +PV,ret-he,RET-HE,result,pg +PV,sirolimus,Sirolimus,result,ng/l +PV,sodium,Sodium,result,mmol/l +PV,sodium_post,Sodium (Post),result,mmol/l +PV,t4,Total T4,result,ng/l +PV,tacrolimus,Tacrolimus,result,ng/ml +PV,testosterone,Serum Testosterone,result,ng/dl +PV,tg,TG,result,mmol/l +PV,tgn,TGN Levels,result +PV,tpmt,TPMT Levels,result,mU/l +PV,transferrin,Transferrin,result,% +PV,trop,Troponin-T,result,ng/ml +PV,tsh,TSH,result,mU/l +PV,ualbumin,Urine Albumin,result,mg/l +PV,ucreatinine,Urine Creatinine,result,mmol/l +PV,updipstick,Urine Protein Dipstick,obs +PV,uprotein,Urine Protein,result,mmol/l +PV,urate,Urate,result,mmol/l +PV,urea,Urea,result,mmol/l +PV,urea_post,Urea (Post),result,mmol/l +PV,urr,URR,result,ratio +PV,urr_post,URR (Post),result +PV,vitb12,Vitamin B12,result,ng/l +PV,vitd,Vitamin D,result,nmol/l +PV,wbc,WBC,result,10^9/l +PV,weight,Weight,obs,kg \ No newline at end of file diff --git a/codes/code_lists/pv_rrtstatus.csv b/codes/code_lists/pv_rrtstatus.csv new file mode 100644 index 0000000..c751833 --- /dev/null +++ b/codes/code_lists/pv_rrtstatus.csv @@ -0,0 +1,5 @@ +PV_RRTSTATUS,GEN,Kidney Care (not Dialysis or Transplant) +PV_RRTSTATUS,HD,Haemodialysis +PV_RRTSTATUS,PD,Peritoneal Dialysis +PV_RRTSTATUS,TP,Transplant Follow up +PV_RRTSTATUS,XFER,Transferred Out diff --git a/codes/code_lists/pv_tpstatus.csv b/codes/code_lists/pv_tpstatus.csv new file mode 100644 index 0000000..1910840 --- /dev/null +++ b/codes/code_lists/pv_tpstatus.csv @@ -0,0 +1,7 @@ +PV_TPSTATUS,A,Active +PV_TPSTATUS,S,Suspended +PV_TPSTATUS,T,Transplanted +PV_TPSTATUS,R,Not on List +PV_TPSTATUS,N,Not on List +PV_TPSTATUS,O,Not on List +PV_TPSTATUS,U,No Status Uploaded diff --git a/codes/code_lists/radar_facilities.csv b/codes/code_lists/radar_facilities.csv new file mode 100644 index 0000000..d564fc2 --- /dev/null +++ b/codes/code_lists/radar_facilities.csv @@ -0,0 +1 @@ +RADAR,RWDDA,LINCOLN COUNTY HOSPITAL diff --git a/codes/code_lists/rawpvrrtstatus.csv b/codes/code_lists/rawpvrrtstatus.csv new file mode 100644 index 0000000..134db9c --- /dev/null +++ b/codes/code_lists/rawpvrrtstatus.csv @@ -0,0 +1,101 @@ +PV_RAW_RRTSTATUS,AAPD +PV_RAW_RRTSTATUS,ACUTE ITU +PV_RAW_RRTSTATUS,ACUTE +PV_RAW_RRTSTATUS,ALD +PV_RAW_RRTSTATUS,APD +PV_RAW_RRTSTATUS,CAPD +PV_RAW_RRTSTATUS,CK +PV_RAW_RRTSTATUS,CKD/TX +PV_RAW_RRTSTATUS,CLINIC +PV_RAW_RRTSTATUS,HD (HOME) +PV_RAW_RRTSTATUS,HD (HOSP) +PV_RAW_RRTSTATUS,HOME APD +PV_RAW_RRTSTATUS,HOME CAPD +PV_RAW_RRTSTATUS,HOME HD NOCTURNAL +PV_RAW_RRTSTATUS,HOME HD +PV_RAW_RRTSTATUS,HOSPITAL HD +PV_RAW_RRTSTATUS,IN-CENTRE HD +PV_RAW_RRTSTATUS,LOST +PV_RAW_RRTSTATUS,LRD +PV_RAW_RRTSTATUS,MOVED OUT +PV_RAW_RRTSTATUS,PR +PV_RAW_RRTSTATUS,PRE +PV_RAW_RRTSTATUS,REC +PV_RAW_RRTSTATUS,T/P RENAL(C) +PV_RAW_RRTSTATUS,T/P RENAL(L) +PV_RAW_RRTSTATUS,TRANSPLANT +PV_RAW_RRTSTATUS,TX (KL) +PV_RAW_RRTSTATUS,TX (PAK) +PV_RAW_RRTSTATUS,TX (PAT) +PV_RAW_RRTSTATUS,TX (SPK) +PV_RAW_RRTSTATUS,0 +PV_RAW_RRTSTATUS,1 +PV_RAW_RRTSTATUS,2 +PV_RAW_RRTSTATUS,3 +PV_RAW_RRTSTATUS,4 +PV_RAW_RRTSTATUS,5 +PV_RAW_RRTSTATUS,9 +PV_RAW_RRTSTATUS,10 +PV_RAW_RRTSTATUS,11 +PV_RAW_RRTSTATUS,12 +PV_RAW_RRTSTATUS,13 +PV_RAW_RRTSTATUS,14 +PV_RAW_RRTSTATUS,15 +PV_RAW_RRTSTATUS,16 +PV_RAW_RRTSTATUS,17 +PV_RAW_RRTSTATUS,19 +PV_RAW_RRTSTATUS,20 +PV_RAW_RRTSTATUS,21 +PV_RAW_RRTSTATUS,22 +PV_RAW_RRTSTATUS,23 +PV_RAW_RRTSTATUS,24 +PV_RAW_RRTSTATUS,25 +PV_RAW_RRTSTATUS,26 +PV_RAW_RRTSTATUS,27 +PV_RAW_RRTSTATUS,28 +PV_RAW_RRTSTATUS,29 +PV_RAW_RRTSTATUS,41 +PV_RAW_RRTSTATUS,42 +PV_RAW_RRTSTATUS,43 +PV_RAW_RRTSTATUS,44 +PV_RAW_RRTSTATUS,45 +PV_RAW_RRTSTATUS,49 +PV_RAW_RRTSTATUS,50 +PV_RAW_RRTSTATUS,51 +PV_RAW_RRTSTATUS,52 +PV_RAW_RRTSTATUS,53 +PV_RAW_RRTSTATUS,54 +PV_RAW_RRTSTATUS,55 +PV_RAW_RRTSTATUS,56 +PV_RAW_RRTSTATUS,57 +PV_RAW_RRTSTATUS,59 +PV_RAW_RRTSTATUS,60 +PV_RAW_RRTSTATUS,61 +PV_RAW_RRTSTATUS,62 +PV_RAW_RRTSTATUS,63 +PV_RAW_RRTSTATUS,64 +PV_RAW_RRTSTATUS,65 +PV_RAW_RRTSTATUS,66 +PV_RAW_RRTSTATUS,68 +PV_RAW_RRTSTATUS,69 +PV_RAW_RRTSTATUS,74 +PV_RAW_RRTSTATUS,75 +PV_RAW_RRTSTATUS,77 +PV_RAW_RRTSTATUS,81 +PV_RAW_RRTSTATUS,82 +PV_RAW_RRTSTATUS,83 +PV_RAW_RRTSTATUS,111 +PV_RAW_RRTSTATUS,114 +PV_RAW_RRTSTATUS,115 +PV_RAW_RRTSTATUS,117 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+RR1+,PKB,PATIENTS KNOW BEST +RR1+,TRACING,UKRDC TRACING RECORD +RR1+,UKRR,UK RENAL REGISTRY +RR1+,RY5K7,CHANDRA MISTRY DIALYSIS UNIT +RR1+,RAJ,MID & SOUTH ESSEX TRUST +RR1+,BAPN,Migrated BAPN Data diff --git a/codes/code_lists/snomed_codes.csv b/codes/code_lists/snomed_codes.csv new file mode 100644 index 0000000..12d25c2 --- /dev/null +++ b/codes/code_lists/snomed_codes.csv @@ -0,0 +1,7 @@ +SNOMED,27113001,Weight,obs,kg +SNOMED,162755006,Height,obs,cm +SNOMED,301331008,BMI,obs,kg/m^2 +SNOMED,162986007,Pulse,obs,bpm +SNOMED,163030003,Systolic Blood Pressure,obs,mmHg (systolic) +SNOMED,163031004,Diastolic Blood Pressure,obs,mmHg (diastolic) +SNOMED,75367002,Blood Pressure,obs \ No newline at end of file diff --git a/codes/code_lists/survey_questions.csv b/codes/code_lists/survey_questions.csv new file mode 100644 index 0000000..5805a46 --- /dev/null +++ b/codes/code_lists/survey_questions.csv @@ -0,0 +1,28 @@ +YOUR_HEALTH,YOHQ1 +YOUR_HEALTH,YOHQ2 +YOUR_HEALTH,YOHQ3 +YOUR_HEALTH,YOHQ4 +YOUR_HEALTH,YOHQ5 +YOUR_HEALTH,YOHQ6 +YOUR_HEALTH,YSQ1 +YOUR_HEALTH,YSQ10 +YOUR_HEALTH,YSQ11 +YOUR_HEALTH,YSQ12 +YOUR_HEALTH,YSQ13 +YOUR_HEALTH,YSQ14 +YOUR_HEALTH,YSQ15 +YOUR_HEALTH,YSQ16 +YOUR_HEALTH,YSQ17 +YOUR_HEALTH,YSQ18 +YOUR_HEALTH,YSQ19 +YOUR_HEALTH,YSQ2 +YOUR_HEALTH,YSQ20 +YOUR_HEALTH,YSQ21 +YOUR_HEALTH,YSQ22 +YOUR_HEALTH,YSQ3 +YOUR_HEALTH,YSQ4 +YOUR_HEALTH,YSQ5 +YOUR_HEALTH,YSQ6 +YOUR_HEALTH,YSQ7 +YOUR_HEALTH,YSQ8 +YOUR_HEALTH,YSQ9 diff --git a/codes/code_lists/survey_types.csv b/codes/code_lists/survey_types.csv new file mode 100644 index 0000000..118ac2d --- /dev/null +++ b/codes/code_lists/survey_types.csv @@ -0,0 +1,4 @@ +SURVEY,EQ5D +SURVEY,PROM +SURVEY,PAM +SURVEY,PREM diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv new file mode 100644 index 0000000..04ff0fa --- /dev/null +++ b/codes/code_lists/ukrr_observations.csv @@ -0,0 +1,61 @@ +UKRR,QBLA1,Serum Creatinine,result +UKRR,QBLA3,Serum Urea,result +UKRR,QBLA4,Serum Bicarbonate,result +UKRR,QBLA6,Serum Sodium,result +UKRR,QBLA9,Serum Potassium,result +UKRR,QBLAB,Lab Calculated eGFR,result +UKRR,QBLAC,Serum Uric Acid (Urate),result +UKRR,QBLAL,Unit Calculated eGFR,result +UKRR,QBLB1,Serum Phosphate,result +UKRR,QBLB3,Serum Calcium,result +UKRR,QBLB4,Corrected Serum Calcium,result +UKRR,QBLB5,Serum Alkaline Phosphatase,result +UKRR,QBLB7,Serum Albumin,result +UKRR,QBLB9,Serum Parathyroid Hormone (PTH),result +UKRR,QBLC1,Urine Protein:Creatinine Ratio,result +UKRR,QBLC3,Urine Albumin:Creatinine Ratio,result +UKRR,QBLD1,Total Serium Cholesterol,result +UKRR,QBLD3,Serum HDL Cholesterol,result +UKRR,QBLD4,Serum LDL Cholesterol,result +UKRR,QBLD5,Serum Triglycerides,result +UKRR,QBLD6,CRP,result +UKRR,QBLD8,Hba1c %,result +UKRR,QBLDA,Hba1c,result +UKRR,QBLE1,Haemoglobin,result +UKRR,QBLE3,MCH,result +UKRR,QBLE4,Platelets,result +UKRR,QBLE5,WBC (from full blood count),result +UKRR,QBLEB,Haemloglobin,result +UKRR,QBLF1,Serum Ferritin,result +UKRR,QBLF3,Transferrin Saturation,result +UKRR,QBLF5,Percentage of Hypochromic Cells,result +UKRR,QBLF7,Serum B12,result +UKRR,QBLF9,Serum Folate,result +UKRR,QBLFB,Red Cell Folate,result +UKRR,QBLFD,Serum Aluminium,result +UKRR,QBLFF,Tacrolimus Blood Concentration Level,result +UKRR,QBLFH,Sirolimus Blood Concentration Level,result +UKRR,QBLFK,Ciclosporin Blood Concentration Level,result +UKRR,QBLFM,Mycophenolate Blood Concentration Level,result +UKRR,QBLG1,Weight,observation +UKRR,QBLG3,Systolic BP,observation +UKRR,QBLG4,Diastolic BP,observation +UKRR,QBLG9,Urea Reduction Ratio,result +UKRR,QBLGG,Kt/V,result +UKRR,QBLGB,Height,observation +UKRR,QBLHA,HBV Antibody Status,result +UKRR,QBLHC,HBV Surface Antigen Status,result +UKRR,QBLHE,HCV Antibody Status,result +UKRR,QBLHG,CMV Antibody Status,result +UKRR,QBLHK,CMV PCR Copies/ML,result +UKRR,QBLHM,HIV Antigen Status,result +UKRR,QBLHN,Varicella,result +UKRR,QBLHR,EBV Status,result +UKRR,QBLHS,EBV Log Count,result +UKRR,QBLHV,Urine Volume in 24 Hours,observation +UKRR,QBLHX,Urinary Creatinine Extraction,result +UKRR,QBLPA,PTH ULN,result +UKRR,QBLPB,PTH / PTHH ULN Ratio,result +UKRR,QBLPC,ALT,result +UKRR,QBLPD,ANC,result +UKRR,QBLPE,ALC,result \ No newline at end of file diff --git a/codes/code_writer.py b/codes/code_writer.py new file mode 100644 index 0000000..8722128 --- /dev/null +++ b/codes/code_writer.py @@ -0,0 +1,67 @@ +# This script converts Shaun's XLS document +# Into 3 CSV files to match the table structure + +import csv +import itertools + + +def main(): + # Code List + + csvreader = csv.reader(open("C:/Temp/PV2_Test_harmonisation.csv", "r")) + + code_list = list() + code_conv_list = list() + unit_conv_list = list() + + next(csvreader) + for row in csvreader: + + test_code = row[0] + unit_code = row[1] + correct_test_code = row[3] + correct_unit_code = row[4] + record_type = row[5] + + # creatinine,µmol/l,68,creatinine,micromol/L,result, + + code_list.append(("PV", correct_test_code, None, record_type)) + if correct_test_code not in ("", None): + code_conv_list.append(("PVMIGRATION", test_code, "PV", correct_test_code)) + if correct_unit_code not in ("", None): + unit_conv_list.append(("PVMIGRATION", unit_code, "PV", correct_unit_code)) + + # Code List + code_list.sort() + code_list = list(code_list for code_list, _ in itertools.groupby(code_list)) + + csvwriter = csv.writer(open("C:/Temp/CodeList.csv", "w", newline="")) + + for row in code_list: + csvwriter.writerow(row) + + # Code Conv List + code_conv_list.sort() + code_conv_list = list( + code_conv_list for code_conv_list, _ in itertools.groupby(code_conv_list) + ) + + csvwriter = csv.writer(open("C:/Temp/CodeConvList.csv", "w", newline="")) + + for row in code_conv_list: + csvwriter.writerow(row) + + # Unit Conv List + unit_conv_list.sort() + unit_conv_list = list( + unit_conv_list for unit_conv_list, _ in itertools.groupby(unit_conv_list) + ) + + csvwriter = csv.writer(open("C:/Temp/UnitConvList.csv", "w", newline="")) + + for row in unit_conv_list: + csvwriter.writerow(row) + + +if __name__ == "__main__": + main() diff --git a/codes/redis_code_importer.py b/codes/redis_code_importer.py new file mode 100644 index 0000000..dcc5a1f --- /dev/null +++ b/codes/redis_code_importer.py @@ -0,0 +1,148 @@ +import csv +import json +import os +from typing import Optional + +import redis +from sshtunnel import SSHTunnelForwarder + +from ukrdc.services.codes import Codes + +UKRDC_INSTANCE = "live_app_ssh" + +code_conv_list_path = "conf/pv2_codes/code_conv_lists/" +code_list_path = "conf/pv2_codes/code_lists/" +code_exclusion_path = "conf/pv2_codes/code_exclusions/" +satellite_map_path = "conf/pv2_codes/satellite_map/satellite_map.csv" + + +def import_codes(host: str, port: int): + r = redis.Redis(host=host, port=port, db=0) + + # Clear Existing Data + r.flushall() + + # Code Map + for filename in os.listdir(code_conv_list_path): + csvreader = csv.reader( + open(code_conv_list_path + filename, "r", newline="", encoding="utf-8") + ) + + print(f"Importing {filename}") + for row in csvreader: + source_coding_standard = row[0] + source_code = row[1] + destination_coding_standard = row[2] + destination_code = row[3] + + Codes().set_code_mapping_item( + r, + source_coding_standard, + source_code, + destination_coding_standard, + destination_code, + ) + + # Code List + for filename in os.listdir(code_list_path): + csvreader = csv.reader( + open(code_list_path + filename, "r", newline="", encoding="utf-8") + ) + + print(f"Importing {filename}") + for row in csvreader: + coding_standard = row[0] + try: + code = row[1] + except Exception: + print(filename) + print(row) + raise + + if len(row) >= 3: + description: Optional[str] = row[2] + else: + description = None + + if len(row) >= 4: + code_type: Optional[str] = row[3] + else: + code_type = None + + if len(row) >= 5: + units: Optional[str] = row[4] + else: + units = None + + key = "CODE_LIST:" + key += coding_standard + ":" + key += code + + if description: + r.hset(key, "description", description) + else: + r.hset(key, "description", code) + + if code_type: + r.hset(key, "code_type", code_type) + + if units: + r.hset(key, "units", units) + + # Code Exclusions + for filename in os.listdir(code_exclusion_path): + csvreader = csv.reader( + open(code_exclusion_path + filename, "r", newline="", encoding="utf-8") + ) + + for row in csvreader: + + coding_standard = row[0] + code = row[1] + system = row[2] + + Codes().set_code_exclusion(r, coding_standard, code, system) + + # Satellite Map + + csvreader = csv.reader(open(satellite_map_path, "r", newline="", encoding="utf-8")) + + for row in csvreader: + satellite_code = row[0] + main_unit_code = row[1] + + key = "SATELLITE_LIST:" + key += satellite_code + + r.set(key, main_unit_code) + + +if __name__ == "__main__": + + import argparse + + parser = argparse.ArgumentParser() + parser.add_argument("--local", action="store_true") + + local: bool = parser.parse_args().local + + if local: + import_codes("localhost", 6379) + + else: + + fname = os.path.expanduser("~/.config/ukrdc/services/db_conf.json") + print("Configuration File: ", fname) + with open(fname) as fhandle: + params = json.load(fhandle) + + with SSHTunnelForwarder( + (params[UKRDC_INSTANCE]["HOST"], 22), + ssh_password=params[UKRDC_INSTANCE]["PASSWORD"], + ssh_username=params[UKRDC_INSTANCE]["USER"], + remote_bind_address=("localhost", 6379), + # Make an SSH Tunnel to Redis on the chosen App Server + ) as ukrdc_redis_tunnel: + host = "localhost" + port = ukrdc_redis_tunnel.local_bind_port + import_codes(host, port) diff --git a/codes/satellite_map/satellite_map.csv b/codes/satellite_map/satellite_map.csv new file mode 100644 index 0000000..fcecfca --- /dev/null +++ b/codes/satellite_map/satellite_map.csv @@ -0,0 +1,221 @@ +RH840,RH8 +9RH05,RH8 +RH8G3,RH8 +9RH06,RH8 +RBZ19,RH8 +9RA911,RH8 +RH802,RH8 +RJ230,RJ121 +TAF21,RJ121 +99RJ121,RJ121 +98CJ06,RJ121 +9RJ121,RJ121 +RJ224,RJ121 +9RPD01,RJ121 +98A713,RJ121 +8RJ121,RJ121 +9RH641,RH641 +9RTQ,RH641 +RL109,RKHA4 +RNLBX,RLGAY +RRBBW,RRBBV +RKM,RRBBV +XXX03,RRBBV +XXX02,RRBBV +9RVEB1,RRBBV +XXX01,RRBBV +99RRBBV,RRBBV +RRS,RRBBV +RDDH1,RDDH0 +9RNA,RNA03 +9RWP31,RNA03 +RBBP3,REE01 +9RH01,REE01 +RD1,REE01 +9RVJ21,REE01 +9RA743,REE01 +RA301,REE01 +9RH02,REE01 +9REE01,REE01 +9RJH01,RL7 +99RL7,RL7 +RNG10,RL7 +RL301,RL7 +9RBD01,RBD01 +9RH03,RBD01 +RDZ00,RBD01 +RRE01,RJE01 +RBT20,RJE01 +99RJ701,RJ701 +9RJ701,RJ701 +98RQY,RJ701 +98RJ701,RJ701 +RFZ20,RQN02 +RTK02,RQN02 +RWG02,RQN02 +RAU31,RQN02 +RFW01,RQN02 +RYJ03,RQN02 +RDA03,RQN02 +RC368,RQN02 +9RCF31,RAE05 +RKZDA,RFBAK +RGN,RFBAK +RFBAT,RFBAK +9RWDLB,RFBAK +RNQ51,RFBAK +RT5DC,RFBAK +9RP7LA,RFBAK +9RFBAK,RFBAK +9RWD,RFBAK +98RFBAK,RFBAK +99RFBAK,RFBAK +RY5K7,RFBAK +9RKD,RHU02 +99RHU02,RHU02 +RDZ15,RHU02 +9RN506,RHU02 +RHS55,RHU02 +RR201,RHU02 +RPK40,RHU02 +RNZ02,RHU02 +9RFU,RAQ01 +RQW,RAQ01 +RC971,RAQ01 +RPW02,RAQ01 +REF01,REF12 +RJ866,REF12 +9RF201,RF201 +RJL,RF201 +RF832,RF201 +9RLNGH,RLNGH +RR9,RLNGH +RJC03,RKB01 +RKB03,RKB01 +RLT01,RKB01 +RJC46,RKB01 +9RQY,RAZ +99RAZ,RAZ +RJ6,RAZ +RTP02,RAZ +9RXX,RAZ +9RAZ,RAZ +99RXX,RAZ +RG303A,RAZ +RVV20,RVVKC +RVVMA,RVVKC +RPA,RVVKC +RVV11,RVVKC +RPC20,RVVKC +9RQBAU,RQBAU +RW5CA,RMF01 +RMB05,RMF01 +RXR01,RMF01 +RXL06,RMF01 +RJU01,RMF01 +RE5BW,RMF01 +RP5BA,RP5 +RP5MM,RP5 +99RJZ,RJZ +RJZW,RJZ +98RJZ,RJZ +9RJZ,RJZ +RN7,RJZ +RXJ06,RJZ +RG222,RJZ +88A713,RJZ +RKTAG,RQHC7 +RKUAJ,RQHC7 +RR6BL,RQHC7 +RGQ03,RGQ02 +RRE14,RL403 +9RL403,RL403 +9RBK,RL403 +9RNA3,RL403 +9RK7CC,RK7CC +RFSDA,RK7CC +RFRPA,RK7CC +RFRAA,RK7CC +9RWX,RHW01 +9RH108,RHW01 +RXC02,RGU01 +9RTP02,RGU01 +RDM03,RGU01 +RPL04,RGU01 +RVL07,RAL01 +98TAF,RAL01 +9RAL01,RAL01 +9TAF,RAL01 +RVL01,RAL01 +RAPNM,RAL01 +8A713,RAL01 +RCC25,RCB55 +RCB23,RCB55 +RCD35,RCB55 +9RBN01,RQ617 +RQ601,RQ617 +RKC81,RQ617 +RBN63,RQ617 +RQQ31,RGT01 +RGR50,RGT01 +RCX01,RGT01 +RBL20,RBL14 +RJR05,RBL14 +RM131,RM102 +RGP75,RM102 +REM26,RW402 +9RW402,RW402 +RVY01,RW402 +RTRNT,RCJAT +9RCJAT,RCJAT +RLBCH,RCJAT +RXWAT,RLZ01 +REFWW,RK950 +R1G55,RK950 +9RJ866,RK950 +8RA911,RK950 +9RWJ,RM574 +RW602,RM574 +RM202,RM574 +RM403,RM574 +9RXV06,RM574 +RJN71,RM574 +RMP01,RM574 +RTD03,RTD01 +RF4DG,RNJ00 +RGCNH,RNJ00 +RGCKH,RNJ00 +9RNJ00,RNJ00 +RWL25,RRK02 +98RRK02,RRK02 +9RRK02,RRK02 +RLW01,RRK02 +9RNA2,RRK02 +RWP31,RRK02 +RLQ02,RRK02 +99RRK02,RRK02 +9RLQ02,RRK02 +97RRK02,RRK02 +98RBK,RRK02 +9RNG2,RRK02 +RXQ50,RNX02 +RVNCA,RNX02 +RBF33,RNX02 +RXQ02,RNX02 +RD816,RNX02 +RMW10,RQR13 +RQR14,RQR13 +9RQR13,RQR13 +RGA02,RQR13 +RXF03,RQR13 +RGB04,RQR13 +9RQR14,RQR13 +REZ02,RM301 +7RM301,RM301 +9RM301,RM301 +RMC00,RM301 +RHANN,RCSLB +9RCSLB,RCSLB +RX1RA,RCSLB +RXM56,RCSLB +RFJBC,RCSLB From f9ef07806d39f89174d01b50d312cc0bcf423633 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 10 Dec 2023 19:49:32 +0000 Subject: [PATCH 071/166] Move code scripts to scripts folder --- {codes => scripts}/code_importer.py | 0 {codes => scripts}/code_writer.py | 0 {codes => scripts}/redis_code_importer.py | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename {codes => scripts}/code_importer.py (100%) rename {codes => scripts}/code_writer.py (100%) rename {codes => scripts}/redis_code_importer.py (100%) diff --git a/codes/code_importer.py b/scripts/code_importer.py similarity index 100% rename from codes/code_importer.py rename to scripts/code_importer.py diff --git a/codes/code_writer.py b/scripts/code_writer.py similarity index 100% rename from codes/code_writer.py rename to scripts/code_writer.py diff --git a/codes/redis_code_importer.py b/scripts/redis_code_importer.py similarity index 100% rename from codes/redis_code_importer.py rename to scripts/redis_code_importer.py From ea153d1304fa59c641384f85b6d394f8a91c862a Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Fri, 22 Dec 2023 10:20:28 +0000 Subject: [PATCH 072/166] Increment versions --- pyxb_build/ukrdc_schema/__init__.py | 2 +- xsdata_build/setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyxb_build/ukrdc_schema/__init__.py b/pyxb_build/ukrdc_schema/__init__.py index ce1305b..7039708 100644 --- a/pyxb_build/ukrdc_schema/__init__.py +++ b/pyxb_build/ukrdc_schema/__init__.py @@ -1 +1 @@ -__version__ = "4.0.0" +__version__ = "4.1.0" diff --git a/xsdata_build/setup.py b/xsdata_build/setup.py index 722a75a..257092f 100644 --- a/xsdata_build/setup.py +++ b/xsdata_build/setup.py @@ -7,7 +7,7 @@ setup( name="ukrdc-xsdata", - version="4.0.0", + version="4.1.0", long_description=long_description, long_description_content_type='text/markdown', author="UK Renal Registry", From b4d47686c4d07d4c42d4d0e21a23c19c99bc857f Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Fri, 22 Dec 2023 10:38:44 +0000 Subject: [PATCH 073/166] Update versions --- pyxb_build/ukrdc_schema/__init__.py | 2 +- schema/ukrdc/CHANGELOG.md | 1 + schema/ukrdc/Procedures/Procedure.xsd | 6 ------ xsdata_build/setup.py | 2 +- 4 files changed, 3 insertions(+), 8 deletions(-) diff --git a/pyxb_build/ukrdc_schema/__init__.py b/pyxb_build/ukrdc_schema/__init__.py index ce1305b..0fd7811 100644 --- a/pyxb_build/ukrdc_schema/__init__.py +++ b/pyxb_build/ukrdc_schema/__init__.py @@ -1 +1 @@ -__version__ = "4.0.0" +__version__ = "4.2.0" diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index 6a72a7a..da054bf 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -6,6 +6,7 @@ - Increased ResultItem/ResultValue to 30 characters - Increased Observation/ObservationValue to 30 characters - Amended Medication UoM to use CF_RR23 type. +- Remove EnteredBy from Procedure ## 4.1.0 - 2023-08-13 ### Changed diff --git a/schema/ukrdc/Procedures/Procedure.xsd b/schema/ukrdc/Procedures/Procedure.xsd index d2eac97..f12c499 100644 --- a/schema/ukrdc/Procedures/Procedure.xsd +++ b/schema/ukrdc/Procedures/Procedure.xsd @@ -21,12 +21,6 @@ The time the Procedure started. - - - - Person entering the diagnosis as a National Clinicial code where possible or other local code if not. - - diff --git a/xsdata_build/setup.py b/xsdata_build/setup.py index 722a75a..3f33540 100644 --- a/xsdata_build/setup.py +++ b/xsdata_build/setup.py @@ -7,7 +7,7 @@ setup( name="ukrdc-xsdata", - version="4.0.0", + version="4.2.0", long_description=long_description, long_description_content_type='text/markdown', author="UK Renal Registry", From d20b2226df7c1a194d63720a7a40df16cee4ecb9 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Fri, 22 Dec 2023 11:03:37 +0000 Subject: [PATCH 074/166] Incremenet Versions (4.1.2) --- pyxb_build/ukrdc_schema/__init__.py | 2 +- xsdata_build/setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyxb_build/ukrdc_schema/__init__.py b/pyxb_build/ukrdc_schema/__init__.py index 7039708..13ffcf4 100644 --- a/pyxb_build/ukrdc_schema/__init__.py +++ b/pyxb_build/ukrdc_schema/__init__.py @@ -1 +1 @@ -__version__ = "4.1.0" +__version__ = "4.1.2" diff --git a/xsdata_build/setup.py b/xsdata_build/setup.py index 257092f..78a0413 100644 --- a/xsdata_build/setup.py +++ b/xsdata_build/setup.py @@ -7,7 +7,7 @@ setup( name="ukrdc-xsdata", - version="4.1.0", + version="4.1.2", long_description=long_description, long_description_content_type='text/markdown', author="UK Renal Registry", From 624293e7be79db697bced8478c8a9be2ae7c9a4e Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Fri, 22 Dec 2023 11:25:54 +0000 Subject: [PATCH 075/166] Update Versions (4.1.3) --- pyxb_build/ukrdc_schema/__init__.py | 2 +- schema/ukrdc/CHANGELOG.md | 4 ++++ schema/ukrdc/Patient.xsd | 2 +- schema/ukrdc/UKRDC.xsd | 2 +- xsdata_build/setup.py | 2 +- 5 files changed, 8 insertions(+), 4 deletions(-) diff --git a/pyxb_build/ukrdc_schema/__init__.py b/pyxb_build/ukrdc_schema/__init__.py index 13ffcf4..3a6bf39 100644 --- a/pyxb_build/ukrdc_schema/__init__.py +++ b/pyxb_build/ukrdc_schema/__init__.py @@ -1 +1 @@ -__version__ = "4.1.2" +__version__ = "4.1.3" diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index f2214a5..fbcf708 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## 4.1.3 - 2023-12-22 +### Changed +- Remove maxOccurs from PatientNumbers to fix PyXB + ## 4.1.0 - 2023-08-13 ### Changed - Added Missing EDTA2 PRD Codes diff --git a/schema/ukrdc/Patient.xsd b/schema/ukrdc/Patient.xsd index 2b726c2..338f72a 100644 --- a/schema/ukrdc/Patient.xsd +++ b/schema/ukrdc/Patient.xsd @@ -15,7 +15,7 @@ - + UKRRv4,UKRRv5 diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 44613da..dd5ce86 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -1,4 +1,4 @@ - + diff --git a/xsdata_build/setup.py b/xsdata_build/setup.py index 78a0413..4e1b153 100644 --- a/xsdata_build/setup.py +++ b/xsdata_build/setup.py @@ -7,7 +7,7 @@ setup( name="ukrdc-xsdata", - version="4.1.2", + version="4.1.3", long_description=long_description, long_description_content_type='text/markdown', author="UK Renal Registry", From b3fb2d32eecdfe3c908f581f2d388a8bc8f00fb3 Mon Sep 17 00:00:00 2001 From: George Date: Thu, 11 Jan 2024 12:27:29 +0000 Subject: [PATCH 076/166] Update README.md --- schema/ukrdc/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schema/ukrdc/README.md b/schema/ukrdc/README.md index c803c69..abf6bac 100644 --- a/schema/ukrdc/README.md +++ b/schema/ukrdc/README.md @@ -6,7 +6,7 @@ [Schema Documentation](https://renalregistry.atlassian.net/wiki/spaces/UD/overview) -[File Transfer Instructions](https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2044133823/UKRDC+File+Transmission) +[Building a Renal Unit to UKRDC Feed]([https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2044133823/UKRDC+File+Transmission](https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2383118357/Building+a+Renal+Unit+to+UKRDC+Feed)) ## Technical References From 6e353ac823373d96f2b81784d3543a370d1fe620 Mon Sep 17 00:00:00 2001 From: George Date: Thu, 11 Jan 2024 12:27:59 +0000 Subject: [PATCH 077/166] Update README.md --- schema/ukrdc/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schema/ukrdc/README.md b/schema/ukrdc/README.md index abf6bac..b31d7e5 100644 --- a/schema/ukrdc/README.md +++ b/schema/ukrdc/README.md @@ -6,7 +6,7 @@ [Schema Documentation](https://renalregistry.atlassian.net/wiki/spaces/UD/overview) -[Building a Renal Unit to UKRDC Feed]([https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2044133823/UKRDC+File+Transmission](https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2383118357/Building+a+Renal+Unit+to+UKRDC+Feed)) +[Building a Renal Unit to UKRDC Feed](https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2383118357/Building+a+Renal+Unit+to+UKRDC+Feed) ## Technical References From 31f446bd79f1729eddd2817b24f89fbfaf3a0abe Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 6 Feb 2024 11:07:06 +0000 Subject: [PATCH 078/166] Allow multiple CoD/PRDs --- schema/ukrdc/CHANGELOG.md | 4 ++-- schema/ukrdc/UKRDC.xsd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index da054bf..3e750c3 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -1,12 +1,13 @@ # Changelog -## 4.2.0 - 2023-12-05 +## 4.2.0 - 2024-02-06 ### Changed - Restricted Treatment/VisitDescription to 255 characters - Increased ResultItem/ResultValue to 30 characters - Increased Observation/ObservationValue to 30 characters - Amended Medication UoM to use CF_RR23 type. - Remove EnteredBy from Procedure +- All Multiple PRD/CoD Records ## 4.1.0 - 2023-08-13 ### Changed @@ -16,7 +17,6 @@ - Changed Mandatory fields in DialysisPrescription - Modified Diagnosis to allow LOCAL/ICD-10 CodingStandards - ## 4.0.0 - 2023-06-13 ### Added - Assessment Element Type diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index 2aef1e5..4f86a46 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -131,7 +131,7 @@ Co-Morbidities - + UKRRv4,UKRRv5,RADAR @@ -139,7 +139,7 @@ Cause of Death - + UKRRv4,UKRRv5,PKB,RADAR From ee4a0d56994c42227a1403ad94f7df3c11d5d47e Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Tue, 6 Feb 2024 11:10:32 +0000 Subject: [PATCH 079/166] Amend test files --- sample_files/ukrdc/fullFile.xml | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/sample_files/ukrdc/fullFile.xml b/sample_files/ukrdc/fullFile.xml index 37adbea..fe1c93d 100644 --- a/sample_files/ukrdc/fullFile.xml +++ b/sample_files/ukrdc/fullFile.xml @@ -278,11 +278,6 @@ Haemodialysis 2006-05-04T18:13:51.0 - - ODS - ABC123 - Dr Foster - RR1+ ABC123 @@ -298,11 +293,6 @@ Description82 2006-05-04T18:13:51.0 - - ODS - Code84 - Description84 - ODS Code85 @@ -319,11 +309,6 @@ PEX 2006-05-04T18:13:51.0 - - ODS - ABC123 - Dr Foster - RR1+ ABC123 @@ -339,11 +324,6 @@ Construction of arteriovenous fistula 2006-05-04T18:13:51.0 - - ODS - ABC123 - Dr Foster - RR1+ ABC123 From 2f5a4775e6967fb4dc6b27a7b0d139f27af02361 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Mon, 26 Feb 2024 16:38:04 +0000 Subject: [PATCH 080/166] Make ObservationTime mandatory --- schema/ukrdc/CHANGELOG.md | 5 +++-- schema/ukrdc/LabOrders/LabOrder.xsd | 2 +- schema/ukrdc/Observations/Observation.xsd | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index 3e750c3..4668968 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -1,13 +1,14 @@ # Changelog -## 4.2.0 - 2024-02-06 +## 4.2.0 - 2024-02-26 ### Changed - Restricted Treatment/VisitDescription to 255 characters - Increased ResultItem/ResultValue to 30 characters - Increased Observation/ObservationValue to 30 characters - Amended Medication UoM to use CF_RR23 type. - Remove EnteredBy from Procedure -- All Multiple PRD/CoD Records +- Allow Multiple PRD/CoD Records +- Make ObservationTime mandatory on ResultItem/Observation ## 4.1.0 - 2023-08-13 ### Changed diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index 365fa9d..67fafcf 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -334,7 +334,7 @@ - + OBX:14 diff --git a/schema/ukrdc/Observations/Observation.xsd b/schema/ukrdc/Observations/Observation.xsd index 5745660..bbaa7ad 100644 --- a/schema/ukrdc/Observations/Observation.xsd +++ b/schema/ukrdc/Observations/Observation.xsd @@ -17,7 +17,7 @@ - + From b20de98026151bd5a40610c1ef9532f6519b797a Mon Sep 17 00:00:00 2001 From: Joel Collins Date: Tue, 27 Feb 2024 10:50:23 +0000 Subject: [PATCH 081/166] Set v4.2.0 version numbers using setversions.sh --- sample_files/ukrdc/fullDemographics.xml | 2 +- sample_files/ukrdc/fullFile.xml | 2 +- sample_files/ukrdc/minimalDemographics.xml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/sample_files/ukrdc/fullDemographics.xml b/sample_files/ukrdc/fullDemographics.xml index 32b78ea..2b60c73 100644 --- a/sample_files/ukrdc/fullDemographics.xml +++ b/sample_files/ukrdc/fullDemographics.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC diff --git a/sample_files/ukrdc/fullFile.xml b/sample_files/ukrdc/fullFile.xml index fe1c93d..2c95a4e 100644 --- a/sample_files/ukrdc/fullFile.xml +++ b/sample_files/ukrdc/fullFile.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC diff --git a/sample_files/ukrdc/minimalDemographics.xml b/sample_files/ukrdc/minimalDemographics.xml index 3295fb1..ef6a0e3 100644 --- a/sample_files/ukrdc/minimalDemographics.xml +++ b/sample_files/ukrdc/minimalDemographics.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC From 7dd3ebc6a64b91a7dde6622dd06929f4a515d625 Mon Sep 17 00:00:00 2001 From: andreoap Date: Wed, 13 Mar 2024 12:19:11 +0000 Subject: [PATCH 082/166] Add RR50/RR51 codes --- codes/code_lists/RR50.csv | 3 +++ codes/code_lists/RR51.csv | 12 ++++++++++++ 2 files changed, 15 insertions(+) create mode 100644 codes/code_lists/RR50.csv create mode 100644 codes/code_lists/RR51.csv diff --git a/codes/code_lists/RR50.csv b/codes/code_lists/RR50.csv new file mode 100644 index 0000000..b9baf89 --- /dev/null +++ b/codes/code_lists/RR50.csv @@ -0,0 +1,3 @@ +RR50,TPLTassess,Suitability for renal transplant +RR50,RRTassess,Shared future RRT choice +RR50,PPDassess,Preferred place of dying \ No newline at end of file diff --git a/codes/code_lists/RR51.csv b/codes/code_lists/RR51.csv new file mode 100644 index 0000000..be6a661 --- /dev/null +++ b/codes/code_lists/RR51.csv @@ -0,0 +1,12 @@ +RR51,1,Unsuitable +RR51,2,Workup commenced +RR51,3,Suitable +RR51,4,Referred for assessment +RR51,5,Assessment in progress +RR51,6,Opts for transplant +RR51,7,Opts for ICHD +RR51,8,Opts for HHD +RR51,9,Opts for PD +RR51,10,Opts for supportive care +RR51,11,Current home +RR51,12,Nursing home \ No newline at end of file From da93c62ce419477da669624bb95268ba264334cf Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 5 May 2024 23:19:33 +0100 Subject: [PATCH 083/166] UKRR Datasets - Normalise filenames of XLS Copies --- ...R-Dataset-v4.2.xls => UKRR DataSet v4_2_0.xls} | Bin ... Renal units.xlsx => UKRR DataSet v5_0_0.xlsx} | Bin .../UKRR/v5/~$DataSet_v5_0_For Renal units.xlsx | Bin 165 -> 0 bytes 3 files changed, 0 insertions(+), 0 deletions(-) rename dataset/UKRR/v4/{RR-Dataset-v4.2.xls => UKRR DataSet v4_2_0.xls} (100%) rename dataset/UKRR/v5/{DataSet_v5_0_For Renal units.xlsx => UKRR DataSet v5_0_0.xlsx} (100%) delete mode 100644 dataset/UKRR/v5/~$DataSet_v5_0_For Renal units.xlsx diff --git a/dataset/UKRR/v4/RR-Dataset-v4.2.xls b/dataset/UKRR/v4/UKRR DataSet v4_2_0.xls similarity index 100% rename from dataset/UKRR/v4/RR-Dataset-v4.2.xls rename to dataset/UKRR/v4/UKRR DataSet v4_2_0.xls diff --git a/dataset/UKRR/v5/DataSet_v5_0_For Renal units.xlsx b/dataset/UKRR/v5/UKRR DataSet v5_0_0.xlsx similarity index 100% rename from dataset/UKRR/v5/DataSet_v5_0_For Renal units.xlsx rename to dataset/UKRR/v5/UKRR DataSet v5_0_0.xlsx diff --git a/dataset/UKRR/v5/~$DataSet_v5_0_For Renal units.xlsx b/dataset/UKRR/v5/~$DataSet_v5_0_For Renal units.xlsx deleted file mode 100644 index 97642d53b44293c5da60358f35e677a69c593db7..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 165 zcmWf1Pt7k%PgMvm&&+Qy>NiGPpCOGUPK9F{A@&1%_aTa)wNXJRnR3ij@Fm J@_?e$f&hyw7Q+Al From 0f1a7695dd56a11e498b63f523b3ec6e47e7faa3 Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 5 May 2024 23:25:42 +0100 Subject: [PATCH 084/166] UKRR Dataset - Create Changelog for V5 --- dataset/UKRR/v5/CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 dataset/UKRR/v5/CHANGELOG.md diff --git a/dataset/UKRR/v5/CHANGELOG.md b/dataset/UKRR/v5/CHANGELOG.md new file mode 100644 index 0000000..eacbb35 --- /dev/null +++ b/dataset/UKRR/v5/CHANGELOG.md @@ -0,0 +1,8 @@ +# Changelog + +## 5.0.0 - 2024-05-05 +### Added +- Initial Version + + > This is the version of the document that was distributed to sites/suppliers post-Consultation. + From dafcfd0bc79ab04bc518b0db2cd10f7c8626a3fb Mon Sep 17 00:00:00 2001 From: andreoap Date: Tue, 28 May 2024 10:59:27 +0100 Subject: [PATCH 085/166] Add RTR45 code --- codes/code_lists/rr1plus_facilities.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index fa1a64e..b65f7e9 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -398,3 +398,4 @@ RR1+,UKRR,UK RENAL REGISTRY RR1+,RY5K7,CHANDRA MISTRY DIALYSIS UNIT RR1+,RAJ,MID & SOUTH ESSEX TRUST RR1+,BAPN,Migrated BAPN Data +RR1+,RTR45,Friarage Dialysis Centre From 96c0f2682ae68043465182e3a0384aa73fc3a28d Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 28 Jul 2024 19:01:24 +0100 Subject: [PATCH 086/166] Move snomed mappings to correct folder --- .../edta2_to_snomed.csv | 566 +++++++++--------- .../snomed_to_edta2.csv | 468 +++++++-------- 2 files changed, 517 insertions(+), 517 deletions(-) rename codes/{code_mappings => code_conv_lists}/edta2_to_snomed.csv (96%) rename codes/{code_mappings => code_conv_lists}/snomed_to_edta2.csv (96%) diff --git a/codes/code_mappings/edta2_to_snomed.csv b/codes/code_conv_lists/edta2_to_snomed.csv similarity index 96% rename from codes/code_mappings/edta2_to_snomed.csv rename to codes/code_conv_lists/edta2_to_snomed.csv index a59e02e..083fa11 100644 --- a/codes/code_mappings/edta2_to_snomed.csv +++ b/codes/code_conv_lists/edta2_to_snomed.csv @@ -1,283 +1,283 @@ -EDTA2,1003,SNOMED,52254009 -EDTA2,1019,SNOMED,445119005 -EDTA2,1026,SNOMED,48796009 -EDTA2,1035,SNOMED,197601003 -EDTA2,1042,SNOMED,197601003 -EDTA2,1057,SNOMED,722369003 -EDTA2,1061,SNOMED,236384008 -EDTA2,1074,SNOMED,236385009 -EDTA2,1088,SNOMED,722118005 -EDTA2,1090,SNOMED,44785005 -EDTA2,1100,SNOMED,44785005 -EDTA2,1116,SNOMED,236407003 -EDTA2,1128,SNOMED,236407003 -EDTA2,1137,SNOMED,445404003 -EDTA2,1144,SNOMED,445404003 -EDTA2,1159,SNOMED,282364005 -EDTA2,1163,SNOMED,282364005 -EDTA2,1171,SNOMED,236411009 -EDTA2,1185,SNOMED,722119002 -EDTA2,1192,SNOMED,722086002 -EDTA2,1205,SNOMED,722120008 -EDTA2,1214,SNOMED,722168002 -EDTA2,1222,SNOMED,75888001 -EDTA2,1233,SNOMED,722760002 -EDTA2,1246,SNOMED,236409000 -EDTA2,1251,SNOMED,197697005 -EDTA2,1267,SNOMED,236404005 -EDTA2,1279,SNOMED,445388002 -EDTA2,1280,SNOMED,445388002 -EDTA2,1298,SNOMED,444977005 -EDTA2,1308,SNOMED,444977005 -EDTA2,1312,SNOMED,1269761000000101 -EDTA2,1320,SNOMED,1269761000000101 -EDTA2,1331,SNOMED,3704008 -EDTA2,1349,SNOMED,35546006 -EDTA2,1354,SNOMED,83866005 -EDTA2,1365,SNOMED,36171008 -EDTA2,1377,SNOMED, 36171008 -EDTA2,1383,SNOMED, 724599009 -EDTA2,1396,SNOMED,722191003 -EDTA2,1401,SNOMED,195353004 -EDTA2,1417,SNOMED,195353004 -EDTA2,1429,SNOMED,1144805008 -EDTA2,1438,SNOMED,82275008 -EDTA2,1440,SNOMED,82275008 -EDTA2,1455,SNOMED,155441006 -EDTA2,1464,SNOMED,50581000 -EDTA2,1472,SNOMED,50581000 -EDTA2,1486,SNOMED,68815009 -EDTA2,1493,SNOMED,68815009 -EDTA2,1504,SNOMED,191306005 -EDTA2,1515,SNOMED,191306005 -EDTA2,1527,SNOMED,236502006 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+SNOMED,118600007,EDTA2,3823 +SNOMED,736992003,EDTA2,3834 +SNOMED,6956008,EDTA2,3847 From 8b5d2af99e706e24c522d1c05a2130352de71c0b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 3 Sep 2024 21:17:07 +0000 Subject: [PATCH 087/166] Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 2 to 4.1.7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v2...v4.1.7) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- .github/workflows/schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/schema.yml b/.github/workflows/schema.yml index 2faa760..4ee419a 100644 --- a/.github/workflows/schema.yml +++ b/.github/workflows/schema.yml @@ -86,7 +86,7 @@ jobs: if: startsWith(github.ref, 'refs/tags/') steps: - - uses: actions/download-artifact@v2 + - uses: actions/download-artifact@v4.1.7 - name: Release uses: softprops/action-gh-release@v1 From cdfc6926c4494d7a77eb5df8eda474d71ac07f02 Mon Sep 17 00:00:00 2001 From: andreoap Date: Wed, 18 Sep 2024 13:13:37 +0100 Subject: [PATCH 088/166] Add non-verbal languages to lookup --- codes/code_lists/nhs_data_dictionary_language_code.csv | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/codes/code_lists/nhs_data_dictionary_language_code.csv b/codes/code_lists/nhs_data_dictionary_language_code.csv index 5de20f8..810b2a0 100644 --- a/codes/code_lists/nhs_data_dictionary_language_code.csv +++ b/codes/code_lists/nhs_data_dictionary_language_code.csv @@ -182,3 +182,8 @@ NHS_DATA_DICTIONARY_LANGUAGE_CODE,yo,Yoruba NHS_DATA_DICTIONARY_LANGUAGE_CODE,za,Zhuang; Chuang NHS_DATA_DICTIONARY_LANGUAGE_CODE,zh,Chinese NHS_DATA_DICTIONARY_LANGUAGE_CODE,zu,Zulu +NHS_DATA_DICTIONARY_LANGUAGE_CODE,q1,Braille - for people who are unable to see +NHS_DATA_DICTIONARY_LANGUAGE_CODE,q2,American Sign Language +NHS_DATA_DICTIONARY_LANGUAGE_CODE,q3,Australian Sign Language +NHS_DATA_DICTIONARY_LANGUAGE_CODE,q4,British Sign Language +NHS_DATA_DICTIONARY_LANGUAGE_CODE,q5,Makaton - devised for children and adults with a variety of communication and Learning Disabilities From 244fecd87bfe48ff2fa6639da807a5c6ddcf4791 Mon Sep 17 00:00:00 2001 From: andreoap Date: Thu, 19 Sep 2024 10:23:29 +0100 Subject: [PATCH 089/166] Update github action version --- .github/workflows/schema.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/schema.yml b/.github/workflows/schema.yml index 2faa760..8b1a228 100644 --- a/.github/workflows/schema.yml +++ b/.github/workflows/schema.yml @@ -29,7 +29,7 @@ jobs: cd pyxb_build python setup.py bdist_wheel - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: ukrdc_schema_wheel path: pyxb_build/dist/*.whl @@ -66,7 +66,7 @@ jobs: ./build.sh python setup.py bdist_wheel - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: ukrdc_xsdata_wheel path: xsdata_build/dist/*.whl From 736aad8197c94bfbe03c01f6b457b1eb7908f65e Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Fri, 18 Oct 2024 10:35:16 +0100 Subject: [PATCH 090/166] feat(TNG-1012): Moved Scripts (#24) moved scripts to new repo https://github.com/renalreg/ukrdc_schema_report --- scripts/run_schema_report.sh | 10 -- scripts/schema_report.py | 340 ----------------------------------- 2 files changed, 350 deletions(-) delete mode 100644 scripts/run_schema_report.sh delete mode 100644 scripts/schema_report.py diff --git a/scripts/run_schema_report.sh b/scripts/run_schema_report.sh deleted file mode 100644 index 631e240..0000000 --- a/scripts/run_schema_report.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh -x -ssh -f -N -M -S /tmp/ukrdc_resources_socket root@10.38.181.121 -L 6000:db.ukrdc.nhs.uk:5432 -source env/bin/activate -pip install ukrdc-services -pip install ukrdc.database -pip install xlwt -pip install lxml -python scripts/schema_report.py -ssh -S /tmp/ukrdc_resources_socket -O exit xxx -exit 0 diff --git a/scripts/schema_report.py b/scripts/schema_report.py deleted file mode 100644 index 7712d05..0000000 --- a/scripts/schema_report.py +++ /dev/null @@ -1,340 +0,0 @@ -"""Produces an XLS Report comparing the UKRDC Schema to -the Repository Database""" - -import csv -import os - -from lxml import etree -import xlwt - -from ukrdc.database import Connection - -# NOTE: This may assume a PostgreSQL DB - - -def get_db_table_list(session): - sqlstring = """ - SELECT DISTINCT - A.table_name - FROM - information_schema.columns A - LEFT JOIN information_schema.tables B - ON A.table_name = B.table_name AND - A.table_schema = B.table_schema - WHERE - A.table_schema = 'extract' AND - B.table_type <> 'VIEW' - """ - - return [row[0] for row in session.execute(sqlstring)] - - -def get_db_column_metadata(session, tablename): - sqlstring = """ - SELECT - tab_columns.column_name, - data_type, - character_maximum_length, - numeric_precision, - is_nullable, - tab_constraints.constraint_type, - col_constraints.constraint_name, - col_check_constraints.check_clause - FROM - information_schema.columns AS tab_columns - LEFT OUTER JOIN - information_schema.constraint_column_usage AS col_constraints ON - tab_columns.table_name = col_constraints.table_name AND - tab_columns.column_name = col_constraints.column_name - LEFT OUTER JOIN - information_schema.table_constraints AS tab_constraints ON - tab_constraints.constraint_name = col_constraints.constraint_name - LEFT OUTER JOIN - information_schema.check_constraints AS col_check_constraints ON - col_check_constraints.constraint_name = tab_constraints.constraint_name - WHERE - tab_columns.table_name = :table_name AND - tab_columns.table_schema = 'extract' - ORDER BY ordinal_position; - """ - - results = session.execute(sqlstring, {"table_name": tablename}) - return results - - -def get_field_contents_stats(session, table_name, column_name): - - # We could add MAX/MIN/AVG here but it wouldn't make much sense - # As ResultValue/ObservationValue will be across all tests - - sql_string = ( - """ - SELECT - COUNT(*) AS ROW_COUNT, - SUM(CASE WHEN """ - + column_name - + """ IS NOT NULL THEN 1 ELSE 0 END) AS VALUE_COUNT, - COUNT(DISTINCT """ - + column_name - + """) AS DISTINCT_VALUE_COUNT - FROM - """ - + table_name - ) - - result = session.execute(sql_string) - return result.fetchone() - - -def get_coded_fields(session): - - sql_string = """ - SELECT - tab_columns.table_name, - tab_columns.column_name - FROM - information_schema.columns AS tab_columns - WHERE - tab_columns.column_name LIKE :column_name_like AND - tab_columns.table_schema = 'extract' - """ - - results = session.execute(sql_string, {"column_name_like": "%codestd"}) - return results - - -def query_coded_fields(session, table_name, column_name): - - # codestd - base_name = column_name[:-7] - - code_std_field = column_name - desc_field = base_name + "desc" - code_field = base_name + "code" - - sql_string = ( - """ - - SELECT - '""" - + table_name - + """', - '""" - + code_std_field - + """', - """ - + code_std_field - + """, - '""" - + code_field - + """', - """ - + code_field - + """, - '""" - + desc_field - + """', - """ - + desc_field - + """, - COUNT(*) - FROM - """ - + table_name - + """ - GROUP BY - """ - + code_std_field - + """, - """ - + code_field - + """, - """ - + desc_field - ) - - results = session.execute(sql_string) - return results - - -class DBMetadata(object): - def __init__(self, session, xsdpath): - self.session = session - self.xsdpath = xsdpath - - def set_db_metadata(self): - - db_metadata = dict() - - session = self.session - table_names = get_db_table_list(session) - - for table_name in table_names: - print(table_name) - db_metadata[table_name] = dict() - for row in get_db_column_metadata(session, table_name): - column_name = row[0] - field_stats = get_field_contents_stats(session, table_name, column_name) - row = list(row) - row.extend(field_stats) - db_metadata[table_name][column_name] = row - - self.db_metadata = db_metadata - - def process_xsd_file(self, fh): - ns = "http://www.w3.org/2001/XMLSchema" - xml_doc = etree.parse(fh) - appinfo_nodes = xml_doc.xpath("//xs:appinfo", namespaces={"xs": ns}) - xml_metadata = self.xml_metadata - for appinfo_node in appinfo_nodes: - appinfo_text = appinfo_node.text - # Assume value in format: - # table_name.column_name - split_appinfo_text = appinfo_text.split(".") - table_name = split_appinfo_text[0] - column_name = split_appinfo_text[1] - - try: - documentation_node = appinfo_node.xpath( - "following-sibling::xs:documentation", namespaces={"xs": ns} - )[-1] - except: # noqa: E722 - print("Error with", table_name, column_name) - continue - - documentation_text = documentation_node.text - - # NOTE: Here we go "up" from the documentation tag looking - # for the first element which doesn't match exclusions - # This may not be necessary and we might just be able to look - # for xs:element nodes. - element_node = appinfo_node.xpath( - "ancestor::*[not(self::xs:annotation)]", namespaces={"xs": ns} - )[-1] - xml_element_name = element_node.attrib["name"] - - xml_element_type = element_node.attrib.get("type", None) - - # If not present minOccurs default is 1 - xml_element_minoccurs = element_node.attrib.get("minOccurs", "1") - - xml_element_maxoccurs = element_node.attrib.get("maxOccurs", None) - - if table_name not in xml_metadata: - xml_metadata[table_name] = dict() - - xml_metadata[table_name][column_name] = ( - xml_element_name, - xml_element_type, - xml_element_minoccurs, - xml_element_maxoccurs, - documentation_text, - ) - - def set_xml_metadata(self): - self.xml_metadata = dict() - for root, dirs, files in os.walk(self.xsdpath, topdown=False): - for name in files: - if not name.endswith(".xsd"): - continue - fp = os.path.join(root, name) - with open(fp) as fh: - self.process_xsd_file(fh) - - def run(self): - self.set_db_metadata() - self.set_xml_metadata() - xml_metadata = self.xml_metadata - db_metadata = self.db_metadata - xml_md_keys = xml_metadata.keys() - for table_name in db_metadata.keys(): - if table_name not in xml_metadata: - continue - xml_md_table_keys = xml_metadata[table_name].keys() - for column_name in db_metadata[table_name].keys(): - extra = all( - (table_name in xml_md_keys, column_name in xml_md_table_keys) - ) - if extra: - # Add the extra XML columns if there's a match - db_column_data = db_metadata[table_name][column_name] - xml_column_data = xml_metadata[table_name][column_name] - db_column_data.extend(xml_column_data) - db_metadata[table_name][column_name] = db_column_data - - -def make_report(db_metadata, filepath): - - work_book = xlwt.Workbook() - fields = ( - "Column Name", - "Data Type", - "Max Length", - "Numeric Precision", - "Is Nullable", - "Constraint Type", - "Constraint Name", - "Check Clause", - "Row Count", - "Value Count", - "Distinct Value Count", - "XML Element Name", - "XML Type", - "XML MinOccurs", - "XML MaxOccurs", - "XML Description", - ) - for table_name in db_metadata.keys(): - work_sheet = work_book.add_sheet(table_name) - row = work_sheet.row(0) - - for x, header in enumerate(fields): - row.write(x, header) - - y = 1 - for column_name in db_metadata[table_name]: - field_row = db_metadata[table_name][column_name] - row = work_sheet.row(y) - for x, value in enumerate(field_row): - row.write(x, value) - y += 1 - work_book.save(filepath) - - -def make_coded_field_report(session, filepath): - - csvwriter = csv.writer(open(filepath, "w", newline="", encoding="utf-8")) - - csvwriter.writerow( - ( - "Table Name", - "Coding Std Field", - "Coding Std Value", - "Code Field", - "Code Value", - "Desc Field", - "Desc", - ) - ) - - coded_fields = get_coded_fields(session) - - for table_name, column_name in coded_fields: - print(table_name, column_name) - results = query_coded_fields(session, table_name, column_name) - for row in results: - csvwriter.writerow(row) - - -def main(): - xsd_path = "schema/ukrdc/" - sessionmaker = Connection.get_sessionmaker_from_file(key="ukrdc_live") - session = sessionmaker() - dbm = DBMetadata(session, xsd_path) - dbm.run() - make_report(dbm.db_metadata, "dataset_report.xls") - make_coded_field_report(session, "coded_field_report.csv") - - -if __name__ == "__main__": - main() From 9a2447a63e54d43cc39c0c766eeff145280cbb6a Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 3 Nov 2024 22:24:55 +0000 Subject: [PATCH 091/166] Update DialysisSession metadata --- schema/ukrdc/DialysisSessions/DialysisSession.xsd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/schema/ukrdc/DialysisSessions/DialysisSession.xsd b/schema/ukrdc/DialysisSessions/DialysisSession.xsd index 797d50c..7c77fc6 100644 --- a/schema/ukrdc/DialysisSessions/DialysisSession.xsd +++ b/schema/ukrdc/DialysisSessions/DialysisSession.xsd @@ -20,7 +20,7 @@ - + Symptomatic hypotension (QHD19) @@ -32,7 +32,7 @@ - + Vascular Access Site (QHD21) From 785a82b87d98c3efe771c0fdbcd0d88f262c98cf Mon Sep 17 00:00:00 2001 From: George Swinnerton Date: Sun, 3 Nov 2024 22:44:19 +0000 Subject: [PATCH 092/166] Update Procedure metadata --- schema/ukrdc/Procedures/Procedure.xsd | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/schema/ukrdc/Procedures/Procedure.xsd b/schema/ukrdc/Procedures/Procedure.xsd index f12c499..4654124 100644 --- a/schema/ukrdc/Procedures/Procedure.xsd +++ b/schema/ukrdc/Procedures/Procedure.xsd @@ -11,19 +11,16 @@ - At least code must be entered - The time the Procedure started. - - + > Location the procedure was performed at. Use National coding e.g. RXF01 From 7b4aa457ea3606f1f6593aff6b0c6b540f6c24ef Mon Sep 17 00:00:00 2001 From: andreoap Date: Tue, 28 Jan 2025 11:10:25 +0000 Subject: [PATCH 093/166] Add RADAR dose unit codes --- codes/code_lists/dose_units.csv | 2 ++ schema/ukrdc/Procedures/Procedure.xsd | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/dose_units.csv b/codes/code_lists/dose_units.csv index 22f8564..58ec28c 100644 --- a/codes/code_lists/dose_units.csv +++ b/codes/code_lists/dose_units.csv @@ -16,3 +16,5 @@ RADAR,patch,patch,dose_unit RADAR,sachet,sachet,dose_unit RADAR,µg,microgram,dose_unit RADAR,tbsp,table_spoon,dose_unit +RADAR,units,units,dose_unit +RADAR,other,other,dose_unit diff --git a/schema/ukrdc/Procedures/Procedure.xsd b/schema/ukrdc/Procedures/Procedure.xsd index 4654124..b1a79d4 100644 --- a/schema/ukrdc/Procedures/Procedure.xsd +++ b/schema/ukrdc/Procedures/Procedure.xsd @@ -20,7 +20,7 @@ - > + Location the procedure was performed at. Use National coding e.g. RXF01 From 1d585be9c7326b3536a8ef2a68538c4b45284720 Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Mon, 10 Feb 2025 14:18:42 +0000 Subject: [PATCH 094/166] added new code conversions (#26) --- codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv diff --git a/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv b/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv new file mode 100644 index 0000000..dda4b15 --- /dev/null +++ b/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv @@ -0,0 +1,5 @@ +CF_RR23, microgram, RADAR, µg +CF_RR23, ug, RADAR, µg +CF_RR23, microg, RADAR, µg +CF_RR23, tablet, RADAR, tab +CF_RR23, tab, RADAR, tab \ No newline at end of file From c82a0b89a8e8ccfa41dda0d1765e5b79fe6a2f22 Mon Sep 17 00:00:00 2001 From: andreoap Date: Thu, 13 Feb 2025 11:59:09 +0000 Subject: [PATCH 095/166] Add RTG54 code and satellite mapping --- codes/code_lists/rr1plus_facilities.csv | 1 + codes/satellite_map/satellite_map.csv | 1 + 2 files changed, 2 insertions(+) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index b65f7e9..e7a896a 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -399,3 +399,4 @@ RR1+,RY5K7,CHANDRA MISTRY DIALYSIS UNIT RR1+,RAJ,MID & SOUTH ESSEX TRUST RR1+,BAPN,Migrated BAPN Data RR1+,RTR45,Friarage Dialysis Centre +RR1+,RTG54,Samuel Johnson Community Hospital (Litchfield) \ No newline at end of file diff --git a/codes/satellite_map/satellite_map.csv b/codes/satellite_map/satellite_map.csv index fcecfca..e12658e 100644 --- a/codes/satellite_map/satellite_map.csv +++ b/codes/satellite_map/satellite_map.csv @@ -219,3 +219,4 @@ RHANN,RCSLB RX1RA,RCSLB RXM56,RCSLB RFJBC,RCSLB +RTG54,RFPFG From 21d251b824025b382102ba749029f5fe7c8f2be3 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 13 Feb 2025 14:05:23 +0000 Subject: [PATCH 096/166] Update descriptions in snomed.csv --- codes/code_lists/snomed.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/codes/code_lists/snomed.csv b/codes/code_lists/snomed.csv index 2b9e460..37cb8ed 100644 --- a/codes/code_lists/snomed.csv +++ b/codes/code_lists/snomed.csv @@ -2,10 +2,10 @@ SNOMED,445119005,Steroid sensitive nephrotic syndrome of childhood SNOMED,48796009,Congenital nephrotic syndrome SNOMED,197601003,Finnish congenital nephrotic syndrome -SNOMED,722369003,Congenital nephrotic syndrome +SNOMED,722369003,Congenital nephrotic syndrome due to diffuse mesangial sclerosis SNOMED,236384008,Congenital nephrotic syndrome with focal glomerulosclerosis SNOMED,236385009,Drash syndrome -SNOMED,722118005,Congenital nephrotic syndrome +SNOMED,722118005,Congenital nephrotic syndrome due to congenital infection SNOMED,44785005,Minimal change disease SNOMED,236407003,IgA nephropathy SNOMED,445404003,Familial immunoglobulin A nephropathy @@ -18,7 +18,7 @@ SNOMED,722168002,Membranous glomerulonephritis with infectious disease SNOMED,75888001,"Mesangiocapillary glomerulonephritis, type I " SNOMED,722760002,"Mesangiocapillary glomerulonephritis, type II " SNOMED,236409000,Mesangiocapillary glomerulonephritis type III -SNOMED,197697005, +SNOMED,197697005,Rapidly progressive nephritic syndrome, diffuse crescentic glomerulonephritis SNOMED,236404005,Classical focal segmental glomerulosclerosis SNOMED,445388002,Autosomal recessive focal segmental glomerulosclerosis SNOMED,444977005,Autosomal dominant focal segmental glomerulosclerosis From 9afb8b4ecc320d294432b3a92224eb31451b46cd Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 13 Feb 2025 14:06:52 +0000 Subject: [PATCH 097/166] Update descriptions in snomed.csv --- codes/code_lists/snomed.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/codes/code_lists/snomed.csv b/codes/code_lists/snomed.csv index 37cb8ed..4c28bde 100644 --- a/codes/code_lists/snomed.csv +++ b/codes/code_lists/snomed.csv @@ -18,7 +18,7 @@ SNOMED,722168002,Membranous glomerulonephritis with infectious disease SNOMED,75888001,"Mesangiocapillary glomerulonephritis, type I " SNOMED,722760002,"Mesangiocapillary glomerulonephritis, type II " SNOMED,236409000,Mesangiocapillary glomerulonephritis type III -SNOMED,197697005,Rapidly progressive nephritic syndrome, diffuse crescentic glomerulonephritis +SNOMED,197697005,Rapidly progressive nephritic syndrome - diffuse crescentic glomerulonephritis SNOMED,236404005,Classical focal segmental glomerulosclerosis SNOMED,445388002,Autosomal recessive focal segmental glomerulosclerosis SNOMED,444977005,Autosomal dominant focal segmental glomerulosclerosis From f8a50bdd2cb8e89a92cdc08b3fca5af2d988bf16 Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Mon, 17 Feb 2025 13:43:24 +0000 Subject: [PATCH 098/166] Update dose_units_cf_rr23_to_radar.csv --- codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv b/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv index dda4b15..26b5596 100644 --- a/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv +++ b/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv @@ -1,5 +1,5 @@ CF_RR23, microgram, RADAR, µg CF_RR23, ug, RADAR, µg +CF_RR23, µg, RADAR, µg CF_RR23, microg, RADAR, µg -CF_RR23, tablet, RADAR, tab -CF_RR23, tab, RADAR, tab \ No newline at end of file +CF_RR23, tab, RADAR, tab From 226bc25b0bc312f3c77c674c1b80effe679901fd Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Mar 2025 12:11:01 +0000 Subject: [PATCH 099/166] Add UKRR Units of Measure to ukrr_observations.csv --- codes/code_lists/ukrr_observations.csv | 122 ++++++++++++------------- 1 file changed, 61 insertions(+), 61 deletions(-) diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv index 04ff0fa..fa89bda 100644 --- a/codes/code_lists/ukrr_observations.csv +++ b/codes/code_lists/ukrr_observations.csv @@ -1,61 +1,61 @@ -UKRR,QBLA1,Serum Creatinine,result -UKRR,QBLA3,Serum Urea,result -UKRR,QBLA4,Serum Bicarbonate,result -UKRR,QBLA6,Serum Sodium,result -UKRR,QBLA9,Serum Potassium,result -UKRR,QBLAB,Lab Calculated eGFR,result -UKRR,QBLAC,Serum Uric Acid (Urate),result -UKRR,QBLAL,Unit Calculated eGFR,result -UKRR,QBLB1,Serum Phosphate,result -UKRR,QBLB3,Serum Calcium,result -UKRR,QBLB4,Corrected Serum Calcium,result -UKRR,QBLB5,Serum Alkaline Phosphatase,result -UKRR,QBLB7,Serum Albumin,result -UKRR,QBLB9,Serum Parathyroid Hormone (PTH),result -UKRR,QBLC1,Urine Protein:Creatinine Ratio,result -UKRR,QBLC3,Urine Albumin:Creatinine Ratio,result -UKRR,QBLD1,Total Serium Cholesterol,result -UKRR,QBLD3,Serum HDL Cholesterol,result -UKRR,QBLD4,Serum LDL Cholesterol,result -UKRR,QBLD5,Serum Triglycerides,result -UKRR,QBLD6,CRP,result -UKRR,QBLD8,Hba1c %,result -UKRR,QBLDA,Hba1c,result -UKRR,QBLE1,Haemoglobin,result -UKRR,QBLE3,MCH,result -UKRR,QBLE4,Platelets,result -UKRR,QBLE5,WBC (from full blood count),result -UKRR,QBLEB,Haemloglobin,result -UKRR,QBLF1,Serum Ferritin,result -UKRR,QBLF3,Transferrin Saturation,result -UKRR,QBLF5,Percentage of Hypochromic Cells,result -UKRR,QBLF7,Serum B12,result -UKRR,QBLF9,Serum Folate,result -UKRR,QBLFB,Red Cell Folate,result -UKRR,QBLFD,Serum Aluminium,result -UKRR,QBLFF,Tacrolimus Blood Concentration Level,result -UKRR,QBLFH,Sirolimus Blood Concentration Level,result -UKRR,QBLFK,Ciclosporin Blood Concentration Level,result -UKRR,QBLFM,Mycophenolate Blood Concentration Level,result -UKRR,QBLG1,Weight,observation -UKRR,QBLG3,Systolic BP,observation -UKRR,QBLG4,Diastolic BP,observation -UKRR,QBLG9,Urea Reduction Ratio,result -UKRR,QBLGG,Kt/V,result -UKRR,QBLGB,Height,observation -UKRR,QBLHA,HBV Antibody Status,result -UKRR,QBLHC,HBV Surface Antigen Status,result -UKRR,QBLHE,HCV Antibody Status,result -UKRR,QBLHG,CMV Antibody Status,result -UKRR,QBLHK,CMV PCR Copies/ML,result -UKRR,QBLHM,HIV Antigen Status,result -UKRR,QBLHN,Varicella,result -UKRR,QBLHR,EBV Status,result -UKRR,QBLHS,EBV Log Count,result -UKRR,QBLHV,Urine Volume in 24 Hours,observation -UKRR,QBLHX,Urinary Creatinine Extraction,result -UKRR,QBLPA,PTH ULN,result -UKRR,QBLPB,PTH / PTHH ULN Ratio,result -UKRR,QBLPC,ALT,result -UKRR,QBLPD,ANC,result -UKRR,QBLPE,ALC,result \ No newline at end of file +UKRR,QBLA1,Serum Creatinine,result,umol/L +UKRR,QBLA3,Serum Urea,result,mmol/L +UKRR,QBLA4,Serum Bicarbonate,result,mmol/L +UKRR,QBLA6,Serum Sodium,result,mmol/L +UKRR,QBLA9,Serum Potassium,result,mmol/L +UKRR,QBLAB,Lab Calculated eGFR,result, +UKRR,QBLAC,Serum Uric Acid (Urate),result,mmol/L +UKRR,QBLAL,Unit Calculated eGFR,result, +UKRR,QBLB1,Serum Phosphate,result,mmol/L +UKRR,QBLB3,Serum Calcium,result,mmol/L +UKRR,QBLB4,Corrected Serum Calcium,result,mmol/L +UKRR,QBLB5,Serum Alkaline Phosphatase,result,IU/L +UKRR,QBLB7,Serum Albumin,result,g/L +UKRR,QBLB9,Serum Parathyroid Hormone (PTH),result,pmol/L +UKRR,QBLC1,Urine Protein:Creatinine Ratio,result, +UKRR,QBLC3,Urine Albumin:Creatinine Ratio,result, +UKRR,QBLD1,Total Serium Cholesterol,result,mmol/L +UKRR,QBLD3,Serum HDL Cholesterol,result,mmol/L +UKRR,QBLD4,Serum LDL Cholesterol,result,mmol/L +UKRR,QBLD5,Serum Triglycerides,result,mmol/L +UKRR,QBLD6,CRP,result,mg/L +UKRR,QBLD8,Hba1c %,result,% +UKRR,QBLDA,Hba1c,result,mmol/mol +UKRR,QBLE1,Haemoglobin,result,g/dL +UKRR,QBLE3,MCH,result, +UKRR,QBLE4,Platelets,result, +UKRR,QBLE5,WBC (from full blood count),result, +UKRR,QBLEB,Haemloglobin,result,g/L +UKRR,QBLF1,Serum Ferritin,result,ug/L = ng/ml +UKRR,QBLF3,Transferrin Saturation,result,% +UKRR,QBLF5,Percentage of Hypochromic Cells,result,% +UKRR,QBLF7,Serum B12,result,ng/L +UKRR,QBLF9,Serum Folate,result,ug/L +UKRR,QBLFB,Red Cell Folate,result,ug/L +UKRR,QBLFD,Serum Aluminium,result, +UKRR,QBLFF,Tacrolimus Blood Concentration Level,result,ng/mL +UKRR,QBLFH,Sirolimus Blood Concentration Level,result,ng/mL +UKRR,QBLFK,Ciclosporin Blood Concentration Level,result,ng/mL +UKRR,QBLFM,Mycophenolate Blood Concentration Level,result,ng/mL +UKRR,QBLG1,Weight,observation,kg +UKRR,QBLG3,Systolic BP,observation,mmHg +UKRR,QBLG4,Diastolic BP,observation,mmHg +UKRR,QBLG9,Urea Reduction Ratio,result, +UKRR,QBLGG,Kt/V,result, +UKRR,QBLGB,Height,observation,cm +UKRR,QBLHA,HBV Antibody Status,result, +UKRR,QBLHC,HBV Surface Antigen Status,result, +UKRR,QBLHE,HCV Antibody Status,result, +UKRR,QBLHG,CMV Antibody Status,result, +UKRR,QBLHK,CMV PCR Copies/ML,result, +UKRR,QBLHM,HIV Antigen Status,result, +UKRR,QBLHN,Varicella,result, +UKRR,QBLHR,EBV Status,result, +UKRR,QBLHS,EBV Log Count,result, +UKRR,QBLHV,Urine Volume in 24 Hours,observation,ml +UKRR,QBLHX,Urinary Creatinine Extraction,result,mmol/L +UKRR,QBLPA,PTH ULN,result, +UKRR,QBLPB,PTH / PTHH ULN Ratio,result, +UKRR,QBLPC,ALT,result,IU/L +UKRR,QBLPD,ANC,result, +UKRR,QBLPE,ALC,result, From 0fe62c41feda3154a828ea5f3d362d324ca4a64f Mon Sep 17 00:00:00 2001 From: George Date: Mon, 14 Apr 2025 20:02:10 +0100 Subject: [PATCH 100/166] Update pv_observations.csv Make "beautiful" --- codes/code_lists/pv_observations.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codes/code_lists/pv_observations.csv b/codes/code_lists/pv_observations.csv index c39ca10..963146b 100644 --- a/codes/code_lists/pv_observations.csv +++ b/codes/code_lists/pv_observations.csv @@ -1,6 +1,6 @@ PV,BodyTemperature,Body Temperature,obs PV,FaecalCalprotectin,Faecal Calprotectin,result,ug/g -PV,TargetWeight,Target Weight,obs +PV,TargetWeight,Target Weight,obs, PV,acr,ACR,result,mg/mmol PV,adjustedcalcium,Adjusted Calcium,result,mmol/L PV,albumin,Albumin,result,g/L @@ -89,4 +89,4 @@ PV,urr_post,URR (Post),result PV,vitb12,Vitamin B12,result,ng/l PV,vitd,Vitamin D,result,nmol/l PV,wbc,WBC,result,10^9/l -PV,weight,Weight,obs,kg \ No newline at end of file +PV,weight,Weight,obs,kg From 30c0ef5f1e3631e4cbf0320e895bea3355446f00 Mon Sep 17 00:00:00 2001 From: George Date: Mon, 14 Apr 2025 20:03:38 +0100 Subject: [PATCH 101/166] Update pv_observations.csv Make "beautiful" #2 --- codes/code_lists/pv_observations.csv | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/codes/code_lists/pv_observations.csv b/codes/code_lists/pv_observations.csv index 963146b..f87327d 100644 --- a/codes/code_lists/pv_observations.csv +++ b/codes/code_lists/pv_observations.csv @@ -1,4 +1,4 @@ -PV,BodyTemperature,Body Temperature,obs +PV,BodyTemperature,Body Temperature,obs, PV,FaecalCalprotectin,Faecal Calprotectin,result,ug/g PV,TargetWeight,Target Weight,obs, PV,acr,ACR,result,mg/mmol @@ -14,14 +14,14 @@ PV,bmi,BMI,obs, PV,bpdia,BP Diastolic,obs,mm Hg PV,bpsys,BP Systolic,obs,mm Hg PV,calcium,Calcium,result,mmol/l -PV,calcium_post,Calcium (Post),result +PV,calcium_post,Calcium (Post),result, PV,cholesterol,Cholesterol,result,mmol/l PV,ciclosporin,Ciclosporin,result,ng/ml -PV,covid19antibody,Covid-19 Antibody,result -PV,covid19lflow,Covid-19 Lateral Flow,result -PV,covid19pcr,Covid-19 PCR,result +PV,covid19antibody,Covid-19 Antibody,result, +PV,covid19lflow,Covid-19 Lateral Flow,result, +PV,covid19pcr,Covid-19 PCR,result, PV,creatinine,Creatinine,result,umol/l -PV,creatinine_post,Creatinine (Post),result +PV,creatinine_post,Creatinine (Post),result, PV,crp,CRP,result,mg/l PV,egfr,eGFR,result,mL/min/1.73m^2 PV,egfr_post,eGFR (Post),result,mL/min/1.73m^2 @@ -33,14 +33,14 @@ PV,ggt,GGT,result,U/l PV,glucose,Glucose Random,result,mmol/l PV,hb,Hb,result,g/l PV,hba1c,HbA1c,result,mmol/mol -PV,hbv,Hep B,result +PV,hbv,Hep B,result, PV,hco3,Bicarb,result,mmol/l -PV,hco3_post,HCO3 (Post),result +PV,hco3_post,HCO3 (Post),result, PV,hct,HCT/PCV,result,I/l -PV,hcv,Hep C,result +PV,hcv,Hep C,result, PV,hdl,HDL,result,mmol/l PV,height,Height,obs,cm -PV,hypotension,Symptomatic Hypotension,obs +PV,hypotension,Symptomatic Hypotension,obs, PV,inr,INR,result,ratio PV,iron,Iron,result,mmol/l PV,ironsat,Fe Sat,result,% @@ -53,7 +53,7 @@ PV,lithium,Lithium,result,mEq/l PV,magnesium,Mg,result,mmol/l PV,mmp,MMP Level,result, PV,neutrophils,Neutrophils,result,10^9/l -PV,odema,Odema,obs +PV,odema,Odema,obs, PV,pcr,PCR,result,mg/mmol PV,phepku,Phenylalanine,result,mg/dl PV,phosphate,Phosphate,result,mmol/l @@ -72,20 +72,20 @@ PV,t4,Total T4,result,ng/l PV,tacrolimus,Tacrolimus,result,ng/ml PV,testosterone,Serum Testosterone,result,ng/dl PV,tg,TG,result,mmol/l -PV,tgn,TGN Levels,result +PV,tgn,TGN Levels,result, PV,tpmt,TPMT Levels,result,mU/l PV,transferrin,Transferrin,result,% PV,trop,Troponin-T,result,ng/ml PV,tsh,TSH,result,mU/l PV,ualbumin,Urine Albumin,result,mg/l PV,ucreatinine,Urine Creatinine,result,mmol/l -PV,updipstick,Urine Protein Dipstick,obs +PV,updipstick,Urine Protein Dipstick,obs, PV,uprotein,Urine Protein,result,mmol/l PV,urate,Urate,result,mmol/l PV,urea,Urea,result,mmol/l PV,urea_post,Urea (Post),result,mmol/l PV,urr,URR,result,ratio -PV,urr_post,URR (Post),result +PV,urr_post,URR (Post),result, PV,vitb12,Vitamin B12,result,ng/l PV,vitd,Vitamin D,result,nmol/l PV,wbc,WBC,result,10^9/l From 5ae27c4c22eb433312f52f45a9434cda46208ef1 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 28 Apr 2025 15:37:42 +0100 Subject: [PATCH 102/166] Add UKRR Units of Measure to ukrr_observations.csv --- codes/code_lists/ukrr_observations.csv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv index fa89bda..8947270 100644 --- a/codes/code_lists/ukrr_observations.csv +++ b/codes/code_lists/ukrr_observations.csv @@ -22,7 +22,7 @@ UKRR,QBLD6,CRP,result,mg/L UKRR,QBLD8,Hba1c %,result,% UKRR,QBLDA,Hba1c,result,mmol/mol UKRR,QBLE1,Haemoglobin,result,g/dL -UKRR,QBLE3,MCH,result, +UKRR,QBLE3,MCH,result,g/dL UKRR,QBLE4,Platelets,result, UKRR,QBLE5,WBC (from full blood count),result, UKRR,QBLEB,Haemloglobin,result,g/L @@ -32,7 +32,7 @@ UKRR,QBLF5,Percentage of Hypochromic Cells,result,% UKRR,QBLF7,Serum B12,result,ng/L UKRR,QBLF9,Serum Folate,result,ug/L UKRR,QBLFB,Red Cell Folate,result,ug/L -UKRR,QBLFD,Serum Aluminium,result, +UKRR,QBLFD,Serum Aluminium,result,umol/L UKRR,QBLFF,Tacrolimus Blood Concentration Level,result,ng/mL UKRR,QBLFH,Sirolimus Blood Concentration Level,result,ng/mL UKRR,QBLFK,Ciclosporin Blood Concentration Level,result,ng/mL @@ -47,13 +47,13 @@ UKRR,QBLHA,HBV Antibody Status,result, UKRR,QBLHC,HBV Surface Antigen Status,result, UKRR,QBLHE,HCV Antibody Status,result, UKRR,QBLHG,CMV Antibody Status,result, -UKRR,QBLHK,CMV PCR Copies/ML,result, +UKRR,QBLHK,CMV PCR Copies/ML,result,IU/mL UKRR,QBLHM,HIV Antigen Status,result, UKRR,QBLHN,Varicella,result, UKRR,QBLHR,EBV Status,result, UKRR,QBLHS,EBV Log Count,result, UKRR,QBLHV,Urine Volume in 24 Hours,observation,ml -UKRR,QBLHX,Urinary Creatinine Extraction,result,mmol/L +UKRR,QBLHX,Urinary Creatinine Excretion,result,mmol/L UKRR,QBLPA,PTH ULN,result, UKRR,QBLPB,PTH / PTHH ULN Ratio,result, UKRR,QBLPC,ALT,result,IU/L From 62e1756d4d5af7d14fdb98141f8daf6962a5c8eb Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 1 May 2025 14:14:57 +0100 Subject: [PATCH 103/166] Add UKRR Units of Measure to ukrr_observations.csv --- codes/code_lists/ukrr_observations.csv | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv index 8947270..4706628 100644 --- a/codes/code_lists/ukrr_observations.csv +++ b/codes/code_lists/ukrr_observations.csv @@ -3,9 +3,9 @@ UKRR,QBLA3,Serum Urea,result,mmol/L UKRR,QBLA4,Serum Bicarbonate,result,mmol/L UKRR,QBLA6,Serum Sodium,result,mmol/L UKRR,QBLA9,Serum Potassium,result,mmol/L -UKRR,QBLAB,Lab Calculated eGFR,result, +UKRR,QBLAB,Lab Calculated eGFR,result,mL/min/1.72m^2 UKRR,QBLAC,Serum Uric Acid (Urate),result,mmol/L -UKRR,QBLAL,Unit Calculated eGFR,result, +UKRR,QBLAL,Unit Calculated eGFR,result,mL/min/1.72m^2 UKRR,QBLB1,Serum Phosphate,result,mmol/L UKRR,QBLB3,Serum Calcium,result,mmol/L UKRR,QBLB4,Corrected Serum Calcium,result,mmol/L @@ -23,8 +23,8 @@ UKRR,QBLD8,Hba1c %,result,% UKRR,QBLDA,Hba1c,result,mmol/mol UKRR,QBLE1,Haemoglobin,result,g/dL UKRR,QBLE3,MCH,result,g/dL -UKRR,QBLE4,Platelets,result, -UKRR,QBLE5,WBC (from full blood count),result, +UKRR,QBLE4,Platelets,result,10^9/L +UKRR,QBLE5,WBC (from full blood count),result,10^9/L UKRR,QBLEB,Haemloglobin,result,g/L UKRR,QBLF1,Serum Ferritin,result,ug/L = ng/ml UKRR,QBLF3,Transferrin Saturation,result,% @@ -54,7 +54,7 @@ UKRR,QBLHR,EBV Status,result, UKRR,QBLHS,EBV Log Count,result, UKRR,QBLHV,Urine Volume in 24 Hours,observation,ml UKRR,QBLHX,Urinary Creatinine Excretion,result,mmol/L -UKRR,QBLPA,PTH ULN,result, +UKRR,QBLPA,PTH ULN,result,pmol/L UKRR,QBLPB,PTH / PTHH ULN Ratio,result, UKRR,QBLPC,ALT,result,IU/L UKRR,QBLPD,ANC,result, From f0bcb506cf9c8fcdd8686fd290b9105bd1ce84c6 Mon Sep 17 00:00:00 2001 From: andreoap Date: Thu, 8 May 2025 10:12:20 +0100 Subject: [PATCH 104/166] Add BHLY codes 996 and 997 --- codes/code_lists/rr1plus_facilities.csv | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index e7a896a..ad23006 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -399,4 +399,6 @@ RR1+,RY5K7,CHANDRA MISTRY DIALYSIS UNIT RR1+,RAJ,MID & SOUTH ESSEX TRUST RR1+,BAPN,Migrated BAPN Data RR1+,RTR45,Friarage Dialysis Centre -RR1+,RTG54,Samuel Johnson Community Hospital (Litchfield) \ No newline at end of file +RR1+,RTG54,Samuel Johnson Community Hospital (Litchfield) +RR1+,996,BHLY - 996 +RR1+,997,BHLY - 997 \ No newline at end of file From 4cf044e18bf3e32e6a6b6c914471ae25b38316d1 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 29 May 2025 10:44:27 +0100 Subject: [PATCH 105/166] Add Units of Measure to ukrr_observations.csv --- codes/code_lists/ukrr_observations.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv index 4706628..8fb0580 100644 --- a/codes/code_lists/ukrr_observations.csv +++ b/codes/code_lists/ukrr_observations.csv @@ -57,5 +57,5 @@ UKRR,QBLHX,Urinary Creatinine Excretion,result,mmol/L UKRR,QBLPA,PTH ULN,result,pmol/L UKRR,QBLPB,PTH / PTHH ULN Ratio,result, UKRR,QBLPC,ALT,result,IU/L -UKRR,QBLPD,ANC,result, -UKRR,QBLPE,ALC,result, +UKRR,QBLPD,ANC,result,10^9/L +UKRR,QBLPE,ALC,result,10^9/L From 4517c81b1f27e064b087a76a0e015f55bb94b9b8 Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Tue, 22 Jul 2025 14:04:16 +0100 Subject: [PATCH 106/166] added pytyped (#30) * added pytyped * added pytyped to build --- pyxb_build/setup.py | 2 +- pyxb_build/ukrdc_schema/py.typed | 0 xsdata_build/build.sh | 3 +++ 3 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 pyxb_build/ukrdc_schema/py.typed diff --git a/pyxb_build/setup.py b/pyxb_build/setup.py index e28ac7b..81e789d 100644 --- a/pyxb_build/setup.py +++ b/pyxb_build/setup.py @@ -6,7 +6,7 @@ match_pat = r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]' version = re.search(match_pat, f.read(), re.MULTILINE).group(1) -data = {'ukrdc_schema': ['transforms/*.xsl'], } +data = {'ukrdc_schema': ['transforms/*.xsl', 'py.typed'], } setup( name='ukrdc_schema', version=version, diff --git a/pyxb_build/ukrdc_schema/py.typed b/pyxb_build/ukrdc_schema/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/xsdata_build/build.sh b/xsdata_build/build.sh index db870fc..2f4d6a0 100755 --- a/xsdata_build/build.sh +++ b/xsdata_build/build.sh @@ -1,3 +1,6 @@ xsdata ../schema/ukrdc/UKRDC.xsd --config .xsdata.xml --package ukrdc_xsdata.ukrdc xsdata ../schema/pv2/PV_2_0.xsd --config .xsdata.xml --package ukrdc_xsdata.pv xsdata ../schema/rrtf/RRTF_4.xsd --config .xsdata.xml --package ukrdc_xsdata.rrtf + +# Add py.typed to top-level package to enable type checking +touch ukrdc_xsdata/py.typed From 408d6a8ad4adeb2ac7c40c6fb4f41b96e0917f64 Mon Sep 17 00:00:00 2001 From: GlebRysev-UKKA Date: Thu, 31 Jul 2025 09:29:25 +0100 Subject: [PATCH 107/166] feat(RR-1438): RR19 picklist for COM82 --- schema/rrtf/RRTF_4.xsd | 147 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 144 insertions(+), 3 deletions(-) diff --git a/schema/rrtf/RRTF_4.xsd b/schema/rrtf/RRTF_4.xsd index e0289aa..edf6104 100644 --- a/schema/rrtf/RRTF_4.xsd +++ b/schema/rrtf/RRTF_4.xsd @@ -1688,6 +1688,116 @@ + + + + + + Non-melanoma skin cancer, BCC, SCC + + + + + + + Melanoma + + + + + + + Breast + + + + + + + Upper GI (oesophagus/stomach) + + + + + + + Lower GI (small/large bowel) + + + + + + + Lung + + + + + + + Urological NOT prostate + + + + + + + Prostate + + + + + + + Testicular + + + + + + + Leukaemia + + + + + + + Lymphoma + + + + + + + Myeloma + + + + + + + CNS Tumour + + + + + + + Musculo-skeletal + + + + + + + Other + + + + + + @@ -3593,6 +3703,37 @@ + + + + RR_DATE_FIRST_CKD1 + + + + + + RR_DATE_FIRST_CKD2 + + + + + + RR_DATE_FIRST_CKD3 + + + + + + RR_DATE_FIRST_CKD4 + + + + + + RR_DATE_FIRST_CKD5 + + + @@ -3654,14 +3795,12 @@ Pre dialysis Creatinine at 1st RRT / ERF treatment - - @@ -4073,7 +4212,7 @@ - + @@ -4970,6 +5109,8 @@ + + From d10481838168d0fca2204faef16a81a03b5a51db Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Fri, 15 Aug 2025 11:24:20 +0100 Subject: [PATCH 108/166] Update rr1plus_facilities_to_radar.csv --- codes/code_conv_lists/rr1plus_facilities_to_radar.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/codes/code_conv_lists/rr1plus_facilities_to_radar.csv b/codes/code_conv_lists/rr1plus_facilities_to_radar.csv index b940cbb..4801101 100644 --- a/codes/code_conv_lists/rr1plus_facilities_to_radar.csv +++ b/codes/code_conv_lists/rr1plus_facilities_to_radar.csv @@ -1,3 +1,4 @@ RR1+,RJ121,RADAR,RJ100 RR1+,SSC02,RADAR,RSC02 RR1+,RCSLB,RADAR,RX1CC +RR1+,RBN63,RADAR,RQ617 From 69d7b82e51b93bad93d52ac78d59bcc857c5d480 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Fri, 15 Aug 2025 12:45:14 +0100 Subject: [PATCH 109/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index ad23006..388ee06 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -401,4 +401,27 @@ RR1+,BAPN,Migrated BAPN Data RR1+,RTR45,Friarage Dialysis Centre RR1+,RTG54,Samuel Johnson Community Hospital (Litchfield) RR1+,996,BHLY - 996 -RR1+,997,BHLY - 997 \ No newline at end of file +RR1+,997,BHLY - 997 +RR1+,RA702,BRISTOL GENERAL HOSPITAL +RR1+,RD304,POOLE GENERAL HOSPITAL +RR1+,RVR50,EPSOM HOSPITAL +RR1+,RNZ36,ST MARYS HOSPITAL (PORTSMOUTH) +RR1+,RLT14,COVENTRY & WARWICKS HOSPITAL FACILITIES +RR1+,E102H,London Hospital +RR1+,RK5BC,KING'S MILL HOSPITAL +RR1+,RG303,FARNBOROUGH HOSPITAL +RR1+,RVN3N,SOUTHMEAD HOSPITAL AWP +RR1+,RGP72,LOWESTOFT HOSPITAL +RR1+,RT302,ROYAL BROMPTON HOSPITAL +RR1+,RED03,PLYMPTON HOSPITAL +RR1+,RD300,POOLE GENERAL HOSPITAL +RR1+,RUE01,STAFFORD DISTRICT GENERAL HOSPITAL +RR1+,RCPAA,BASSETLAW HOSPITAL +RR1+,RA503,GLOUCESTERSHIRE ROYAL HOSPITAL +RR1+,RT301,HAREFIELD HOSPITAL +RR1+,RJD01,STAFFORD HOSPITAL +RR1+,RLY02,STOKE CITY GENERAL HOSPITAL +RR1+,RFJBL,MANSFIELD COMMUNITY HOSPITAL +RR1+,RP1L2,JOHN RADCLIFFE HOSPITAL + + From 45ee401322d7c88c40cbef857a9ba314c64a8b47 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 19 Aug 2025 12:46:43 +0100 Subject: [PATCH 110/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 388ee06..9a7d9b3 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -423,5 +423,7 @@ RR1+,RJD01,STAFFORD HOSPITAL RR1+,RLY02,STOKE CITY GENERAL HOSPITAL RR1+,RFJBL,MANSFIELD COMMUNITY HOSPITAL RR1+,RP1L2,JOHN RADCLIFFE HOSPITAL +RR1+,RKB13,WARWICK NUFFIELD +RR1+,RKB28,Oxford University Hospitals NHS Foundation Trust From a08a6eb1b904374a9f483e77102c79dfb71badb6 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 26 Aug 2025 10:13:53 +0100 Subject: [PATCH 111/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 9a7d9b3..323cad0 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -425,5 +425,8 @@ RR1+,RFJBL,MANSFIELD COMMUNITY HOSPITAL RR1+,RP1L2,JOHN RADCLIFFE HOSPITAL RR1+,RKB13,WARWICK NUFFIELD RR1+,RKB28,Oxford University Hospitals NHS Foundation Trust - +RR1+,M5O5A,Somers Place Kidney Unit +RR1+,RJE55,Burton Hospital +RR1+,RTG08,Long Eaton Health Centre +RR1+,RTG05,St Oswalds Hospital From 9cdbb9e2eb5fe92d7e6c496db0ee50edb07638e5 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 23 Sep 2025 10:08:05 +0100 Subject: [PATCH 112/166] Update ukrr_observations.csv --- codes/code_lists/ukrr_observations.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv index 8fb0580..f4ea78e 100644 --- a/codes/code_lists/ukrr_observations.csv +++ b/codes/code_lists/ukrr_observations.csv @@ -12,8 +12,8 @@ UKRR,QBLB4,Corrected Serum Calcium,result,mmol/L UKRR,QBLB5,Serum Alkaline Phosphatase,result,IU/L UKRR,QBLB7,Serum Albumin,result,g/L UKRR,QBLB9,Serum Parathyroid Hormone (PTH),result,pmol/L -UKRR,QBLC1,Urine Protein:Creatinine Ratio,result, -UKRR,QBLC3,Urine Albumin:Creatinine Ratio,result, +UKRR,QBLC1,Urine Protein:Creatinine Ratio,result,mg/mmol +UKRR,QBLC3,Urine Albumin:Creatinine Ratio,result,mg/mmol UKRR,QBLD1,Total Serium Cholesterol,result,mmol/L UKRR,QBLD3,Serum HDL Cholesterol,result,mmol/L UKRR,QBLD4,Serum LDL Cholesterol,result,mmol/L From 1866132f400dc4fd14872ace92e23072ae9c1208 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 29 Sep 2025 11:16:29 +0100 Subject: [PATCH 113/166] Update snomed_codes.csv --- codes/code_lists/snomed_codes.csv | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/snomed_codes.csv b/codes/code_lists/snomed_codes.csv index 12d25c2..f216b95 100644 --- a/codes/code_lists/snomed_codes.csv +++ b/codes/code_lists/snomed_codes.csv @@ -4,4 +4,7 @@ SNOMED,301331008,BMI,obs,kg/m^2 SNOMED,162986007,Pulse,obs,bpm SNOMED,163030003,Systolic Blood Pressure,obs,mmHg (systolic) SNOMED,163031004,Diastolic Blood Pressure,obs,mmHg (diastolic) -SNOMED,75367002,Blood Pressure,obs \ No newline at end of file +SNOMED,75367002,Blood Pressure,obs +SNOMED,763264000,Canadian Study of Health and Aging Clinical Frailty Scale score (observable entity),obs +SNOMED,1366111000000102,Kidney Failure Risk Equation (4 Variable ) 2 year risk score (observable entity),obs +SNOMED,1365921000000102,Kidney Failure Risk Equation (4 Variable) 5 year risk score (observable entity),obs From c8d833e0299ff6c5c9fbc61951f2d7ac0ce7935a Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 13 Oct 2025 10:18:46 +0100 Subject: [PATCH 114/166] Update satellite_map.csv --- codes/satellite_map/satellite_map.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/codes/satellite_map/satellite_map.csv b/codes/satellite_map/satellite_map.csv index e12658e..cd81cf7 100644 --- a/codes/satellite_map/satellite_map.csv +++ b/codes/satellite_map/satellite_map.csv @@ -123,6 +123,7 @@ RJZW,RJZ RN7,RJZ RXJ06,RJZ RG222,RJZ +R7Y4J,RJZ 88A713,RJZ RKTAG,RQHC7 RKUAJ,RQHC7 From c2492e86ba5a1f584438e047389872be33c97849 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 13 Oct 2025 10:18:52 +0100 Subject: [PATCH 115/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 323cad0..0b31ab5 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -429,4 +429,4 @@ RR1+,M5O5A,Somers Place Kidney Unit RR1+,RJE55,Burton Hospital RR1+,RTG08,Long Eaton Health Centre RR1+,RTG05,St Oswalds Hospital - +RR1+,R7Y4J,Somers Place Kidney Unit From 3384cdd1203299fa9fcc888196762b20e48f91ac Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Fri, 17 Oct 2025 13:09:45 +0100 Subject: [PATCH 116/166] added ukrr testcodes to snomed (#32) --- .../ukrr_testcodes_to_snomed.csv | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 codes/code_conv_lists/ukrr_testcodes_to_snomed.csv diff --git a/codes/code_conv_lists/ukrr_testcodes_to_snomed.csv b/codes/code_conv_lists/ukrr_testcodes_to_snomed.csv new file mode 100644 index 0000000..53e37cc --- /dev/null +++ b/codes/code_conv_lists/ukrr_testcodes_to_snomed.csv @@ -0,0 +1,52 @@ +UKRR,QBLA1,SNOMED,1107001000000108 +UKRR,QBLA3,SNOMED,1110281000000107 +UKRR,QBLA4,SNOMED,1106011000000107 +UKRR,QBLA6,SNOMED,1107871000000107 +UKRR,QBLA9,SNOMED,1107761000000109 +UKRR,QBLAB,SNOMED,1107411000000104 +UKRR,QBLAC,SNOMED,1109851000000106 +UKRR,QBLAL,SNOMED,857971000000104 +UKRR,QBLAL,SNOMED,1020291000000106 +UKRR,QBLB1,SNOMED,1107711000000107 +UKRR,QBLB3,SNOMED,1106621000000109 +UKRR,QBLB4,SNOMED,1107251000000104 +UKRR,QBLB5,SNOMED,1106051000000106 +UKRR,QBLB7,SNOMED,1105861000000106 +UKRR,QBLB9,SNOMED,1109581000000102 +UKRR,QBLC3,SNOMED,1023491000000104 +UKRR,QBLD1,SNOMED,1106541000000101 +UKRR,QBLD3,SNOMED,1107681000000108 +UKRR,QBLD4,SNOMED,1108551000000102 +UKRR,QBLD5,SNOMED,1109831000000104 +UKRR,QBLD6,SNOMED,1106741000000105 +UKRR,QBLDA,SNOMED,1107481000000106 +UKRR,QBLE3,SNOMED,1022471000000107 +UKRR,QBLE4,SNOMED,1108041000000107 +UKRR,QBLE5,SNOMED,1110441000000100 +UKRR,QBLF1,SNOMED,1108611000000102 +UKRR,QBLF5,SNOMED,1111581000000104 +UKRR,QBLF9,SNOMED,1108651000000103 +UKRR,QBLFB,SNOMED,1108641000000101 +UKRR,QBLFD,SNOMED,12711000237100 +UKRR,QBLFF,SNOMED,1111311000000103 +UKRR,QBLFH,SNOMED,1107851000000103 +UKRR,QBLFK,SNOMED,1107021000000104 +UKRR,QBLFM,SNOMED,1109271000000101 +UKRR,QBLFM,SNOMED,1109281000000104 +UKRR,QBLG1,SNOMED,27113001 +UKRR,QBLG9,SNOMED,1110411000000101 +UKRR,QBLGG,SNOMED,1110501000000104 +UKRR,QBLGG,SNOMED,1110511000000102 +UKRR,QBLHA,SNOMED,1111161000000103 +UKRR,QBLHC,SNOMED,1111171000000105 +UKRR,QBLHE,SNOMED,1111131000000108 +UKRR,QBLHG,SNOMED,1111211000000108 +UKRR,QBLHK,SNOMED,1107381000000101 +UKRR,QBLHM,SNOMED,1111341000000102 +UKRR,QBLHN,SNOMED,1111351000000104 +UKRR,QBLHR,SNOMED,1111041000000100 +UKRR,QBLHS,SNOMED,996101000000106 +UKRR,QBLHX,SNOMED,1107011000000105 +UKRR,QBLPC,SNOMED,1106081000000100 +UKRR,QBLPD,SNOMED,1108071000000101 +UKRR,QBLPE,SNOMED,1107961000000106 \ No newline at end of file From aa24b90ad0e0668524815c66f57c89d2040d3713 Mon Sep 17 00:00:00 2001 From: andreoap Date: Mon, 20 Oct 2025 14:55:17 +0100 Subject: [PATCH 117/166] Add historical units RF202 and RF316 --- codes/code_lists/rr1plus_facilities.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 0b31ab5..2436c4c 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -430,3 +430,5 @@ RR1+,RJE55,Burton Hospital RR1+,RTG08,Long Eaton Health Centre RR1+,RTG05,St Oswalds Hospital RR1+,R7Y4J,Somers Place Kidney Unit +RR1+,RF202,PRINCESS ROYAL HOSPITAL +RR1+,RF316,CASTLE HILL HOSPITAL \ No newline at end of file From 639d091c7cb8dd0379e1d78cdb107a6a2372691b Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Thu, 23 Oct 2025 12:27:08 +0100 Subject: [PATCH 118/166] added ukrr testcodes to conversion ratio (#34) * added ukrr testcodes to conversion ratio --- codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv diff --git a/codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv b/codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv new file mode 100644 index 0000000..4d88fcd --- /dev/null +++ b/codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv @@ -0,0 +1,7 @@ +Coding_Standard,Code,Value +RATIO,QBLA1,8.841 +RATIO,QBLA3,16.65 +RATIO,QBLA6,43.48 +RATIO,QBLA9,25.7 +RATIO,QBLB9,9.5 +RATIO,QBLF7,1.355 \ No newline at end of file From 00a357ad13816c90de530ff819a8d3165aedc103 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 28 Oct 2025 16:39:04 +0000 Subject: [PATCH 119/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 2436c4c..90f21db 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -431,4 +431,5 @@ RR1+,RTG08,Long Eaton Health Centre RR1+,RTG05,St Oswalds Hospital RR1+,R7Y4J,Somers Place Kidney Unit RR1+,RF202,PRINCESS ROYAL HOSPITAL -RR1+,RF316,CASTLE HILL HOSPITAL \ No newline at end of file +RR1+,RF316,CASTLE HILL HOSPITAL +RR1+,RNS,Northampton General Hospital NHS Trust From a07f3fabf2f3b3e5805f6f3710032cfbf662ac64 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:00:14 +0000 Subject: [PATCH 120/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 3 +++ 1 file changed, 3 insertions(+) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 90f21db..6926bf4 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -433,3 +433,6 @@ RR1+,R7Y4J,Somers Place Kidney Unit RR1+,RF202,PRINCESS ROYAL HOSPITAL RR1+,RF316,CASTLE HILL HOSPITAL RR1+,RNS,Northampton General Hospital NHS Trust +RR1+,RQ309,Birmingham Children's 'Dialysis Provider' +RR1+,RJE55,Burton Hospital +RR1+,RTG05,St Oswald's Hospital From b640ef7ca93d21637a330159fcdb9864f1c96c8f Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:02:09 +0000 Subject: [PATCH 121/166] Update satellite_map.csv --- codes/satellite_map/satellite_map.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/codes/satellite_map/satellite_map.csv b/codes/satellite_map/satellite_map.csv index cd81cf7..6938d00 100644 --- a/codes/satellite_map/satellite_map.csv +++ b/codes/satellite_map/satellite_map.csv @@ -221,3 +221,5 @@ RX1RA,RCSLB RXM56,RCSLB RFJBC,RCSLB RTG54,RFPFG +RJE55,RFPFG +RTG05,RFPFG From 01cab4d6faa0a30a2e396490a744b31d3a00d7b5 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:03:45 +0000 Subject: [PATCH 122/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 2 -- 1 file changed, 2 deletions(-) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 6926bf4..60ac18f 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -434,5 +434,3 @@ RR1+,RF202,PRINCESS ROYAL HOSPITAL RR1+,RF316,CASTLE HILL HOSPITAL RR1+,RNS,Northampton General Hospital NHS Trust RR1+,RQ309,Birmingham Children's 'Dialysis Provider' -RR1+,RJE55,Burton Hospital -RR1+,RTG05,St Oswald's Hospital From 45f3af94a0aee8870c54ec1b9476f36b82a661e5 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:35:54 +0000 Subject: [PATCH 123/166] Update snomed_codes.csv --- codes/code_lists/snomed_codes.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/codes/code_lists/snomed_codes.csv b/codes/code_lists/snomed_codes.csv index f216b95..2bd446a 100644 --- a/codes/code_lists/snomed_codes.csv +++ b/codes/code_lists/snomed_codes.csv @@ -8,3 +8,4 @@ SNOMED,75367002,Blood Pressure,obs SNOMED,763264000,Canadian Study of Health and Aging Clinical Frailty Scale score (observable entity),obs SNOMED,1366111000000102,Kidney Failure Risk Equation (4 Variable ) 2 year risk score (observable entity),obs SNOMED,1365921000000102,Kidney Failure Risk Equation (4 Variable) 5 year risk score (observable entity),obs +SNOMED,386725007,Body temperature (observable entity),obs From 26f7e5179eecf61b147ba4152377e9fc5e957a31 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:48:28 +0000 Subject: [PATCH 124/166] Rename snomed_codes.csv to snomed_observation.csv --- codes/code_lists/{snomed_codes.csv => snomed_observation.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_codes.csv => snomed_observation.csv} (100%) diff --git a/codes/code_lists/snomed_codes.csv b/codes/code_lists/snomed_observation.csv similarity index 100% rename from codes/code_lists/snomed_codes.csv rename to codes/code_lists/snomed_observation.csv From 569be9ec8bdb6916b61af105bf40c1608b376dc8 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:49:04 +0000 Subject: [PATCH 125/166] Update and rename snomed.csv to snomed_renal_diagnosis.csv --- codes/code_lists/{snomed.csv => snomed_renal_diagnosis.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed.csv => snomed_renal_diagnosis.csv} (100%) diff --git a/codes/code_lists/snomed.csv b/codes/code_lists/snomed_renal_diagnosis.csv similarity index 100% rename from codes/code_lists/snomed.csv rename to codes/code_lists/snomed_renal_diagnosis.csv From 1c4baf6f0ce8a6f213afa447268cc3643278b450 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:49:34 +0000 Subject: [PATCH 126/166] Create snomed_diabetes --- codes/code_lists/snomed_diabetes | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 codes/code_lists/snomed_diabetes diff --git a/codes/code_lists/snomed_diabetes b/codes/code_lists/snomed_diabetes new file mode 100644 index 0000000..c9d9f3f --- /dev/null +++ b/codes/code_lists/snomed_diabetes @@ -0,0 +1,3 @@ +SNOMED,73211009,Diabetes - Unspecified +SNOMED,46635009,Diabetes - Type I +SNOMED,44054006,Diabetes - Type II From fe0490760b014e8b000c08e53af3cd1bc186fa09 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 30 Oct 2025 11:54:44 +0000 Subject: [PATCH 127/166] Create snomed_diagnosis --- codes/code_lists/snomed_diagnosis | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 codes/code_lists/snomed_diagnosis diff --git a/codes/code_lists/snomed_diagnosis b/codes/code_lists/snomed_diagnosis new file mode 100644 index 0000000..15abe54 --- /dev/null +++ b/codes/code_lists/snomed_diagnosis @@ -0,0 +1,28 @@ +SNOMED,73211009,Diabetes - Unspecified +SNOMED,46635009,Diabetes - Type I +SNOMED,44054006,Diabetes - Type II +SNOMED,414545008,Ischaemic Heart Disease +SNOMED,401303003,STEMI First Date +SNOMED,401314000,NSTEMI First Date +SNOMED,194828000,Angina Date First Diagnosed +SNOMED,232717009,CABG or Coronary Angioplasty +SNOMED,84114007,Episode of Heart Failure +SNOMED,49436004,Arterial Fibrillation Date First Diagnosed +SNOMED,86049000,Malignancy Date First Diagnosed +SNOMED,62914000,Cerebrovascular Disease +SNOMED,266257000,TIA First Date +SNOMED,230690007,CVE / Stroke First Date +SNOMED,77176002,Smoking - Current +SNOMED,8517006,Smoking - Ex +SNOMED,8392000,Smoking - Non +SNOMED,13645005,COPD Date Diagnosed +SNOMED,235856003,Liver Disease Date Diagnosed +SNOMED,400047006,PVD Date Diagnosed +SNOMED,81723002,Date of Amputation for PVD +SNOMED,275520000,Claudication Date Diagnosed +SNOMED,13954005,Ischaemic or Neuropathic Ulcers +SNOMED,418285008,Non-Coronary Vascular Intervention - Angioplasty +SNOMED,312288001,Non-Coronary Vascular Intervention - Vascular graft +SNOMED,432119003,Non-Coronary Vascular Intervention - Aneurysm +SNOMED,360042007,Non-Coronary Vascular Intervention - Stent +SNOMED,52448006,Dementia Date Diagnosed From d5b7a7b24fdd8748e97272d7afb5ff62cbe9501e Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 09:56:54 +0000 Subject: [PATCH 128/166] Create snomed_dialysis --- codes/code_lists/snomed_dialysis | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 codes/code_lists/snomed_dialysis diff --git a/codes/code_lists/snomed_dialysis b/codes/code_lists/snomed_dialysis new file mode 100644 index 0000000..3ddcd94 --- /dev/null +++ b/codes/code_lists/snomed_dialysis @@ -0,0 +1,2 @@ +SNOMED,302497006,Haemodialyis +SNOMED,19647005,Plasma Exchange From 150d90f996f5a8083690d8fe2c3f1231902b71a2 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 10:54:43 +0000 Subject: [PATCH 129/166] Create snomed_graft_type --- codes/code_lists/snomed_graft_type | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 codes/code_lists/snomed_graft_type diff --git a/codes/code_lists/snomed_graft_type b/codes/code_lists/snomed_graft_type new file mode 100644 index 0000000..d3e7e34 --- /dev/null +++ b/codes/code_lists/snomed_graft_type @@ -0,0 +1,3 @@ +SNOMED,62438007,Pancreas Transplant +SNOMED,70536003,Kidney Transplant +SNOMED,6471000179103,Kidney & Pancreas Transplant From 41422c7ba06f3aa6ef1f1d5ab906da5b36f185de Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 10:57:08 +0000 Subject: [PATCH 130/166] Create snomed_relationship --- codes/code_lists/snomed_relationship | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 codes/code_lists/snomed_relationship diff --git a/codes/code_lists/snomed_relationship b/codes/code_lists/snomed_relationship new file mode 100644 index 0000000..a0aaaa7 --- /dev/null +++ b/codes/code_lists/snomed_relationship @@ -0,0 +1,9 @@ +SNOMED,1076781000000103,Cadaver donor with donation after brain stem death +SNOMED,1128041000000103,Live related sibling donor +SNOMED,1128051000000100,Live related father donor +SNOMED,1128071000000109,Live related mother donor +SNOMED,1128061000000102,Live related child donor +SNOMED,220751000000102,Live Related Donor +SNOMED,220741000000100,Live Unrelated Donor +SNOMED,1076791000000101,Cadaver donor with donation after cardiac death +SNOMED,105455006,Donor for medical or surgical procedure From 85c70517eef62f77907da1c285b087ed8d8a2fdf Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:01:14 +0000 Subject: [PATCH 131/166] Create snomed_units_of_measure --- codes/code_lists/snomed_units_of_measure | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 codes/code_lists/snomed_units_of_measure diff --git a/codes/code_lists/snomed_units_of_measure b/codes/code_lists/snomed_units_of_measure new file mode 100644 index 0000000..9b2fcbb --- /dev/null +++ b/codes/code_lists/snomed_units_of_measure @@ -0,0 +1,11 @@ +SNOMED,258771000,Deciliters +SNOMED,258682000,Grams +SNOMED,258770004,Litres +SNOMED,258684004,Milligrams +SNOMED,258773002,Milliliters +SNOMED,258718000,Millimols +SNOMED,258686002,Nanograms +SNOMED,767524001,Other - please specify in comments +SNOMED,428673006,Tablets +SNOMED,258997004,International Units (i.e. for Epoetins) +SNOMED,258685003,Micro-grams From 1444393df2a1496492c8edf5c4fb299bc5897cc5 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:40:10 +0000 Subject: [PATCH 132/166] Create snomed_result.csv SNOMED Codes in Red (pending confirmation) not included --- codes/code_lists/snomed_result.csv | 47 ++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 codes/code_lists/snomed_result.csv diff --git a/codes/code_lists/snomed_result.csv b/codes/code_lists/snomed_result.csv new file mode 100644 index 0000000..482acf0 --- /dev/null +++ b/codes/code_lists/snomed_result.csv @@ -0,0 +1,47 @@ +SNOMED,1107001000000108,Substance concentration of creatinine in serum +SNOMED,1110281000000107,Substance concentration of urea in serum +SNOMED,1106011000000107,Substance concentration of bicarbonate in serum +SNOMED,1107871000000107,Substance concentration of sodium in serum +SNOMED,1107761000000109,Substance concentration of potassium in serum +SNOMED,1107411000000104,Estimated glomerular filtration rate by laboratory calculation +SNOMED,1109851000000106,Substance concentration of urate in serum +SNOMED,857971000000104,Estimated glomerular filtration rate using Chronic Kidney Disease Epidemiology Collaboration formula +SNOMED,1020291000000106,Glomerular filtration rate calculated by abbreviated Modification of Diet in Renal Disease Study Group calculation +SNOMED,1107711000000107,Substance concentration of phosphate in serum +SNOMED,1106621000000109,Substance concentration of calcium in serum +SNOMED,1107251000000104,Substance concentration of calcium in serum adjusted for albumin +SNOMED,1106051000000106,Enzyme activity of alkaline phosphatase in serum +SNOMED,1105861000000106,Albumin mass concentration in serum +SNOMED,1109581000000102,Mass concentration of parathyroid hormone in serum +SNOMED,1023491000000104,Urine albumin:creatinine ratio +SNOMED,1106541000000101,Substance concentration of cholesterol in serum +SNOMED,1107681000000108,Substance concentration of high density lipoprotein cholesterol in serum +SNOMED,1108551000000102,Substance concentration of low density lipoprotein cholesterol in serum +SNOMED,1109831000000104,Substance concentration of triglyceride in serum +SNOMED,1106741000000105,Mass concentration of C reactive protein in serum +SNOMED,999791000000106,Haemoglobin A1c level - IFCC standardised +SNOMED,1022471000000107,Mean corpuscular haemoglobin +SNOMED,1108041000000107,Platelet count in blood +SNOMED,1110441000000100,White blood cell count in blood +SNOMED,1108611000000102,Mass concentration of ferritin in serum +SNOMED,1111581000000104,Hypochromic red blood cells percent count in blood +SNOMED,1108651000000103,Mass concentration of folate in serum +SNOMED,1108641000000101,Mass concentration of folate in red blood cells +SNOMED,12711000237100,Substance concentration of aluminium in serum +SNOMED,1111311000000103,Mass concentration of tacrolimus in whole blood +SNOMED,1107851000000103,Mass concentration of sirolimus in whole blood +SNOMED,1107021000000104,Mass concentration of cyclosporin in whole blood +SNOMED,1110411000000101,Urea reduction ratio in serum +SNOMED,1107011000000105,Substance concentration of creatinine in urine +SNOMED,1106081000000100,Enzyme activity of alanine aminotransferase in serum +SNOMED,1108071000000101,Neutrophil count in blood +SNOMED,1107961000000106,Lymphocyte count in blood +SNOMED,1111161000000103,Presence of hepatitis B virus core antibody in serum +SNOMED,1111171000000105,Presence of hepatitis B virus surface antigen in serum +SNOMED,1111131000000108,Presence of hepatitis C virus antibody in serum +SNOMED,1111211000000108,Presence of cytomegalovirus antibody in serum +SNOMED,1111341000000102,Presence of human immunodeficiency virus 1 antibody in serum +SNOMED,1111351000000104,Presence of varicella zoster virus antibody in serum +SNOMED,1111041000000100,Presence of Epstein-Barr virus antibody in serum +SNOMED,996101000000106,Epstein-Barr virus viral load +SNOMED,165581004,International normalized ratio From 8c11828b1b2ca7cc7d12c04cf6dd1a91ab4b9f64 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:45:22 +0000 Subject: [PATCH 133/166] Create snomed_access_procedure.csv SNOMED codes in red not included --- codes/code_lists/snomed_access_procedure.csv | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 codes/code_lists/snomed_access_procedure.csv diff --git a/codes/code_lists/snomed_access_procedure.csv b/codes/code_lists/snomed_access_procedure.csv new file mode 100644 index 0000000..eebc874 --- /dev/null +++ b/codes/code_lists/snomed_access_procedure.csv @@ -0,0 +1,5 @@ +SNOMED,449860009,Insertion of nontunneled central venous catheter +SNOMED,442309004,Insertion of tunneled venous catheter +SNOMED,27929005,Construction of arteriovenous fistula +SNOMED,46196009,Surgical construction of arteriovenous shunt +SNOMED,180277007,Insertion of temporary peritoneal dialysis catheter From fa806f9dfc665c47f2d07e7b8c13c412e159750a Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:46:00 +0000 Subject: [PATCH 134/166] Rename snomed_diabetes to snomed_diabetes.csv --- codes/code_lists/{snomed_diabetes => snomed_diabetes.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_diabetes => snomed_diabetes.csv} (100%) diff --git a/codes/code_lists/snomed_diabetes b/codes/code_lists/snomed_diabetes.csv similarity index 100% rename from codes/code_lists/snomed_diabetes rename to codes/code_lists/snomed_diabetes.csv From 8e77f7036700f1ca4064a077a3491e5df6224dde Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:46:15 +0000 Subject: [PATCH 135/166] Rename snomed_diagnosis to snomed_diagnosis.csv --- codes/code_lists/{snomed_diagnosis => snomed_diagnosis.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_diagnosis => snomed_diagnosis.csv} (100%) diff --git a/codes/code_lists/snomed_diagnosis b/codes/code_lists/snomed_diagnosis.csv similarity index 100% rename from codes/code_lists/snomed_diagnosis rename to codes/code_lists/snomed_diagnosis.csv From 2b76789e44c286d778f70c38978b73dc5b54b400 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:46:29 +0000 Subject: [PATCH 136/166] Rename snomed_dialysis to snomed_dialysis.csv --- codes/code_lists/{snomed_dialysis => snomed_dialysis.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_dialysis => snomed_dialysis.csv} (100%) diff --git a/codes/code_lists/snomed_dialysis b/codes/code_lists/snomed_dialysis.csv similarity index 100% rename from codes/code_lists/snomed_dialysis rename to codes/code_lists/snomed_dialysis.csv From 70edf69e0e57655c8d61cb37b36f75f1896aa0e4 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:46:41 +0000 Subject: [PATCH 137/166] Rename snomed_graft_type to snomed_graft_type.csv --- codes/code_lists/{snomed_graft_type => snomed_graft_type.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_graft_type => snomed_graft_type.csv} (100%) diff --git a/codes/code_lists/snomed_graft_type b/codes/code_lists/snomed_graft_type.csv similarity index 100% rename from codes/code_lists/snomed_graft_type rename to codes/code_lists/snomed_graft_type.csv From 483759ae52fda85371f1dcdb34070ced8d30a506 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:46:55 +0000 Subject: [PATCH 138/166] Rename snomed_relationship to snomed_relationship.csv --- codes/code_lists/{snomed_relationship => snomed_relationship.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_relationship => snomed_relationship.csv} (100%) diff --git a/codes/code_lists/snomed_relationship b/codes/code_lists/snomed_relationship.csv similarity index 100% rename from codes/code_lists/snomed_relationship rename to codes/code_lists/snomed_relationship.csv From 6955de5b8ced502eea717ea348b0b6594748aeb8 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:47:11 +0000 Subject: [PATCH 139/166] Rename snomed_units_of_measure to snomed_units_of_measure.csv --- .../{snomed_units_of_measure => snomed_units_of_measure.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_units_of_measure => snomed_units_of_measure.csv} (100%) diff --git a/codes/code_lists/snomed_units_of_measure b/codes/code_lists/snomed_units_of_measure.csv similarity index 100% rename from codes/code_lists/snomed_units_of_measure rename to codes/code_lists/snomed_units_of_measure.csv From 397e675cd7440daadaf5b54cb71cd3d0bf6e8fbf Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:52:25 +0000 Subject: [PATCH 140/166] Create snomed_access_finding.csv --- codes/code_lists/snomed_access_finding.csv | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 codes/code_lists/snomed_access_finding.csv diff --git a/codes/code_lists/snomed_access_finding.csv b/codes/code_lists/snomed_access_finding.csv new file mode 100644 index 0000000..dbf9e57 --- /dev/null +++ b/codes/code_lists/snomed_access_finding.csv @@ -0,0 +1,6 @@ +SNOMED,440535009,Nontunneled central venous catheter in situ +SNOMED,439012009,Tunneled central venous catheter in situ +SNOMED,439784005,Surgically constructed arteriovenous fistula +SNOMED,699007002,Arteriovenous shunt in situ +SNOMED,366161000000100,Surgically created vein loop +SNOMED,440926006,Temporary peritoneal dialysis catheter in situ From e10f48b5caeca654e2e0766df8ed0c14f89065d4 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:56:36 +0000 Subject: [PATCH 141/166] Create snomed_access_device.csv --- codes/code_lists/snomed_access_device | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 codes/code_lists/snomed_access_device diff --git a/codes/code_lists/snomed_access_device b/codes/code_lists/snomed_access_device new file mode 100644 index 0000000..6d5b97a --- /dev/null +++ b/codes/code_lists/snomed_access_device @@ -0,0 +1,3 @@ +SNOMED,449859004,Non-Tunneled central venous catheter +SNOMED,445085009,Tunnelled central venous catheter +SNOMED,258622003,Arteriovenous shunt From 68ed35fdb5b9b555766916e1bc1aeb8498749451 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 11:59:16 +0000 Subject: [PATCH 142/166] Rename snomed_access_device to snomed_access_device.csv --- .../code_lists/{snomed_access_device => snomed_access_device.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename codes/code_lists/{snomed_access_device => snomed_access_device.csv} (100%) diff --git a/codes/code_lists/snomed_access_device b/codes/code_lists/snomed_access_device.csv similarity index 100% rename from codes/code_lists/snomed_access_device rename to codes/code_lists/snomed_access_device.csv From 05270c506b51feabe9a7d4b8ff7025c2a8234176 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 12:00:54 +0000 Subject: [PATCH 143/166] Update snomed_access_device.csv SNOMED codes in red not included From 180bbc618e38f8c33a41bc190306676842b916cd Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Sun, 2 Nov 2025 12:03:24 +0000 Subject: [PATCH 144/166] Create snomed_malignancy.csv --- codes/code_lists/snomed_malignancy.csv | 30 ++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 codes/code_lists/snomed_malignancy.csv diff --git a/codes/code_lists/snomed_malignancy.csv b/codes/code_lists/snomed_malignancy.csv new file mode 100644 index 0000000..863106a --- /dev/null +++ b/codes/code_lists/snomed_malignancy.csv @@ -0,0 +1,30 @@ +SNOMED,254701007,Malignant basal cell neoplasm of skin (disorder) +SNOMED,254651007,Squamous cell carcinoma of skin (disorder) +SNOMED,93655004,Malignant melanoma of skin (disorder) +SNOMED,254837009,Malignant neoplasm of breast (disorder) +SNOMED,363402007,Malignant tumor of esophagus (disorder) +SNOMED,363349007,Malignant tumor of stomach (disorder) +SNOMED,363509000,Malignant tumor of small intestine (disorder) +SNOMED,363418001,Malignant tumor of pancreas (disorder) +SNOMED,363353009,Malignant tumor of gallbladder (disorder) +SNOMED,93870000,Malignant neoplasm of liver (disorder) +SNOMED,363510005,Malignant tumor of large intestine (disorder) +SNOMED,363351006,Malignant tumor of rectum (disorder) +SNOMED,363358000,Malignant tumor of lung (disorder) +SNOMED,363518003,Malignant tumor of kidney (disorder) +SNOMED,399326009,Malignant tumor of urinary bladder (disorder) +SNOMED,399068003,Malignant tumor of prostate (disorder) +SNOMED,363449006,Malignant tumor of testis (disorder) +SNOMED,371973000,Malignant neoplasm of uterus (disorder) +SNOMED,93143009,Leukemia, disease (disorder) +SNOMED,118600007,Malignant lymphoma (disorder) +SNOMED,109989006,Multiple myeloma (disorder) +SNOMED,372062007,Malignant neoplasm of central nervous system (disorder) +SNOMED,363475005,Malignant tumor of spinal cord (disorder) +SNOMED,372063002,Malignant neoplasm of nervous system (disorder) +SNOMED,428061005,Malignant neoplasm of brain (disorder) +SNOMED,363229000,Neoplasm of musculoskeletal system (disorder) +SNOMED,428281000,Malignant neoplasm of bone (disorder) +SNOMED,363495004,Malignant tumor of muscle (disorder) +SNOMED,255056009,Malignant tumor of head and/or neck (disorder) +SNOMED,363346000,Malignant neoplastic disease (disorder) From 7cf26632a852f580054926aad2b666caa5e4585d Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 4 Nov 2025 10:43:20 +0000 Subject: [PATCH 145/166] Update rr1plus_facilities.csv --- codes/code_lists/rr1plus_facilities.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv index 60ac18f..64b5b32 100644 --- a/codes/code_lists/rr1plus_facilities.csv +++ b/codes/code_lists/rr1plus_facilities.csv @@ -434,3 +434,4 @@ RR1+,RF202,PRINCESS ROYAL HOSPITAL RR1+,RF316,CASTLE HILL HOSPITAL RR1+,RNS,Northampton General Hospital NHS Trust RR1+,RQ309,Birmingham Children's 'Dialysis Provider' +RR1+,P7U2H,LEICESTER SOUTH DIALYSIS UNIT - Wigston South From 72e744939f8da24e3dca8290cbb42e7525565af8 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 4 Nov 2025 10:45:47 +0000 Subject: [PATCH 146/166] Update satellite_map.csv --- codes/satellite_map/satellite_map.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/codes/satellite_map/satellite_map.csv b/codes/satellite_map/satellite_map.csv index 6938d00..070d7ac 100644 --- a/codes/satellite_map/satellite_map.csv +++ b/codes/satellite_map/satellite_map.csv @@ -71,6 +71,7 @@ RT5DC,RFBAK 98RFBAK,RFBAK 99RFBAK,RFBAK RY5K7,RFBAK +P7U2H,RFBAK 9RKD,RHU02 99RHU02,RHU02 RDZ15,RHU02 From f4fa9f52bb1a63686a411a16b8aaa6cbc948293c Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 6 Nov 2025 21:47:20 +0000 Subject: [PATCH 147/166] Create edta_to_edta2.csv --- codes/code_conv_lists/edta_to_edta2.csv | 65 +++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 codes/code_conv_lists/edta_to_edta2.csv diff --git a/codes/code_conv_lists/edta_to_edta2.csv b/codes/code_conv_lists/edta_to_edta2.csv new file mode 100644 index 0000000..ee01d23 --- /dev/null +++ b/codes/code_conv_lists/edta_to_edta2.csv @@ -0,0 +1,65 @@ +EDTA,0,EDTA2,3555 +EDTA,10,EDTA2,3749 +EDTA,11,EDTA2,1061 +EDTA,12,EDTA2,1128 +EDTA,13,EDTA2,1233 +EDTA,14,EDTA2,1185 +EDTA,15,EDTA2,1222 +EDTA,16,EDTA2,1251 +EDTA,17,EDTA2,1267 +EDTA,19,EDTA2,1377 +EDTA,20,EDTA2,1602 +EDTA,21,EDTA2,1706 +EDTA,22,EDTA2,1673 +EDTA,23,EDTA2,1752 +EDTA,24,EDTA2,1602 +EDTA,25,EDTA2,1832 +EDTA,29,EDTA2,3555 +EDTA,30,EDTA2,1884 +EDTA,31,EDTA2,2022 +EDTA,32,EDTA2,2120 +EDTA,33,EDTA2,2046 +EDTA,34,EDTA2,2165 +EDTA,39,EDTA2,2005 +EDTA,40,EDTA2,2794 +EDTA,41,EDTA2,2718 +EDTA,42,EDTA2,2741 +EDTA,43,EDTA2,2804 +EDTA,49,EDTA2,2794 +EDTA,50,EDTA2,3379 +EDTA,51,EDTA2,2756 +EDTA,52,EDTA2,2964 +EDTA,53,EDTA2,3194 +EDTA,54,EDTA2,3224 +EDTA,59,EDTA2,3379 +EDTA,60,EDTA2,1625 +EDTA,61,EDTA2,1734 +EDTA,63,EDTA2,1625 +EDTA,66,EDTA2,1694 +EDTA,70,EDTA2,2430 +EDTA,71,EDTA2,2371 +EDTA,72,EDTA2,2359 +EDTA,73,EDTA2,1455 +EDTA,74,EDTA2,1401 +EDTA,75,EDTA2,2430 +EDTA,76,EDTA2,1159 +EDTA,78,EDTA2,1543 +EDTA,79,EDTA2,2411 +EDTA,80,EDTA2,2316 +EDTA,81,EDTA2,2337 +EDTA,82,EDTA2,2578 +EDTA,83,EDTA2,2509 +EDTA,84,EDTA2,1486 +EDTA,85,EDTA2,1504 +EDTA,86,EDTA2,1464 +EDTA,87,EDTA2,1527 +EDTA,88,EDTA2,2623 +EDTA,89,EDTA2,3555 +EDTA,90,EDTA2,3442 +EDTA,91,EDTA2,2235 +EDTA,92,EDTA2,3636 +EDTA,93,EDTA2,3555 +EDTA,94,EDTA2,1982 +EDTA,95,EDTA2,3461 +EDTA,96,EDTA2,3538 +EDTA,99,EDTA2,3691 From 4ca7dba95de629261f3266b0a2c9341fa0dcffc2 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 6 Nov 2025 22:03:45 +0000 Subject: [PATCH 148/166] Create edta2_to_edta.csv --- codes/code_conv_lists/edta2_to_edta.csv | 284 ++++++++++++++++++++++++ 1 file changed, 284 insertions(+) create mode 100644 codes/code_conv_lists/edta2_to_edta.csv diff --git a/codes/code_conv_lists/edta2_to_edta.csv b/codes/code_conv_lists/edta2_to_edta.csv new file mode 100644 index 0000000..aea3d40 --- /dev/null +++ b/codes/code_conv_lists/edta2_to_edta.csv @@ -0,0 +1,284 @@ +EDTA2,1003,EDTA,10 +EDTA2,1019,EDTA,10 +EDTA2,1026,EDTA,10 +EDTA2,1035,EDTA,10 +EDTA2,1042,EDTA,19 +EDTA2,1057,EDTA,19 +EDTA2,1061,EDTA,11 +EDTA2,1074,EDTA,99 +EDTA2,1088,EDTA,10 +EDTA2,1090,EDTA,10 +EDTA2,1100,EDTA,19 +EDTA2,1116,EDTA,10 +EDTA2,1128,EDTA,12 +EDTA2,1137,EDTA,10 +EDTA2,1144,EDTA,12 +EDTA2,1159,EDTA,10 +EDTA2,1163,EDTA,12 +EDTA2,1171,EDTA,19 +EDTA2,1185,EDTA,14 +EDTA2,1192,EDTA,14 +EDTA2,1205,EDTA,14 +EDTA2,1214,EDTA,14 +EDTA2,1222,EDTA,15 +EDTA2,1233,EDTA,13 +EDTA2,1246,EDTA,19 +EDTA2,1251,EDTA,16 +EDTA2,1267,EDTA,17 +EDTA2,1279,EDTA,50 +EDTA2,1280,EDTA,11 +EDTA2,1298,EDTA,50 +EDTA2,1308,EDTA,11 +EDTA2,1312,EDTA,17 +EDTA2,1320,EDTA,17 +EDTA2,1331,EDTA,19 +EDTA2,1349,EDTA,19 +EDTA2,1354,EDTA,19 +EDTA2,1365,EDTA,10 +EDTA2,1377,EDTA,19 +EDTA2,1383,EDTA,70 +EDTA2,1396,EDTA,74 +EDTA2,1401,EDTA,74 +EDTA2,1417,EDTA,74 +EDTA2,1429,EDTA,74 +EDTA2,1438,EDTA,74 +EDTA2,1440,EDTA,74 +EDTA2,1455,EDTA,73 +EDTA2,1464,EDTA,86 +EDTA2,1472,EDTA,86 +EDTA2,1486,EDTA,84 +EDTA2,1493,EDTA,84 +EDTA2,1504,EDTA,85 +EDTA2,1515,EDTA,85 +EDTA2,1527,EDTA,87 +EDTA2,1536,EDTA,87 +EDTA2,1543,EDTA,78 +EDTA2,1558,EDTA,78 +EDTA2,1562,EDTA,78 +EDTA2,1570,EDTA,78 +EDTA2,1589,EDTA,78 +EDTA2,1591,EDTA,78 +EDTA2,1602,EDTA,24 +EDTA2,1618,EDTA,24 +EDTA2,1625,EDTA,60 +EDTA2,1639,EDTA,40 +EDTA2,1641,EDTA,99 +EDTA2,1656,EDTA,99 +EDTA2,1660,EDTA,99 +EDTA2,1673,EDTA,99 +EDTA2,1687,EDTA,99 +EDTA2,1694,EDTA,66 +EDTA2,1706,EDTA,99 +EDTA2,1710,EDTA,99 +EDTA2,1723,EDTA,99 +EDTA2,1734,EDTA,61 +EDTA2,1747,EDTA,99 +EDTA2,1752,EDTA,23 +EDTA2,1768,EDTA,23 +EDTA2,1775,EDTA,23 +EDTA2,1781,EDTA,23 +EDTA2,1799,EDTA,23 +EDTA2,1809,EDTA,23 +EDTA2,1813,EDTA,23 +EDTA2,1821,EDTA,23 +EDTA2,1832,EDTA,25 +EDTA2,1845,EDTA,99 +EDTA2,1850,EDTA,99 +EDTA2,1866,EDTA,25 +EDTA2,1878,EDTA,99 +EDTA2,1884,EDTA,30 +EDTA2,1897,EDTA,30 +EDTA2,1907,EDTA,50 +EDTA2,1911,EDTA,50 +EDTA2,1924,EDTA,30 +EDTA2,1930,EDTA,30 +EDTA2,1948,EDTA,30 +EDTA2,1953,EDTA,30 +EDTA2,1969,EDTA,99 +EDTA2,1976,EDTA,99 +EDTA2,1982,EDTA,94 +EDTA2,1995,EDTA,94 +EDTA2,2005,EDTA,39 +EDTA2,2014,EDTA,39 +EDTA2,2022,EDTA,31 +EDTA2,2033,EDTA,31 +EDTA2,2046,EDTA,33 +EDTA2,2051,EDTA,33 +EDTA2,2067,EDTA,39 +EDTA2,2079,EDTA,39 +EDTA2,2080,EDTA,39 +EDTA2,2098,EDTA,39 +EDTA2,2108,EDTA,39 +EDTA2,2112,EDTA,39 +EDTA2,2120,EDTA,32 +EDTA2,2131,EDTA,32 +EDTA2,2149,EDTA,39 +EDTA2,2154,EDTA,39 +EDTA2,2165,EDTA,34 +EDTA2,2177,EDTA,34 +EDTA2,2183,EDTA,92 +EDTA2,2196,EDTA,92 +EDTA2,2203,EDTA,92 +EDTA2,2219,EDTA,99 +EDTA2,2226,EDTA,99 +EDTA2,2235,EDTA,91 +EDTA2,2242,EDTA,99 +EDTA2,2257,EDTA,99 +EDTA2,2261,EDTA,99 +EDTA2,2274,EDTA,99 +EDTA2,2288,EDTA,99 +EDTA2,2290,EDTA,99 +EDTA2,2300,EDTA,99 +EDTA2,2316,EDTA,80 +EDTA2,2328,EDTA,80 +EDTA2,2337,EDTA,81 +EDTA2,2344,EDTA,81 +EDTA2,2359,EDTA,72 +EDTA2,2363,EDTA,72 +EDTA2,2371,EDTA,71 +EDTA2,2385,EDTA,71 +EDTA2,2392,EDTA,70 +EDTA2,2407,EDTA,75 +EDTA2,2411,EDTA,75 +EDTA2,2424,EDTA,70 +EDTA2,2430,EDTA,75 +EDTA2,2448,EDTA,75 +EDTA2,2453,EDTA,70 +EDTA2,2469,EDTA,70 +EDTA2,2476,EDTA,99 +EDTA2,2482,EDTA,99 +EDTA2,2495,EDTA,99 +EDTA2,2509,EDTA,83 +EDTA2,2513,EDTA,83 +EDTA2,2521,EDTA,83 +EDTA2,2532,EDTA,83 +EDTA2,2545,EDTA,83 +EDTA2,2550,EDTA,83 +EDTA2,2566,EDTA,83 +EDTA2,2578,EDTA,82 +EDTA2,2584,EDTA,82 +EDTA2,2597,EDTA,82 +EDTA2,2606,EDTA,99 +EDTA2,2610,EDTA,88 +EDTA2,2623,EDTA,88 +EDTA2,2634,EDTA,88 +EDTA2,2647,EDTA,88 +EDTA2,2652,EDTA,88 +EDTA2,2668,EDTA,88 +EDTA2,2675,EDTA,88 +EDTA2,2681,EDTA,99 +EDTA2,2699,EDTA,99 +EDTA2,2702,EDTA,99 +EDTA2,2718,EDTA,41 +EDTA2,2725,EDTA,41 +EDTA2,2739,EDTA,41 +EDTA2,2741,EDTA,42 +EDTA2,2756,EDTA,51 +EDTA2,2760,EDTA,51 +EDTA2,2773,EDTA,99 +EDTA2,2787,EDTA,99 +EDTA2,2794,EDTA,40 +EDTA2,2804,EDTA,43 +EDTA2,2815,EDTA,43 +EDTA2,2827,EDTA,49 +EDTA2,2836,EDTA,43 +EDTA2,2843,EDTA,43 +EDTA2,2858,EDTA,43 +EDTA2,2862,EDTA,43 +EDTA2,2870,EDTA,43 +EDTA2,2889,EDTA,43 +EDTA2,2891,EDTA,43 +EDTA2,2901,EDTA,59 +EDTA2,2917,EDTA,59 +EDTA2,2929,EDTA,99 +EDTA2,2938,EDTA,59 +EDTA2,2940,EDTA,59 +EDTA2,2955,EDTA,99 +EDTA2,2964,EDTA,52 +EDTA2,2972,EDTA,59 +EDTA2,2986,EDTA,59 +EDTA2,2993,EDTA,59 +EDTA2,3000,EDTA,59 +EDTA2,3016,EDTA,59 +EDTA2,3028,EDTA,59 +EDTA2,3037,EDTA,59 +EDTA2,3044,EDTA,59 +EDTA2,3059,EDTA,59 +EDTA2,3063,EDTA,59 +EDTA2,3071,EDTA,59 +EDTA2,3085,EDTA,59 +EDTA2,3092,EDTA,59 +EDTA2,3102,EDTA,59 +EDTA2,3118,EDTA,59 +EDTA2,3125,EDTA,59 +EDTA2,3139,EDTA,59 +EDTA2,3141,EDTA,59 +EDTA2,3156,EDTA,59 +EDTA2,3160,EDTA,59 +EDTA2,3173,EDTA,59 +EDTA2,3187,EDTA,59 +EDTA2,3194,EDTA,53 +EDTA2,3207,EDTA,53 +EDTA2,3211,EDTA,53 +EDTA2,3224,EDTA,54 +EDTA2,3230,EDTA,54 +EDTA2,3248,EDTA,59 +EDTA2,3253,EDTA,59 +EDTA2,3269,EDTA,99 +EDTA2,3276,EDTA,59 +EDTA2,3282,EDTA,59 +EDTA2,3295,EDTA,99 +EDTA2,3305,EDTA,99 +EDTA2,3314,EDTA,99 +EDTA2,3322,EDTA,59 +EDTA2,3333,EDTA,59 +EDTA2,3346,EDTA,59 +EDTA2,3351,EDTA,59 +EDTA2,3367,EDTA,59 +EDTA2,3379,EDTA,59 +EDTA2,3380,EDTA,90 +EDTA2,3398,EDTA,90 +EDTA2,3403,EDTA,90 +EDTA2,3419,EDTA,90 +EDTA2,3426,EDTA,90 +EDTA2,3435,EDTA,90 +EDTA2,3442,EDTA,90 +EDTA2,3457,EDTA,99 +EDTA2,3461,EDTA,95 +EDTA2,3474,EDTA,95 +EDTA2,3488,EDTA,95 +EDTA2,3490,EDTA,95 +EDTA2,3501,EDTA,95 +EDTA2,3517,EDTA,99 +EDTA2,3529,EDTA,96 +EDTA2,3538,EDTA,96 +EDTA2,3540,EDTA,0 +EDTA2,3555,EDTA,0 +EDTA2,3564,EDTA,0 +EDTA2,3572,EDTA,0 +EDTA2,3604,EDTA,10 +EDTA2,3615,EDTA,10 +EDTA2,3627,EDTA,99 +EDTA2,3636,EDTA,92 +EDTA2,3643,EDTA,0 +EDTA2,3658,EDTA,59 +EDTA2,3662,EDTA,93 +EDTA2,3670,EDTA,23 +EDTA2,3689,EDTA,23 +EDTA2,3691,EDTA,0 +EDTA2,3708,EDTA,0 +EDTA2,3712,EDTA,0 +EDTA2,3720,EDTA,0 +EDTA2,3731,EDTA,53 +EDTA2,3749,EDTA,10 +EDTA2,3754,EDTA,17 +EDTA2,3765,EDTA,17 +EDTA2,3777,EDTA,17 +EDTA2,3783,EDTA,99 +EDTA2,3796,EDTA,99 +EDTA2,3806,EDTA,99 +EDTA2,3810,EDTA,25 +EDTA2,3823,EDTA,99 +EDTA2,3834,EDTA,99 +EDTA2,3847,EDTA,70 +EDTA2,3852,EDTA,74 From 84e4f9e6bceed4b2f896dc953cd1f19cae7cee31 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Nov 2025 15:29:00 +0000 Subject: [PATCH 149/166] Add files via upload --- codes/code_conv_lists/pkbsite_to_pkbmain.csv | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 codes/code_conv_lists/pkbsite_to_pkbmain.csv diff --git a/codes/code_conv_lists/pkbsite_to_pkbmain.csv b/codes/code_conv_lists/pkbsite_to_pkbmain.csv new file mode 100644 index 0000000..67f3144 --- /dev/null +++ b/codes/code_conv_lists/pkbsite_to_pkbmain.csv @@ -0,0 +1,10 @@ +PKB_SITE,2020,PKB_MAIN,11023 +PKB_SITE,99RCSLB,PKB_MAIN,RCSLB +PKB_SITE,99RQR13,PKB_MAIN,RQR13 +PKB_SITE,RDEE4,PKB_MAIN,RGQ02 +PKB_SITE,RL7,PKB_MAIN,RRK02 +PKB_SITE,RQ601,PKB_MAIN,RQ617 +PKB_SITE,RW402,PKB_MAIN,RQ617 +PKB_SITE,RW3RM,PKB_MAIN,RM574 +PKB_SITE,SGC02,PKB_MAIN,SGC04 +PKB_SITE,RBL20,PKB_MAIN,RBL14 \ No newline at end of file From 66468e659a60f8884209a0e2befab1b1b04a2395 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Nov 2025 15:33:02 +0000 Subject: [PATCH 150/166] Add files via upload --- codes/code_exclusions/pkb_observations.csv | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 codes/code_exclusions/pkb_observations.csv diff --git a/codes/code_exclusions/pkb_observations.csv b/codes/code_exclusions/pkb_observations.csv new file mode 100644 index 0000000..cfc410d --- /dev/null +++ b/codes/code_exclusions/pkb_observations.csv @@ -0,0 +1,11 @@ +LOINC,732-8,PKB +LOINC,76069-4,PKB +LOINC,59467-1,PKB +LOINC,2283-0,PKB +LOINC,69949-6,PKB +LOINC,56888-1,PKB +LOINC,55972-4,PKB +LOINC,59148-7,PKB +LOINC,21594-7,PKB +LOINC,30247-1,PKB +LOINC,14593-8,PKB From 0c3d9f1df7d84a5bafbe69967dc13f8867f2d16f Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Nov 2025 15:35:41 +0000 Subject: [PATCH 151/166] Add files via upload --- codes/code_lists/pkb_main.csv | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 codes/code_lists/pkb_main.csv diff --git a/codes/code_lists/pkb_main.csv b/codes/code_lists/pkb_main.csv new file mode 100644 index 0000000..baa7883 --- /dev/null +++ b/codes/code_lists/pkb_main.csv @@ -0,0 +1,9 @@ +PKB_MAIN,11023 +PKB_MAIN,RCSLB +PKB_MAIN,RGQ02 +PKB_MAIN,RM574 +PKB_MAIN,RQ617 +PKB_MAIN,RQR13 +PKB_MAIN,RRK02 +PKB_MAIN,SGC04 +PKB_MAIN,RBL14 \ No newline at end of file From 0852423d824fc1342c60a7e1caaa313d9d1c79f8 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Nov 2025 15:42:57 +0000 Subject: [PATCH 152/166] Update pkb_main.csv --- codes/code_lists/pkb_main.csv | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/codes/code_lists/pkb_main.csv b/codes/code_lists/pkb_main.csv index baa7883..e435fe5 100644 --- a/codes/code_lists/pkb_main.csv +++ b/codes/code_lists/pkb_main.csv @@ -6,4 +6,7 @@ PKB_MAIN,RQ617 PKB_MAIN,RQR13 PKB_MAIN,RRK02 PKB_MAIN,SGC04 -PKB_MAIN,RBL14 \ No newline at end of file +PKB_MAIN,RBL14 +PKB_MAIN,RAJ +PKB_MAIN,NHSWLS +PKB_MAIN,45020,Altnagelvin From c1175f373eb78c0b8e9f26bdbcd4da801e4eda29 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Nov 2025 15:47:23 +0000 Subject: [PATCH 153/166] Update pkb_observations.csv --- codes/code_exclusions/pkb_observations.csv | 3 +++ 1 file changed, 3 insertions(+) diff --git a/codes/code_exclusions/pkb_observations.csv b/codes/code_exclusions/pkb_observations.csv index cfc410d..7efd06e 100644 --- a/codes/code_exclusions/pkb_observations.csv +++ b/codes/code_exclusions/pkb_observations.csv @@ -9,3 +9,6 @@ LOINC,59148-7,PKB LOINC,21594-7,PKB LOINC,30247-1,PKB LOINC,14593-8,PKB +LOINC,95209-3,PKB +LOINC,95542-7,PKB +LOINC,94500-6,PKB From 3d4ec839166d5b9dde896ba5369a296314cb0a95 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 10 Nov 2025 16:57:45 +0000 Subject: [PATCH 154/166] Update pkbsite_to_pkbmain.csv --- codes/code_conv_lists/pkbsite_to_pkbmain.csv | 26 ++++++++++++++++---- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/codes/code_conv_lists/pkbsite_to_pkbmain.csv b/codes/code_conv_lists/pkbsite_to_pkbmain.csv index 67f3144..88d4e5e 100644 --- a/codes/code_conv_lists/pkbsite_to_pkbmain.csv +++ b/codes/code_conv_lists/pkbsite_to_pkbmain.csv @@ -1,10 +1,26 @@ PKB_SITE,2020,PKB_MAIN,11023 -PKB_SITE,99RCSLB,PKB_MAIN,RCSLB -PKB_SITE,99RQR13,PKB_MAIN,RQR13 +PKB_SITE,48021,PKB_MAIN,45020 +PKB_SITE,45021,PKB_MAIN,45020 +PKB_SITE,RKGA1,PKB_MAIN,NHSWLS +PKB_SITE,RQHC7,PKB_MAIN,NHSWLS +PKB_SITE,RKHA4,PKB_MAIN,NHSWLS +PKB_SITE,RQBAU,PKB_MAIN,NHSWLS +PKB_SITE,RRBBV,PKB_MAIN,NHSWLS +PKB_SITE,RDDH0,PKB_MAIN,RAJ +PKB_SITE,RQ8L0,PKB_MAIN,RAJ +PKB_SITE,RAJ01,PKB_MAIN,RAJ +PKB_SITE,RBL20,PKB_MAIN,RBL14 PKB_SITE,RDEE4,PKB_MAIN,RGQ02 -PKB_SITE,RL7,PKB_MAIN,RRK02 +PKB_SITE,RW3RM,PKB_MAIN,RM574 PKB_SITE,RQ601,PKB_MAIN,RQ617 PKB_SITE,RW402,PKB_MAIN,RQ617 -PKB_SITE,RW3RM,PKB_MAIN,RM574 +PKB_SITE,RVY01,PKB_MAIN,RQ617 +PKB_SITE,RKC81,PKB_MAIN,RQ617 +PKB_SITE,REM26,PKB_MAIN,RQ617 +PKB_SITE,RBN63,PKB_MAIN,RQ617 +PKB_SITE,9RW402,PKB_MAIN,RQ617 +PKB_SITE,9RBN01,PKB_MAIN,RQ617 +PKB_SITE,99RQR13,PKB_MAIN,RQR13 +PKB_SITE,RL7,PKB_MAIN,RRK02 PKB_SITE,SGC02,PKB_MAIN,SGC04 -PKB_SITE,RBL20,PKB_MAIN,RBL14 \ No newline at end of file +PKB_SITE,99RCSLB,PKB_MAIN,RCSLB From 21b93f19f8cc525811b4441975458b5a46f03c80 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Thu, 27 Nov 2025 13:48:22 +0000 Subject: [PATCH 155/166] Create icd10_to_rr19.csv --- codes/code_conv_lists/icd10_to_rr19.csv | 56 +++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 codes/code_conv_lists/icd10_to_rr19.csv diff --git a/codes/code_conv_lists/icd10_to_rr19.csv b/codes/code_conv_lists/icd10_to_rr19.csv new file mode 100644 index 0000000..d826961 --- /dev/null +++ b/codes/code_conv_lists/icd10_to_rr19.csv @@ -0,0 +1,56 @@ +ICD-10,C02.9,RR19,115 +ICD-10,C15,RR19,104 +ICD-10,C15.0,RR19,104 +ICD-10,C16,RR19,104 +ICD-10,C18,RR19,105 +ICD-10,C18.0,RR19,105 +ICD-10,C18.2,RR19,105 +ICD-10,C18.7,RR19,105 +ICD-10,C20,RR19,105 +ICD-10,C21,RR19,105 +ICD-10,C25,RR19,115 +ICD-10,C34,RR19,106 +ICD-10,C41.2,RR19,115 +ICD-10,C43,RR19,102 +ICD-10,C43.5,RR19,102 +ICD-10,C44,RR19,101 +ICD-10,C44.1,RR19,101 +ICD-10,C44.2,RR19,101 +ICD-10,C44.3,RR19,101 +ICD-10,C44.4,RR19,101 +ICD-10,C44.5,RR19,101 +ICD-10,C44.9,RR19,101 +ICD-10,C46.0,RR19,101 +ICD-10,C47.9,RR19,115 +ICD-10,C50,RR19,103 +ICD-10,C50.9,RR19,103 +ICD-10,C51,RR19,115 +ICD-10,C53,RR19,115 +ICD-10,C54.1,RR19,115 +ICD-10,C55,RR19,115 +ICD-10,C56,RR19,115 +ICD-10,C60.1,RR19,115 +ICD-10,C61,RR19,108 +ICD-10,C64,RR19,107 +ICD-10,C66,RR19,107 +ICD-10,C67,RR19,107 +ICD-10,C67.9,RR19,107 +ICD-10,C68.9,RR19,107 +ICD-10,C71,RR19,113 +ICD-10,C73,RR19,115 +ICD-10,C79.1,RR19,107 +ICD-10,C81.9,RR19,111 +ICD-10,C83.1,RR19,111 +ICD-10,C83.3,RR19,111 +ICD-10,C85.7,RR19,111 +ICD-10,C88.0,RR19,110 +ICD-10,C90.0,RR19,110 +ICD-10,C91,RR19,110 +ICD-10,C91.0,RR19,110 +ICD-10,C91.1,RR19,110 +ICD-10,C91.4,RR19,110 +ICD-10,C92,RR19,110 +ICD-10,C92.1,RR19,110 +ICD-10,C93.1,RR19,110 +ICD-10,C95,RR19,110 +ICD-10,C96.2,RR19,110 From e9d8655a13c87167416d968fa4008b0845fb6c5c Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 1 Dec 2025 15:13:17 +0000 Subject: [PATCH 156/166] Create ukt3.csv --- codes/code_lists/ukt3.csv | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 codes/code_lists/ukt3.csv diff --git a/codes/code_lists/ukt3.csv b/codes/code_lists/ukt3.csv new file mode 100644 index 0000000..cbbe869 --- /dev/null +++ b/codes/code_lists/ukt3.csv @@ -0,0 +1,2 @@ +UKT3,K,Kidney +UKT3,KP,Kidney & Pancreas From 11c281e8ab54e3fa7d42440bf8fa85d92554d53c Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 1 Dec 2025 15:15:45 +0000 Subject: [PATCH 157/166] Create ukt4.csv --- codes/code_lists/ukt4.csv | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 codes/code_lists/ukt4.csv diff --git a/codes/code_lists/ukt4.csv b/codes/code_lists/ukt4.csv new file mode 100644 index 0000000..71504d7 --- /dev/null +++ b/codes/code_lists/ukt4.csv @@ -0,0 +1,14 @@ +UKT4,A,Active +UKT4,DA,Died while Active +UKT4,DS,Died while Suspended +UKT4,L,Live Transplant +UKT4,LA,Live Transplant while Active +UKT4,LS,Live Transplant while Suspended +UKT4,RA,Removed from Active +UKT4,RS,Removed from Suspended +UKT4,S,Suspended +UKT4,SA,Suspended from Active +UKT4,T,Transplanted +UKT4,TA,Transplanted while Active +UKT4,TR,Transplanted when Removed +UKT4,TS,Transplanted while Suspended From 257162f4a9440d1c5cfcc1b1c7f43a872690c1be Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 8 Dec 2025 12:29:36 +0000 Subject: [PATCH 158/166] Create phosphate_to_rr1plus_facilities.csv --- .../phosphate_to_rr1plus_facilities.csv | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv diff --git a/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv b/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv new file mode 100644 index 0000000..80b7e74 --- /dev/null +++ b/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv @@ -0,0 +1,44 @@ +PHOSPHATE_UNIT,P001,RR1+,RGT01 +PHOSPHATE_UNIT,P001,RR1+,RGT01 +PHOSPHATE_UNIT,P004,RR1+,RAE05 +PHOSPHATE_UNIT,P006,RR1+,RP5 +PHOSPHATE_UNIT,P007,RR1+,RVVKC +PHOSPHATE_UNIT,P008,RR1+,RTD01 +PHOSPHATE_UNIT,P009,RR1+,SGC04 +PHOSPHATE_UNIT,P010,RR1+,RH641 +PHOSPHATE_UNIT,P011,RR1+,RJ121 +PHOSPHATE_UNIT,P012,RR1+,RF201 +PHOSPHATE_UNIT,P013,RR1+,RGQ02 +PHOSPHATE_UNIT,P014,RR1+,RJZ +PHOSPHATE_UNIT,P015,RR1+,RFBAK +PHOSPHATE_UNIT,P016,RR1+,RM574 +PHOSPHATE_UNIT,P018,RR1+,RK7CC +PHOSPHATE_UNIT,P019,RR1+,RCSLB +PHOSPHATE_UNIT,P021,RR1+,RQ617 +PHOSPHATE_UNIT,P022,RR1+,RLZ01 +PHOSPHATE_UNIT,P027,RR1+,RJ701 +PHOSPHATE_UNIT,P029,RR1+,RAQ01 +PHOSPHATE_UNIT,P031,RR1+,RW402 +PHOSPHATE_UNIT,P032,RR1+,RRBBV +PHOSPHATE_UNIT,P036,RR1+,RH8 +PHOSPHATE_UNIT,P037,RR1+,RJE01 +PHOSPHATE_UNIT,P038,RR1+,RK950 +PHOSPHATE_UNIT,P039,RR1+,RFPFG +PHOSPHATE_UNIT,P041,RR1+,RBL14 +PHOSPHATE_UNIT,P042,RR1+,RAZ +PHOSPHATE_UNIT,P044,RR1+,SHC01 +PHOSPHATE_UNIT,P046,RR1+,RRK02 +PHOSPHATE_UNIT,P047,RR1+,RHW01 +PHOSPHATE_UNIT,P048,RR1+,SAC02 +PHOSPHATE_UNIT,P051,RR1+,SLC01 +PHOSPHATE_UNIT,P052,RR1+,RL403 +PHOSPHATE_UNIT,P053,RR1+,RGP75 +PHOSPHATE_UNIT,P054,RR1+,RCJAT +PHOSPHATE_UNIT,P094,RR1+,RBD01 +PHOSPHATE_UNIT,P146,RR1+,RLGAY +PHOSPHATE_UNIT,P187,RR1+,RLNGH +PHOSPHATE_UNIT,P207,RR1+,RNA03 +PHOSPHATE_UNIT,P219,RR1+,RKB01 +PHOSPHATE_UNIT,P256,RR1+,RAJ +PHOSPHATE_UNIT,P257,RR1+,RCB55 +PHOSPHATE_UNIT,P258,RR1+,RGU01 From 4cc4408eaaa09fb9912e403ba128b2c11ddb1a68 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 8 Dec 2025 12:33:07 +0000 Subject: [PATCH 159/166] Create simplified_to_rr1plus_facilities.csv --- .../simplified_to_rr1plus_facilities.csv | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 codes/code_conv_lists/simplified_to_rr1plus_facilities.csv diff --git a/codes/code_conv_lists/simplified_to_rr1plus_facilities.csv b/codes/code_conv_lists/simplified_to_rr1plus_facilities.csv new file mode 100644 index 0000000..eff9da9 --- /dev/null +++ b/codes/code_conv_lists/simplified_to_rr1plus_facilities.csv @@ -0,0 +1,55 @@ +SIMPLIFIED_UNIT,S001,RR1+,RGT01 +SIMPLIFIED_UNIT,S002,RR1+,RQN02 +SIMPLIFIED_UNIT,S003,RR1+,RNJ00 +SIMPLIFIED_UNIT,S004,RR1+,RAE05 +SIMPLIFIED_UNIT,S005,RR1+,RAJ +SIMPLIFIED_UNIT,S006,RR1+,RP5 +SIMPLIFIED_UNIT,S007,RR1+,RVVKC +SIMPLIFIED_UNIT,S008,RR1+,RTD01 +SIMPLIFIED_UNIT,S009,RR1+,SGC04 +SIMPLIFIED_UNIT,S010,RR1+,RH641 +SIMPLIFIED_UNIT,S011,RR1+,RJ121 +SIMPLIFIED_UNIT,S014,RR1+,RJZ +SIMPLIFIED_UNIT,S015,RR1+,RFBAK +SIMPLIFIED_UNIT,S016,RR1+,RM574 +SIMPLIFIED_UNIT,S017,RR1+,RM102 +SIMPLIFIED_UNIT,S018,RR1+,RK7CC +SIMPLIFIED_UNIT,S019,RR1+,RCSLB +SIMPLIFIED_UNIT,S020,RR1+,RAL01 +SIMPLIFIED_UNIT,S021,RR1+,RQ617 +SIMPLIFIED_UNIT,S022,RR1+,RLZ01 +SIMPLIFIED_UNIT,S023,RR1+,RGU01 +SIMPLIFIED_UNIT,S024,RR1+,RM301 +SIMPLIFIED_UNIT,S025,RR1+,RAJ +SIMPLIFIED_UNIT,S026,RR1+,REE01 +SIMPLIFIED_UNIT,S027,RR1+,RJ701 +SIMPLIFIED_UNIT,S029,RR1+,RAQ01 +SIMPLIFIED_UNIT,S030,RR1+,RLNGH +SIMPLIFIED_UNIT,S031,RR1+,RW402 +SIMPLIFIED_UNIT,S032,RR1+,RRBBV +SIMPLIFIED_UNIT,S033,RR1+,RAJ +SIMPLIFIED_UNIT,S035,RR1+,RMF01 +SIMPLIFIED_UNIT,S036,RR1+,RH8 +SIMPLIFIED_UNIT,S037,RR1+,RJE01 +SIMPLIFIED_UNIT,S038,RR1+,RK950 +SIMPLIFIED_UNIT,S039,RR1+,RFPFG +SIMPLIFIED_UNIT,S040,RR1+,RQHC7 +SIMPLIFIED_UNIT,S041,RR1+,RBL14 +SIMPLIFIED_UNIT,S042,RR1+,RAZ +SIMPLIFIED_UNIT,S043,RR1+,STC01 +SIMPLIFIED_UNIT,S044,RR1+,SHC01 +SIMPLIFIED_UNIT,S045,RR1+,RGT01 +SIMPLIFIED_UNIT,S046,RR1+,RL7 +SIMPLIFIED_UNIT,S047,RR1+,RHW01 +SIMPLIFIED_UNIT,S048,RR1+,SAC02 +SIMPLIFIED_UNIT,S049,RR1+,RH8 +SIMPLIFIED_UNIT,S050,RR1+,RHU02 +SIMPLIFIED_UNIT,S051,RR1+,SLC01 +SIMPLIFIED_UNIT,S052,RR1+,RL403 +SIMPLIFIED_UNIT,S053,RR1+,RM102 +SIMPLIFIED_UNIT,S054,RR1+,RCJAT +SIMPLIFIED_UNIT,S146,RR1+,RLGAY +SIMPLIFIED_UNIT,S207,RR1+,RNA03 +SIMPLIFIED_UNIT,S238,RR1+, +SIMPLIFIED_UNIT,S249,RR1+,SFC01 +SIMPLIFIED_UNIT,S252,RR1+,SSC02 From 2fe0ac3b050a0bc34f99de8568f51c3bebeec5b4 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 8 Dec 2025 12:51:21 +0000 Subject: [PATCH 160/166] Update phosphate_to_rr1plus_facilities.csv --- codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv | 1 - 1 file changed, 1 deletion(-) diff --git a/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv b/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv index 80b7e74..7741b43 100644 --- a/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv +++ b/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv @@ -1,5 +1,4 @@ PHOSPHATE_UNIT,P001,RR1+,RGT01 -PHOSPHATE_UNIT,P001,RR1+,RGT01 PHOSPHATE_UNIT,P004,RR1+,RAE05 PHOSPHATE_UNIT,P006,RR1+,RP5 PHOSPHATE_UNIT,P007,RR1+,RVVKC From 519a4834d3222ebe1a77049e15493b6186a34c38 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 8 Dec 2025 14:59:08 +0000 Subject: [PATCH 161/166] Create rr1plus_facilities_to_statistician_code.csv --- ...r1plus_facilities_to_statistician_code.csv | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv diff --git a/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv b/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv new file mode 100644 index 0000000..b70e814 --- /dev/null +++ b/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv @@ -0,0 +1,69 @@ +RR1+,2020,STATISTICIAN_CODE,Belfast +RR1+,7021,STATISTICIAN_CODE,Ulster +RR1+,24027,STATISTICIAN_CODE,Antrim +RR1+,33020,STATISTICIAN_CODE,Newry +RR1+,45021,STATISTICIAN_CODE,West NI +RR1+,RAE05,STATISTICIAN_CODE,Bradfd +RR1+,RAJ,STATISTICIAN_CODE,EssexMS +RR1+,RAL01,STATISTICIAN_CODE,L Rfree +RR1+,RAQ01,STATISTICIAN_CODE,Stevng +RR1+,RAZ,STATISTICIAN_CODE,Carsh +RR1+,RBD01,STATISTICIAN_CODE,Dorset +RR1+,RBL14,STATISTICIAN_CODE,Wirral +RR1+,RCB55,STATISTICIAN_CODE,York +RR1+,RCJAT,STATISTICIAN_CODE,Middlbr +RR1+,RCSLB,STATISTICIAN_CODE,Nottm +RR1+,RDEE4,STATISTICIAN_CODE,Colchr +RR1+,REE01,STATISTICIAN_CODE,Bristol +RR1+,REF12,STATISTICIAN_CODE,Truro +RR1+,RF201,STATISTICIAN_CODE,Hull +RR1+,RFBAK,STATISTICIAN_CODE,Leic +RR1+,RFPFG,STATISTICIAN_CODE,Derby +RR1+,RGQ02,STATISTICIAN_CODE,Ipswi +RR1+,RGT01,STATISTICIAN_CODE,Camb +RR1+,RGU01,STATISTICIAN_CODE,Brightn +RR1+,RH641,STATISTICIAN_CODE,Glouc +RR1+,RH8,STATISTICIAN_CODE,Exeter +RR1+,RHU02,STATISTICIAN_CODE,Ports +RR1+,RHW01,STATISTICIAN_CODE,Redng +RR1+,RJ121,STATISTICIAN_CODE,L Guys +RR1+,RQN02,STATISTICIAN_CODE,L West +RR1+,RJ701,STATISTICIAN_CODE,L St.G +RR1+,RJE01,STATISTICIAN_CODE,Stoke +RR1+,RJZ,STATISTICIAN_CODE,L Kings +RR1+,RK7CC,STATISTICIAN_CODE,Sheff +RR1+,RK950,STATISTICIAN_CODE,Plymth +RR1+,RKB01,STATISTICIAN_CODE,Covnt +RR1+,RKGA1,STATISTICIAN_CODE,Clwyd +RR1+,RKHA4,STATISTICIAN_CODE,Wrexm +RR1+,RL403,STATISTICIAN_CODE,Wolve +RR1+,RL7,STATISTICIAN_CODE,Bham +RR1+,RLGAY,STATISTICIAN_CODE,Carlis +RR1+,RLNGH,STATISTICIAN_CODE,Sund +RR1+,RLZ01,STATISTICIAN_CODE,Shrew +RR1+,RM102,STATISTICIAN_CODE,Norwch +RR1+,RM301,STATISTICIAN_CODE,Salford +RR1+,RM574,STATISTICIAN_CODE,M RI +RR1+,RMF01,STATISTICIAN_CODE,Prestn +RR1+,RNA03,STATISTICIAN_CODE,Dudley +RR1+,RNJ00,STATISTICIAN_CODE,L Barts +RR1+,RNX02,STATISTICIAN_CODE,Oxford +RR1+,RP5,STATISTICIAN_CODE,Donc +RR1+,RQR13,STATISTICIAN_CODE,Leeds +RR1+,RQ617,STATISTICIAN_CODE,Liv UH +RR1+,RQBAU,STATISTICIAN_CODE,Bangor +RR1+,RQHC7,STATISTICIAN_CODE,Swanse +RR1+,RRBBV,STATISTICIAN_CODE,Cardff +RR1+,RRK02,STATISTICIAN_CODE,Bham +RR1+,RTD01,STATISTICIAN_CODE,Newc +RR1+,RVVKC,STATISTICIAN_CODE,Kent +RR1+,RW402,STATISTICIAN_CODE,Liv UH +RR1+,SAC02,STATISTICIAN_CODE,Klmarnk +RR1+,SFC01,STATISTICIAN_CODE,Krkcldy +RR1+,SGC04,STATISTICIAN_CODE,Glasgw +RR1+,SHC01,STATISTICIAN_CODE,Inverns +RR1+,SLC01,STATISTICIAN_CODE,Airdrie +RR1+,SNC01,STATISTICIAN_CODE,Abrdn +RR1+,SSC02,STATISTICIAN_CODE,Edinb +RR1+,STC01,STATISTICIAN_CODE,Dundee +RR1+,SYC02,STATISTICIAN_CODE,D&Gall From ec3cce445951d167199421ecb58f2988a7a3134f Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 9 Dec 2025 10:27:36 +0000 Subject: [PATCH 162/166] Update rr1plus_facilities_to_statistician_code.csv --- .../rr1plus_facilities_to_statistician_code.csv | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv b/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv index b70e814..30ca493 100644 --- a/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv +++ b/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv @@ -67,3 +67,16 @@ RR1+,SNC01,STATISTICIAN_CODE,Abrdn RR1+,SSC02,STATISTICIAN_CODE,Edinb RR1+,STC01,STATISTICIAN_CODE,Dundee RR1+,SYC02,STATISTICIAN_CODE,D&Gall +RR1+,11023,STATISTICIAN_CODE,Blfst_P +RR1+,99RCSLB,STATISTICIAN_CODE,Nottm_P +RR1+,99RHM01,STATISTICIAN_CODE,Soton_P +RR1+,99RQR13,STATISTICIAN_CODE,Leeds_P +RR1+,RA723,STATISTICIAN_CODE,Brstl_P +RR1+,RBS25,STATISTICIAN_CODE,Livpl_P +RR1+,RJ122,STATISTICIAN_CODE,L Eve_P +RR1+,RP4,STATISTICIAN_CODE,L GOSH_P +RR1+,RQ3,STATISTICIAN_CODE,Bham_P +RR1+,RTD02,STATISTICIAN_CODE,Newc_P +RR1+,RW3RM,STATISTICIAN_CODE,Manch_P +RR1+,RWM51,STATISTICIAN_CODE,Cardf_P +RR1+,SGC02,STATISTICIAN_CODE,Glasg_P From 0e95df7c8892301f5afbee9306a5e4dc2342aaef Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Tue, 30 Dec 2025 10:02:34 +0000 Subject: [PATCH 163/166] Create snomed_unofficial_to_edta2.csv --- .../code_conv_lists/snomed_unofficial_to_edta2.csv | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 codes/code_conv_lists/snomed_unofficial_to_edta2.csv diff --git a/codes/code_conv_lists/snomed_unofficial_to_edta2.csv b/codes/code_conv_lists/snomed_unofficial_to_edta2.csv new file mode 100644 index 0000000..712ab93 --- /dev/null +++ b/codes/code_conv_lists/snomed_unofficial_to_edta2.csv @@ -0,0 +1,13 @@ +SNOMED, 111411000119103, EDTA2, 2359 +SNOMED, 236403004, EDTA2, 1267 +SNOMED, 68779003, EDTA2, 1116 +SNOMED, 285841000119104, EDTA2, 2371 +SNOMED, 90791000119104, EDTA2, 2337 +SNOMED, 308751000119106, EDTA2, 1486 +SNOMED, 104931000119100, EDTA2, 2359 +SNOMED, 236398000, EDTA2, 1251 +SNOMED, 722278006, EDTA2, 3419 +SNOMED, 711000119100, EDTA2, 2337 +SNOMED, 717742006, EDTA2, 1625 +SNOMED, 788613004, EDTA2, 1464 +SNOMED, 86211000119102, EDTA2, 1602 From 0e86608f927b44bcfc0633b23658d412eee6e661 Mon Sep 17 00:00:00 2001 From: phil Date: Mon, 12 Jan 2026 10:14:41 +0000 Subject: [PATCH 164/166] removed codes to prevent falling out of sync with registry codes --- codes/README.md | 3 + .../dose_units_cf_rr23_to_radar.csv | 5 - .../dose_units_snomed_to_radar.csv | 17 - codes/code_conv_lists/edta2_to_edta.csv | 284 ------------ codes/code_conv_lists/edta2_to_snomed.csv | 283 ------------ codes/code_conv_lists/edta_to_edta2.csv | 65 --- codes/code_conv_lists/icd10_to_rr19.csv | 56 --- .../phosphate_to_rr1plus_facilities.csv | 43 -- codes/code_conv_lists/pkbsite_to_pkbmain.csv | 26 -- .../pv_facilities_to_rr1plus.csv | 9 - .../code_conv_lists/pv_testcodes_to_loinc.csv | 82 ---- .../pv_testcodes_to_snomed.csv | 7 - .../code_conv_lists/pvmig_testcodes_to_pv.csv | 83 ---- .../code_conv_lists/pvmig_testunits_to_pv.csv | 53 --- .../code_conv_lists/pvraw_testcodes_to_pv.csv | 3 - .../radar_facilities_to_rr1plus.csv | 26 -- .../rawpvrrtstatus_to_pvrrtstatus.csv | 101 ---- .../rr1plus_facilities_to_pv.csv | 7 - .../rr1plus_facilities_to_radar.csv | 4 - ...r1plus_facilities_to_statistician_code.csv | 82 ---- .../simplified_to_rr1plus_facilities.csv | 55 --- .../snomed_testcodes_to_pv.csv | 1 - codes/code_conv_lists/snomed_to_edta2.csv | 234 ---------- .../snomed_to_survey_types.csv | 5 - .../survey_types_to_snomed.csv | 5 - .../survey_units_to_rr1plus.csv | 72 --- .../ukrr_testcodes_to_loinc.csv | 50 -- .../code_conv_lists/ukrr_testcodes_to_pv.csv | 46 -- .../ukrr_testcodes_to_snomed.csv | 52 --- codes/code_exclusions/pkb_observations.csv | 14 - codes/code_exclusions/pv_observations.csv | 3 - codes/code_lists/RR22.csv | 7 - codes/code_lists/RR23.csv | 11 - codes/code_lists/RR50.csv | 3 - codes/code_lists/RR51.csv | 12 - codes/code_lists/cf_rr7_discharge.csv | 9 - codes/code_lists/cf_rr7_treatment.csv | 51 -- codes/code_lists/dose_units.csv | 20 - codes/code_lists/edta2.csv | 284 ------------ codes/code_lists/edta_cod.csv | 65 --- codes/code_lists/edta_prd.csv | 339 -------------- codes/code_lists/loinc_observations.csv | 86 ---- .../nhs_data_dictionary_employment_status.csv | 9 - .../nhs_data_dictionary_ethnicity.csv | 17 - .../nhs_data_dictionary_language_code.csv | 189 -------- codes/code_lists/pkb_main.csv | 12 - codes/code_lists/pv_admit_reason.csv | 2 - codes/code_lists/pv_groups.csv | 175 ------- codes/code_lists/pv_observations.csv | 92 ---- codes/code_lists/pv_rrtstatus.csv | 5 - codes/code_lists/pv_tpstatus.csv | 7 - codes/code_lists/radar_facilities.csv | 1 - codes/code_lists/rawpvrrtstatus.csv | 101 ---- codes/code_lists/rr1plus_facilities.csv | 437 ------------------ codes/code_lists/snomed_access_device.csv | 3 - codes/code_lists/snomed_access_finding.csv | 6 - codes/code_lists/snomed_access_procedure.csv | 5 - codes/code_lists/snomed_diabetes.csv | 3 - codes/code_lists/snomed_diagnosis.csv | 28 -- codes/code_lists/snomed_dialysis.csv | 2 - codes/code_lists/snomed_graft_type.csv | 3 - codes/code_lists/snomed_malignancy.csv | 30 -- codes/code_lists/snomed_observation.csv | 11 - codes/code_lists/snomed_relationship.csv | 9 - codes/code_lists/snomed_renal_diagnosis.csv | 232 ---------- codes/code_lists/snomed_result.csv | 47 -- codes/code_lists/snomed_units_of_measure.csv | 11 - codes/code_lists/survey_questions.csv | 28 -- codes/code_lists/survey_types.csv | 4 - codes/code_lists/ukrr_observations.csv | 61 --- .../ukrr_testcodes_to_gl_mmoll_ratio.csv | 7 - codes/code_lists/ukt3.csv | 2 - codes/code_lists/ukt4.csv | 14 - codes/satellite_map/satellite_map.csv | 226 --------- 74 files changed, 3 insertions(+), 4439 deletions(-) create mode 100644 codes/README.md delete mode 100644 codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv delete mode 100644 codes/code_conv_lists/dose_units_snomed_to_radar.csv delete mode 100644 codes/code_conv_lists/edta2_to_edta.csv delete mode 100644 codes/code_conv_lists/edta2_to_snomed.csv delete mode 100644 codes/code_conv_lists/edta_to_edta2.csv delete mode 100644 codes/code_conv_lists/icd10_to_rr19.csv delete mode 100644 codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv delete mode 100644 codes/code_conv_lists/pkbsite_to_pkbmain.csv delete mode 100644 codes/code_conv_lists/pv_facilities_to_rr1plus.csv delete mode 100644 codes/code_conv_lists/pv_testcodes_to_loinc.csv delete mode 100644 codes/code_conv_lists/pv_testcodes_to_snomed.csv delete mode 100644 codes/code_conv_lists/pvmig_testcodes_to_pv.csv delete mode 100644 codes/code_conv_lists/pvmig_testunits_to_pv.csv delete mode 100644 codes/code_conv_lists/pvraw_testcodes_to_pv.csv delete mode 100644 codes/code_conv_lists/radar_facilities_to_rr1plus.csv delete mode 100644 codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv delete mode 100644 codes/code_conv_lists/rr1plus_facilities_to_pv.csv delete mode 100644 codes/code_conv_lists/rr1plus_facilities_to_radar.csv delete mode 100644 codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv delete mode 100644 codes/code_conv_lists/simplified_to_rr1plus_facilities.csv delete mode 100644 codes/code_conv_lists/snomed_testcodes_to_pv.csv delete mode 100644 codes/code_conv_lists/snomed_to_edta2.csv delete mode 100644 codes/code_conv_lists/snomed_to_survey_types.csv delete mode 100644 codes/code_conv_lists/survey_types_to_snomed.csv delete mode 100644 codes/code_conv_lists/survey_units_to_rr1plus.csv delete mode 100644 codes/code_conv_lists/ukrr_testcodes_to_loinc.csv delete mode 100644 codes/code_conv_lists/ukrr_testcodes_to_pv.csv delete mode 100644 codes/code_conv_lists/ukrr_testcodes_to_snomed.csv delete mode 100644 codes/code_exclusions/pkb_observations.csv delete mode 100644 codes/code_exclusions/pv_observations.csv delete mode 100644 codes/code_lists/RR22.csv delete mode 100644 codes/code_lists/RR23.csv delete mode 100644 codes/code_lists/RR50.csv delete mode 100644 codes/code_lists/RR51.csv delete mode 100644 codes/code_lists/cf_rr7_discharge.csv delete mode 100644 codes/code_lists/cf_rr7_treatment.csv delete mode 100644 codes/code_lists/dose_units.csv delete mode 100644 codes/code_lists/edta2.csv delete mode 100644 codes/code_lists/edta_cod.csv delete mode 100644 codes/code_lists/edta_prd.csv delete mode 100644 codes/code_lists/loinc_observations.csv delete mode 100644 codes/code_lists/nhs_data_dictionary_employment_status.csv delete mode 100644 codes/code_lists/nhs_data_dictionary_ethnicity.csv delete mode 100644 codes/code_lists/nhs_data_dictionary_language_code.csv delete mode 100644 codes/code_lists/pkb_main.csv delete mode 100644 codes/code_lists/pv_admit_reason.csv delete mode 100644 codes/code_lists/pv_groups.csv delete mode 100644 codes/code_lists/pv_observations.csv delete mode 100644 codes/code_lists/pv_rrtstatus.csv delete mode 100644 codes/code_lists/pv_tpstatus.csv delete mode 100644 codes/code_lists/radar_facilities.csv delete mode 100644 codes/code_lists/rawpvrrtstatus.csv delete mode 100644 codes/code_lists/rr1plus_facilities.csv delete mode 100644 codes/code_lists/snomed_access_device.csv delete mode 100644 codes/code_lists/snomed_access_finding.csv delete mode 100644 codes/code_lists/snomed_access_procedure.csv delete mode 100644 codes/code_lists/snomed_diabetes.csv delete mode 100644 codes/code_lists/snomed_diagnosis.csv delete mode 100644 codes/code_lists/snomed_dialysis.csv delete mode 100644 codes/code_lists/snomed_graft_type.csv delete mode 100644 codes/code_lists/snomed_malignancy.csv delete mode 100644 codes/code_lists/snomed_observation.csv delete mode 100644 codes/code_lists/snomed_relationship.csv delete mode 100644 codes/code_lists/snomed_renal_diagnosis.csv delete mode 100644 codes/code_lists/snomed_result.csv delete mode 100644 codes/code_lists/snomed_units_of_measure.csv delete mode 100644 codes/code_lists/survey_questions.csv delete mode 100644 codes/code_lists/survey_types.csv delete mode 100644 codes/code_lists/ukrr_observations.csv delete mode 100644 codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv delete mode 100644 codes/code_lists/ukt3.csv delete mode 100644 codes/code_lists/ukt4.csv delete mode 100644 codes/satellite_map/satellite_map.csv diff --git a/codes/README.md b/codes/README.md new file mode 100644 index 0000000..79b7fd0 --- /dev/null +++ b/codes/README.md @@ -0,0 +1,3 @@ +# Registry codes +Historically this directory was used to store csv files containing picklists and mappings for the codes which were used by the UKRDC. They have been now moved to a repo exclusively for this purpose which can be found [here](https://github.com/renalreg/registry-codes). + diff --git a/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv b/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv deleted file mode 100644 index 26b5596..0000000 --- a/codes/code_conv_lists/dose_units_cf_rr23_to_radar.csv +++ /dev/null @@ -1,5 +0,0 @@ -CF_RR23, microgram, RADAR, µg -CF_RR23, ug, RADAR, µg -CF_RR23, µg, RADAR, µg -CF_RR23, microg, RADAR, µg -CF_RR23, tab, RADAR, tab diff --git a/codes/code_conv_lists/dose_units_snomed_to_radar.csv b/codes/code_conv_lists/dose_units_snomed_to_radar.csv deleted file mode 100644 index a88d2c6..0000000 --- a/codes/code_conv_lists/dose_units_snomed_to_radar.csv +++ /dev/null @@ -1,17 +0,0 @@ -SNOMED,258770004,RADAR,l -SNOMED,258771000,RADAR,dl -SNOMED,258773002,RADAR,ml -SNOMED,258682000,RADAR,g -SNOMED,258684004,RADAR,mg -SNOMED,258685003,RADAR,µg -SNOMED,258686002,RADAR,ng -SNOMED,428673006,RADAR,tab -SNOMED,258997004,RADAR,iu -SNOMED,258718000,RADAR,mmol -SNOMED,415215001,RADAR,puff -SNOMED,767525000,RADAR,unit -SNOMED,413516001,RADAR,ampoule -SNOMED,404218003,RADAR,drop -SNOMED,428641000,RADAR,capsule -SNOMED,419702001,RADAR,patch -SNOMED,733013000,RADAR,sachet diff --git a/codes/code_conv_lists/edta2_to_edta.csv b/codes/code_conv_lists/edta2_to_edta.csv deleted file mode 100644 index aea3d40..0000000 --- a/codes/code_conv_lists/edta2_to_edta.csv +++ /dev/null @@ -1,284 +0,0 @@ -EDTA2,1003,EDTA,10 -EDTA2,1019,EDTA,10 -EDTA2,1026,EDTA,10 -EDTA2,1035,EDTA,10 -EDTA2,1042,EDTA,19 -EDTA2,1057,EDTA,19 -EDTA2,1061,EDTA,11 -EDTA2,1074,EDTA,99 -EDTA2,1088,EDTA,10 -EDTA2,1090,EDTA,10 -EDTA2,1100,EDTA,19 -EDTA2,1116,EDTA,10 -EDTA2,1128,EDTA,12 -EDTA2,1137,EDTA,10 -EDTA2,1144,EDTA,12 -EDTA2,1159,EDTA,10 -EDTA2,1163,EDTA,12 -EDTA2,1171,EDTA,19 -EDTA2,1185,EDTA,14 -EDTA2,1192,EDTA,14 -EDTA2,1205,EDTA,14 -EDTA2,1214,EDTA,14 -EDTA2,1222,EDTA,15 -EDTA2,1233,EDTA,13 -EDTA2,1246,EDTA,19 -EDTA2,1251,EDTA,16 -EDTA2,1267,EDTA,17 -EDTA2,1279,EDTA,50 -EDTA2,1280,EDTA,11 -EDTA2,1298,EDTA,50 -EDTA2,1308,EDTA,11 -EDTA2,1312,EDTA,17 -EDTA2,1320,EDTA,17 -EDTA2,1331,EDTA,19 -EDTA2,1349,EDTA,19 -EDTA2,1354,EDTA,19 -EDTA2,1365,EDTA,10 -EDTA2,1377,EDTA,19 -EDTA2,1383,EDTA,70 -EDTA2,1396,EDTA,74 -EDTA2,1401,EDTA,74 -EDTA2,1417,EDTA,74 -EDTA2,1429,EDTA,74 -EDTA2,1438,EDTA,74 -EDTA2,1440,EDTA,74 -EDTA2,1455,EDTA,73 -EDTA2,1464,EDTA,86 -EDTA2,1472,EDTA,86 -EDTA2,1486,EDTA,84 -EDTA2,1493,EDTA,84 -EDTA2,1504,EDTA,85 -EDTA2,1515,EDTA,85 -EDTA2,1527,EDTA,87 -EDTA2,1536,EDTA,87 -EDTA2,1543,EDTA,78 -EDTA2,1558,EDTA,78 -EDTA2,1562,EDTA,78 -EDTA2,1570,EDTA,78 -EDTA2,1589,EDTA,78 -EDTA2,1591,EDTA,78 -EDTA2,1602,EDTA,24 -EDTA2,1618,EDTA,24 -EDTA2,1625,EDTA,60 -EDTA2,1639,EDTA,40 -EDTA2,1641,EDTA,99 -EDTA2,1656,EDTA,99 -EDTA2,1660,EDTA,99 -EDTA2,1673,EDTA,99 -EDTA2,1687,EDTA,99 -EDTA2,1694,EDTA,66 -EDTA2,1706,EDTA,99 -EDTA2,1710,EDTA,99 -EDTA2,1723,EDTA,99 -EDTA2,1734,EDTA,61 -EDTA2,1747,EDTA,99 -EDTA2,1752,EDTA,23 -EDTA2,1768,EDTA,23 -EDTA2,1775,EDTA,23 -EDTA2,1781,EDTA,23 -EDTA2,1799,EDTA,23 -EDTA2,1809,EDTA,23 -EDTA2,1813,EDTA,23 -EDTA2,1821,EDTA,23 -EDTA2,1832,EDTA,25 -EDTA2,1845,EDTA,99 -EDTA2,1850,EDTA,99 -EDTA2,1866,EDTA,25 -EDTA2,1878,EDTA,99 -EDTA2,1884,EDTA,30 -EDTA2,1897,EDTA,30 -EDTA2,1907,EDTA,50 -EDTA2,1911,EDTA,50 -EDTA2,1924,EDTA,30 -EDTA2,1930,EDTA,30 -EDTA2,1948,EDTA,30 -EDTA2,1953,EDTA,30 -EDTA2,1969,EDTA,99 -EDTA2,1976,EDTA,99 -EDTA2,1982,EDTA,94 -EDTA2,1995,EDTA,94 -EDTA2,2005,EDTA,39 -EDTA2,2014,EDTA,39 -EDTA2,2022,EDTA,31 -EDTA2,2033,EDTA,31 -EDTA2,2046,EDTA,33 -EDTA2,2051,EDTA,33 -EDTA2,2067,EDTA,39 -EDTA2,2079,EDTA,39 -EDTA2,2080,EDTA,39 -EDTA2,2098,EDTA,39 -EDTA2,2108,EDTA,39 -EDTA2,2112,EDTA,39 -EDTA2,2120,EDTA,32 -EDTA2,2131,EDTA,32 -EDTA2,2149,EDTA,39 -EDTA2,2154,EDTA,39 -EDTA2,2165,EDTA,34 -EDTA2,2177,EDTA,34 -EDTA2,2183,EDTA,92 -EDTA2,2196,EDTA,92 -EDTA2,2203,EDTA,92 -EDTA2,2219,EDTA,99 -EDTA2,2226,EDTA,99 -EDTA2,2235,EDTA,91 -EDTA2,2242,EDTA,99 -EDTA2,2257,EDTA,99 -EDTA2,2261,EDTA,99 -EDTA2,2274,EDTA,99 -EDTA2,2288,EDTA,99 -EDTA2,2290,EDTA,99 -EDTA2,2300,EDTA,99 -EDTA2,2316,EDTA,80 -EDTA2,2328,EDTA,80 -EDTA2,2337,EDTA,81 -EDTA2,2344,EDTA,81 -EDTA2,2359,EDTA,72 -EDTA2,2363,EDTA,72 -EDTA2,2371,EDTA,71 -EDTA2,2385,EDTA,71 -EDTA2,2392,EDTA,70 -EDTA2,2407,EDTA,75 -EDTA2,2411,EDTA,75 -EDTA2,2424,EDTA,70 -EDTA2,2430,EDTA,75 -EDTA2,2448,EDTA,75 -EDTA2,2453,EDTA,70 -EDTA2,2469,EDTA,70 -EDTA2,2476,EDTA,99 -EDTA2,2482,EDTA,99 -EDTA2,2495,EDTA,99 -EDTA2,2509,EDTA,83 -EDTA2,2513,EDTA,83 -EDTA2,2521,EDTA,83 -EDTA2,2532,EDTA,83 -EDTA2,2545,EDTA,83 -EDTA2,2550,EDTA,83 -EDTA2,2566,EDTA,83 -EDTA2,2578,EDTA,82 -EDTA2,2584,EDTA,82 -EDTA2,2597,EDTA,82 -EDTA2,2606,EDTA,99 -EDTA2,2610,EDTA,88 -EDTA2,2623,EDTA,88 -EDTA2,2634,EDTA,88 -EDTA2,2647,EDTA,88 -EDTA2,2652,EDTA,88 -EDTA2,2668,EDTA,88 -EDTA2,2675,EDTA,88 -EDTA2,2681,EDTA,99 -EDTA2,2699,EDTA,99 -EDTA2,2702,EDTA,99 -EDTA2,2718,EDTA,41 -EDTA2,2725,EDTA,41 -EDTA2,2739,EDTA,41 -EDTA2,2741,EDTA,42 -EDTA2,2756,EDTA,51 -EDTA2,2760,EDTA,51 -EDTA2,2773,EDTA,99 -EDTA2,2787,EDTA,99 -EDTA2,2794,EDTA,40 -EDTA2,2804,EDTA,43 -EDTA2,2815,EDTA,43 -EDTA2,2827,EDTA,49 -EDTA2,2836,EDTA,43 -EDTA2,2843,EDTA,43 -EDTA2,2858,EDTA,43 -EDTA2,2862,EDTA,43 -EDTA2,2870,EDTA,43 -EDTA2,2889,EDTA,43 -EDTA2,2891,EDTA,43 -EDTA2,2901,EDTA,59 -EDTA2,2917,EDTA,59 -EDTA2,2929,EDTA,99 -EDTA2,2938,EDTA,59 -EDTA2,2940,EDTA,59 -EDTA2,2955,EDTA,99 -EDTA2,2964,EDTA,52 -EDTA2,2972,EDTA,59 -EDTA2,2986,EDTA,59 -EDTA2,2993,EDTA,59 -EDTA2,3000,EDTA,59 -EDTA2,3016,EDTA,59 -EDTA2,3028,EDTA,59 -EDTA2,3037,EDTA,59 -EDTA2,3044,EDTA,59 -EDTA2,3059,EDTA,59 -EDTA2,3063,EDTA,59 -EDTA2,3071,EDTA,59 -EDTA2,3085,EDTA,59 -EDTA2,3092,EDTA,59 -EDTA2,3102,EDTA,59 -EDTA2,3118,EDTA,59 -EDTA2,3125,EDTA,59 -EDTA2,3139,EDTA,59 -EDTA2,3141,EDTA,59 -EDTA2,3156,EDTA,59 -EDTA2,3160,EDTA,59 -EDTA2,3173,EDTA,59 -EDTA2,3187,EDTA,59 -EDTA2,3194,EDTA,53 -EDTA2,3207,EDTA,53 -EDTA2,3211,EDTA,53 -EDTA2,3224,EDTA,54 -EDTA2,3230,EDTA,54 -EDTA2,3248,EDTA,59 -EDTA2,3253,EDTA,59 -EDTA2,3269,EDTA,99 -EDTA2,3276,EDTA,59 -EDTA2,3282,EDTA,59 -EDTA2,3295,EDTA,99 -EDTA2,3305,EDTA,99 -EDTA2,3314,EDTA,99 -EDTA2,3322,EDTA,59 -EDTA2,3333,EDTA,59 -EDTA2,3346,EDTA,59 -EDTA2,3351,EDTA,59 -EDTA2,3367,EDTA,59 -EDTA2,3379,EDTA,59 -EDTA2,3380,EDTA,90 -EDTA2,3398,EDTA,90 -EDTA2,3403,EDTA,90 -EDTA2,3419,EDTA,90 -EDTA2,3426,EDTA,90 -EDTA2,3435,EDTA,90 -EDTA2,3442,EDTA,90 -EDTA2,3457,EDTA,99 -EDTA2,3461,EDTA,95 -EDTA2,3474,EDTA,95 -EDTA2,3488,EDTA,95 -EDTA2,3490,EDTA,95 -EDTA2,3501,EDTA,95 -EDTA2,3517,EDTA,99 -EDTA2,3529,EDTA,96 -EDTA2,3538,EDTA,96 -EDTA2,3540,EDTA,0 -EDTA2,3555,EDTA,0 -EDTA2,3564,EDTA,0 -EDTA2,3572,EDTA,0 -EDTA2,3604,EDTA,10 -EDTA2,3615,EDTA,10 -EDTA2,3627,EDTA,99 -EDTA2,3636,EDTA,92 -EDTA2,3643,EDTA,0 -EDTA2,3658,EDTA,59 -EDTA2,3662,EDTA,93 -EDTA2,3670,EDTA,23 -EDTA2,3689,EDTA,23 -EDTA2,3691,EDTA,0 -EDTA2,3708,EDTA,0 -EDTA2,3712,EDTA,0 -EDTA2,3720,EDTA,0 -EDTA2,3731,EDTA,53 -EDTA2,3749,EDTA,10 -EDTA2,3754,EDTA,17 -EDTA2,3765,EDTA,17 -EDTA2,3777,EDTA,17 -EDTA2,3783,EDTA,99 -EDTA2,3796,EDTA,99 -EDTA2,3806,EDTA,99 -EDTA2,3810,EDTA,25 -EDTA2,3823,EDTA,99 -EDTA2,3834,EDTA,99 -EDTA2,3847,EDTA,70 -EDTA2,3852,EDTA,74 diff --git a/codes/code_conv_lists/edta2_to_snomed.csv b/codes/code_conv_lists/edta2_to_snomed.csv deleted file mode 100644 index 083fa11..0000000 --- a/codes/code_conv_lists/edta2_to_snomed.csv +++ /dev/null @@ -1,283 +0,0 @@ -EDTA2,1003,SNOMED,52254009 -EDTA2,1019,SNOMED,445119005 -EDTA2,1026,SNOMED,48796009 -EDTA2,1035,SNOMED,197601003 -EDTA2,1042,SNOMED,197601003 -EDTA2,1057,SNOMED,722369003 -EDTA2,1061,SNOMED,236384008 -EDTA2,1074,SNOMED,236385009 -EDTA2,1088,SNOMED,722118005 -EDTA2,1090,SNOMED,44785005 -EDTA2,1100,SNOMED,44785005 -EDTA2,1116,SNOMED,236407003 -EDTA2,1128,SNOMED,236407003 -EDTA2,1137,SNOMED,445404003 -EDTA2,1144,SNOMED,445404003 -EDTA2,1159,SNOMED,282364005 -EDTA2,1163,SNOMED,282364005 -EDTA2,1171,SNOMED,236411009 -EDTA2,1185,SNOMED,722119002 -EDTA2,1192,SNOMED,722086002 -EDTA2,1205,SNOMED,722120008 -EDTA2,1214,SNOMED,722168002 -EDTA2,1222,SNOMED,75888001 -EDTA2,1233,SNOMED,722760002 -EDTA2,1246,SNOMED,236409000 -EDTA2,1251,SNOMED,197697005 -EDTA2,1267,SNOMED,236404005 -EDTA2,1279,SNOMED,445388002 -EDTA2,1280,SNOMED,445388002 -EDTA2,1298,SNOMED,444977005 -EDTA2,1308,SNOMED,444977005 -EDTA2,1312,SNOMED,1269761000000101 -EDTA2,1320,SNOMED,1269761000000101 -EDTA2,1331,SNOMED,3704008 -EDTA2,1349,SNOMED,35546006 -EDTA2,1354,SNOMED,83866005 -EDTA2,1365,SNOMED,36171008 -EDTA2,1377,SNOMED, 36171008 -EDTA2,1383,SNOMED, 724599009 -EDTA2,1396,SNOMED,722191003 -EDTA2,1401,SNOMED,195353004 -EDTA2,1417,SNOMED,195353004 -EDTA2,1429,SNOMED,1144805008 -EDTA2,1438,SNOMED,82275008 -EDTA2,1440,SNOMED,82275008 -EDTA2,1455,SNOMED,155441006 -EDTA2,1464,SNOMED,50581000 -EDTA2,1472,SNOMED,50581000 -EDTA2,1486,SNOMED,68815009 -EDTA2,1493,SNOMED,68815009 -EDTA2,1504,SNOMED,191306005 -EDTA2,1515,SNOMED,191306005 -EDTA2,1527,SNOMED,236502006 -EDTA2,1536,SNOMED,236502006 -EDTA2,1543,SNOMED,239947001 -EDTA2,1558,SNOMED,239947001 -EDTA2,1562,SNOMED,128971000119101 -EDTA2,1570,SNOMED,128971000119101 -EDTA2,1589,SNOMED,30911005 -EDTA2,1591,SNOMED,30911005 -EDTA2,1602,SNOMED,197764002 -EDTA2,1618,SNOMED,707208009 -EDTA2,1625,SNOMED,204949001 -EDTA2,1639,SNOMED,737562008 -EDTA2,1641,SNOMED,710571007 -EDTA2,1656,SNOMED,253864004 -EDTA2,1660,SNOMED,373584008 -EDTA2,1673,SNOMED,373585009 -EDTA2,1687,SNOMED,253900005 -EDTA2,1694,SNOMED,5187006 -EDTA2,1706,SNOMED,445387007 -EDTA2,1710,SNOMED,61758007 -EDTA2,1723,SNOMED,253904001 -EDTA2,1734,SNOMED,18417009 -EDTA2,1747,SNOMED,90241004 -EDTA2,1752,SNOMED,86249007 -EDTA2,1768,SNOMED,722078002 -EDTA2,1775,SNOMED,722082000 -EDTA2,1781,SNOMED,722081007 -EDTA2,1799,SNOMED,722089009 -EDTA2,1809,SNOMED,722088001 -EDTA2,1813,SNOMED,197808006 -EDTA2,1821,SNOMED,236017004 -EDTA2,1832,SNOMED,95566004 -EDTA2,1845,SNOMED,444717006 -EDTA2,1850,SNOMED,37497004 -EDTA2,1866,SNOMED,444690001 -EDTA2,1878,SNOMED,267441009 -EDTA2,1884,SNOMED,428255004 -EDTA2,1897,SNOMED,428255004 -EDTA2,1907,SNOMED,83923004 -EDTA2,1911,SNOMED,83923004 -EDTA2,1924,SNOMED,45927004 -EDTA2,1930,SNOMED,45927004 -EDTA2,1948,SNOMED,418839003 -EDTA2,1953,SNOMED,418839003 -EDTA2,1969,SNOMED,37061001 -EDTA2,1976,SNOMED,37061001 -EDTA2,1982,SNOMED,717770008 -EDTA2,1995,SNOMED,717770008 -EDTA2,2005,SNOMED,439990003 -EDTA2,2014,SNOMED,439990003 -EDTA2,2022,SNOMED,59400006 -EDTA2,2033,SNOMED,59400006 -EDTA2,2046,SNOMED,704203009 -EDTA2,2051,SNOMED,704203009 -EDTA2,2067,SNOMED,704205002 -EDTA2,2079,SNOMED,704205002 -EDTA2,2080,SNOMED,704206001 -EDTA2,2098,SNOMED,704206001 -EDTA2,2108,SNOMED,704055002 -EDTA2,2112,SNOMED,704055002 -EDTA2,2120,SNOMED,53556002 -EDTA2,2131,SNOMED,53556002 -EDTA2,2149,SNOMED,4390004 -EDTA2,2154,SNOMED,4390004 -EDTA2,2165,SNOMED,704204003 -EDTA2,2177,SNOMED,704204003 -EDTA2,2183,SNOMED,236496000 -EDTA2,2196,SNOMED,236496000 -EDTA2,2203,SNOMED,190829000 -EDTA2,2219,SNOMED,7725007 -EDTA2,2226,SNOMED,197772000 -EDTA2,2235,SNOMED,44323002 -EDTA2,2242,SNOMED,77377001 -EDTA2,2257,SNOMED,716864001 -EDTA2,2261,SNOMED,38898003 -EDTA2,2274,SNOMED,713504001 -EDTA2,2288,SNOMED,713504001 -EDTA2,2290,SNOMED,236706006 -EDTA2,2300,SNOMED,40733004 -EDTA2,2316,SNOMED,96441000119101 -EDTA2,2328,SNOMED,96441000119101 -EDTA2,2337,SNOMED,771000119108 -EDTA2,2344,SNOMED,771000119108 -EDTA2,2359,SNOMED,38481006 -EDTA2,2363,SNOMED,38481006 -EDTA2,2371,SNOMED,65443008 -EDTA2,2385,SNOMED,65443008 -EDTA2,2392,SNOMED,445108007 -EDTA2,2407,SNOMED,710565001 -EDTA2,2411,SNOMED,710565001 -EDTA2,2424,SNOMED,302233006 -EDTA2,2430,SNOMED,51677000 -EDTA2,2448,SNOMED,51677000 -EDTA2,2453,SNOMED,783730009 -EDTA2,2469,SNOMED,236488005 -EDTA2,2476,SNOMED,15842009 -EDTA2,2482,SNOMED,445236007 -EDTA2,2495,SNOMED,51292008 -EDTA2,2509,SNOMED,48713002 -EDTA2,2513,SNOMED,274945004 -EDTA2,2521,SNOMED,23132008 -EDTA2,2532,SNOMED,66451004 -EDTA2,2545,SNOMED,66451004 -EDTA2,2550,SNOMED,367528006 -EDTA2,2566,SNOMED,367528006 -EDTA2,2578,SNOMED,32278006 -EDTA2,2584,SNOMED,32278006 -EDTA2,2597,SNOMED,373604002 -EDTA2,2606,SNOMED,73305009 -EDTA2,2610,SNOMED,373421000 -EDTA2,2623,SNOMED,373422007 -EDTA2,2634,SNOMED,78129009 -EDTA2,2647,SNOMED, 111407006 -EDTA2,2652,SNOMED,444976001 -EDTA2,2668,SNOMED,722721004 -EDTA2,2675,SNOMED,373420004 -EDTA2,2681,SNOMED,736993008 -EDTA2,2699,SNOMED,13886001 -EDTA2,2702,SNOMED,13886001 -EDTA2,2718,SNOMED,765330003 -EDTA2,2725,SNOMED,253878003 -EDTA2,2739,SNOMED,253879006 -EDTA2,2741,SNOMED,28770003 -EDTA2,2756,SNOMED,770414008 -EDTA2,2760,SNOMED,770414008 -EDTA2,2773,SNOMED,236418003 -EDTA2,2787,SNOMED,236418003 -EDTA2,2794,SNOMED, 722223000 -EDTA2,2804,SNOMED,726017001 -EDTA2,2815,SNOMED,723373006 -EDTA2,2827,SNOMED,46785007 -EDTA2,2836,SNOMED,204958008 -EDTA2,2843,SNOMED,444830001 -EDTA2,2858,SNOMED,444558002 -EDTA2,2862,SNOMED,444749006 -EDTA2,2870,SNOMED,446989009 -EDTA2,2889,SNOMED,446991001 -EDTA2,2891,SNOMED,447335007 -EDTA2,2901,SNOMED,236466005 -EDTA2,2917,SNOMED,197744007 -EDTA2,2929,SNOMED,444645005 -EDTA2,2938,SNOMED,79385002 -EDTA2,2940,SNOMED,698953004 -EDTA2,2955,SNOMED,85020001 -EDTA2,2964,SNOMED,190681003 -EDTA2,2972,SNOMED,226309007 -EDTA2,2986,SNOMED,82236004 -EDTA2,2993,SNOMED,726080006 -EDTA2,3000,SNOMED,1776003 -EDTA2,3016,SNOMED,24790002 -EDTA2,3028,SNOMED,236461000 -EDTA2,3037,SNOMED,722468005 -EDTA2,3044,SNOMED,111395007 -EDTA2,3059,SNOMED,10406007 -EDTA2,3063,SNOMED,35759001 -EDTA2,3071,SNOMED,31742004 -EDTA2,3085,SNOMED,707742001 -EDTA2,3092,SNOMED,707756004 -EDTA2,3102,SNOMED,707747007 -EDTA2,3118,SNOMED,237770005 -EDTA2,3125,SNOMED,237743003 -EDTA2,3139,SNOMED,237604008 -EDTA2,3141,SNOMED,43941006 -EDTA2,3156,SNOMED,15689008 -EDTA2,3160,SNOMED,237885008 -EDTA2,3173,SNOMED,711152006 -EDTA2,3187,SNOMED,48655003 -EDTA2,3194,SNOMED,17901006 -EDTA2,3207,SNOMED,65520001 -EDTA2,3211,SNOMED,40951006 -EDTA2,3224,SNOMED,16652001 -EDTA2,3230,SNOMED,16652001 -EDTA2,3248,SNOMED,190919008 -EDTA2,3253,SNOMED,22199006 -EDTA2,3269,SNOMED,45582004 -EDTA2,3276,SNOMED,7199000 -EDTA2,3282,SNOMED,46659004 -EDTA2,3295,SNOMED,236443009 -EDTA2,3305,SNOMED,41729002 -EDTA2,3314,SNOMED,445431000 -EDTA2,3322,SNOMED,290006 -EDTA2,3333,SNOMED,63247009 -EDTA2,3346,SNOMED,24750000 -EDTA2,3351,SNOMED,5619004 -EDTA2,3367,SNOMED,240096000 -EDTA2,3379,SNOMED,236419006 -EDTA2,3380,SNOMED,14669001 -EDTA2,3398,SNOMED,1048451000000103 -EDTA2,3403,SNOMED,1048481000000109 -EDTA2,3419,SNOMED,1048491000000106 -EDTA2,3426,SNOMED,23697004 -EDTA2,3435,SNOMED,236428007 -EDTA2,3442,SNOMED,444794000 -EDTA2,3457,SNOMED,36689008 -EDTA2,3461,SNOMED,126880001 -EDTA2,3474,SNOMED,702391001 -EDTA2,3488,SNOMED,408642003 -EDTA2,3490,SNOMED,302849000 -EDTA2,3501,SNOMED,307604008 -EDTA2,3517,SNOMED,824131000000108 -EDTA2,3529,SNOMED,722149000 -EDTA2,3538,SNOMED,722467000 -EDTA2,3540,SNOMED,722098007 -EDTA2,3555,SNOMED,709044004 -EDTA2,3564,SNOMED,709044004 -EDTA2,3604,SNOMED,449820008 -EDTA2,3615,SNOMED,705065000 -EDTA2,3627,SNOMED,609572000 -EDTA2,3636,SNOMED,190829000 -EDTA2,3643,SNOMED,722150000 -EDTA2,3658,SNOMED,446449009 -EDTA2,3662,SNOMED,33763006 -EDTA2,3670,SNOMED,49120005 -EDTA2,3689,SNOMED,236015007 -EDTA2,3691,SNOMED,42399005 -EDTA2,3708,SNOMED,90688005 -EDTA2,3712,SNOMED,53298000 -EDTA2,3720,SNOMED,12491000132101 -EDTA2,3731,SNOMED,734990008 -EDTA2,3749,SNOMED,36171008 -EDTA2,3754,SNOMED, 713887002 -EDTA2,3765,SNOMED, 722139003 -EDTA2,3777,SNOMED,722147003 -EDTA2,3783,SNOMED,723074006 -EDTA2,3796,SNOMED,722077007 -EDTA2,3806,SNOMED, 722085003 -EDTA2,3810,SNOMED, 95570007 -EDTA2,3823,SNOMED,118600007 -EDTA2,3834,SNOMED,736992003 -EDTA2,3847,SNOMED,6956008 -EDTA2,3852,SNOMED,6956008 diff --git a/codes/code_conv_lists/edta_to_edta2.csv b/codes/code_conv_lists/edta_to_edta2.csv deleted file mode 100644 index ee01d23..0000000 --- a/codes/code_conv_lists/edta_to_edta2.csv +++ /dev/null @@ -1,65 +0,0 @@ -EDTA,0,EDTA2,3555 -EDTA,10,EDTA2,3749 -EDTA,11,EDTA2,1061 -EDTA,12,EDTA2,1128 -EDTA,13,EDTA2,1233 -EDTA,14,EDTA2,1185 -EDTA,15,EDTA2,1222 -EDTA,16,EDTA2,1251 -EDTA,17,EDTA2,1267 -EDTA,19,EDTA2,1377 -EDTA,20,EDTA2,1602 -EDTA,21,EDTA2,1706 -EDTA,22,EDTA2,1673 -EDTA,23,EDTA2,1752 -EDTA,24,EDTA2,1602 -EDTA,25,EDTA2,1832 -EDTA,29,EDTA2,3555 -EDTA,30,EDTA2,1884 -EDTA,31,EDTA2,2022 -EDTA,32,EDTA2,2120 -EDTA,33,EDTA2,2046 -EDTA,34,EDTA2,2165 -EDTA,39,EDTA2,2005 -EDTA,40,EDTA2,2794 -EDTA,41,EDTA2,2718 -EDTA,42,EDTA2,2741 -EDTA,43,EDTA2,2804 -EDTA,49,EDTA2,2794 -EDTA,50,EDTA2,3379 -EDTA,51,EDTA2,2756 -EDTA,52,EDTA2,2964 -EDTA,53,EDTA2,3194 -EDTA,54,EDTA2,3224 -EDTA,59,EDTA2,3379 -EDTA,60,EDTA2,1625 -EDTA,61,EDTA2,1734 -EDTA,63,EDTA2,1625 -EDTA,66,EDTA2,1694 -EDTA,70,EDTA2,2430 -EDTA,71,EDTA2,2371 -EDTA,72,EDTA2,2359 -EDTA,73,EDTA2,1455 -EDTA,74,EDTA2,1401 -EDTA,75,EDTA2,2430 -EDTA,76,EDTA2,1159 -EDTA,78,EDTA2,1543 -EDTA,79,EDTA2,2411 -EDTA,80,EDTA2,2316 -EDTA,81,EDTA2,2337 -EDTA,82,EDTA2,2578 -EDTA,83,EDTA2,2509 -EDTA,84,EDTA2,1486 -EDTA,85,EDTA2,1504 -EDTA,86,EDTA2,1464 -EDTA,87,EDTA2,1527 -EDTA,88,EDTA2,2623 -EDTA,89,EDTA2,3555 -EDTA,90,EDTA2,3442 -EDTA,91,EDTA2,2235 -EDTA,92,EDTA2,3636 -EDTA,93,EDTA2,3555 -EDTA,94,EDTA2,1982 -EDTA,95,EDTA2,3461 -EDTA,96,EDTA2,3538 -EDTA,99,EDTA2,3691 diff --git a/codes/code_conv_lists/icd10_to_rr19.csv b/codes/code_conv_lists/icd10_to_rr19.csv deleted file mode 100644 index d826961..0000000 --- a/codes/code_conv_lists/icd10_to_rr19.csv +++ /dev/null @@ -1,56 +0,0 @@ -ICD-10,C02.9,RR19,115 -ICD-10,C15,RR19,104 -ICD-10,C15.0,RR19,104 -ICD-10,C16,RR19,104 -ICD-10,C18,RR19,105 -ICD-10,C18.0,RR19,105 -ICD-10,C18.2,RR19,105 -ICD-10,C18.7,RR19,105 -ICD-10,C20,RR19,105 -ICD-10,C21,RR19,105 -ICD-10,C25,RR19,115 -ICD-10,C34,RR19,106 -ICD-10,C41.2,RR19,115 -ICD-10,C43,RR19,102 -ICD-10,C43.5,RR19,102 -ICD-10,C44,RR19,101 -ICD-10,C44.1,RR19,101 -ICD-10,C44.2,RR19,101 -ICD-10,C44.3,RR19,101 -ICD-10,C44.4,RR19,101 -ICD-10,C44.5,RR19,101 -ICD-10,C44.9,RR19,101 -ICD-10,C46.0,RR19,101 -ICD-10,C47.9,RR19,115 -ICD-10,C50,RR19,103 -ICD-10,C50.9,RR19,103 -ICD-10,C51,RR19,115 -ICD-10,C53,RR19,115 -ICD-10,C54.1,RR19,115 -ICD-10,C55,RR19,115 -ICD-10,C56,RR19,115 -ICD-10,C60.1,RR19,115 -ICD-10,C61,RR19,108 -ICD-10,C64,RR19,107 -ICD-10,C66,RR19,107 -ICD-10,C67,RR19,107 -ICD-10,C67.9,RR19,107 -ICD-10,C68.9,RR19,107 -ICD-10,C71,RR19,113 -ICD-10,C73,RR19,115 -ICD-10,C79.1,RR19,107 -ICD-10,C81.9,RR19,111 -ICD-10,C83.1,RR19,111 -ICD-10,C83.3,RR19,111 -ICD-10,C85.7,RR19,111 -ICD-10,C88.0,RR19,110 -ICD-10,C90.0,RR19,110 -ICD-10,C91,RR19,110 -ICD-10,C91.0,RR19,110 -ICD-10,C91.1,RR19,110 -ICD-10,C91.4,RR19,110 -ICD-10,C92,RR19,110 -ICD-10,C92.1,RR19,110 -ICD-10,C93.1,RR19,110 -ICD-10,C95,RR19,110 -ICD-10,C96.2,RR19,110 diff --git a/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv b/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv deleted file mode 100644 index 7741b43..0000000 --- a/codes/code_conv_lists/phosphate_to_rr1plus_facilities.csv +++ /dev/null @@ -1,43 +0,0 @@ -PHOSPHATE_UNIT,P001,RR1+,RGT01 -PHOSPHATE_UNIT,P004,RR1+,RAE05 -PHOSPHATE_UNIT,P006,RR1+,RP5 -PHOSPHATE_UNIT,P007,RR1+,RVVKC -PHOSPHATE_UNIT,P008,RR1+,RTD01 -PHOSPHATE_UNIT,P009,RR1+,SGC04 -PHOSPHATE_UNIT,P010,RR1+,RH641 -PHOSPHATE_UNIT,P011,RR1+,RJ121 -PHOSPHATE_UNIT,P012,RR1+,RF201 -PHOSPHATE_UNIT,P013,RR1+,RGQ02 -PHOSPHATE_UNIT,P014,RR1+,RJZ -PHOSPHATE_UNIT,P015,RR1+,RFBAK -PHOSPHATE_UNIT,P016,RR1+,RM574 -PHOSPHATE_UNIT,P018,RR1+,RK7CC -PHOSPHATE_UNIT,P019,RR1+,RCSLB -PHOSPHATE_UNIT,P021,RR1+,RQ617 -PHOSPHATE_UNIT,P022,RR1+,RLZ01 -PHOSPHATE_UNIT,P027,RR1+,RJ701 -PHOSPHATE_UNIT,P029,RR1+,RAQ01 -PHOSPHATE_UNIT,P031,RR1+,RW402 -PHOSPHATE_UNIT,P032,RR1+,RRBBV -PHOSPHATE_UNIT,P036,RR1+,RH8 -PHOSPHATE_UNIT,P037,RR1+,RJE01 -PHOSPHATE_UNIT,P038,RR1+,RK950 -PHOSPHATE_UNIT,P039,RR1+,RFPFG -PHOSPHATE_UNIT,P041,RR1+,RBL14 -PHOSPHATE_UNIT,P042,RR1+,RAZ -PHOSPHATE_UNIT,P044,RR1+,SHC01 -PHOSPHATE_UNIT,P046,RR1+,RRK02 -PHOSPHATE_UNIT,P047,RR1+,RHW01 -PHOSPHATE_UNIT,P048,RR1+,SAC02 -PHOSPHATE_UNIT,P051,RR1+,SLC01 -PHOSPHATE_UNIT,P052,RR1+,RL403 -PHOSPHATE_UNIT,P053,RR1+,RGP75 -PHOSPHATE_UNIT,P054,RR1+,RCJAT -PHOSPHATE_UNIT,P094,RR1+,RBD01 -PHOSPHATE_UNIT,P146,RR1+,RLGAY -PHOSPHATE_UNIT,P187,RR1+,RLNGH -PHOSPHATE_UNIT,P207,RR1+,RNA03 -PHOSPHATE_UNIT,P219,RR1+,RKB01 -PHOSPHATE_UNIT,P256,RR1+,RAJ -PHOSPHATE_UNIT,P257,RR1+,RCB55 -PHOSPHATE_UNIT,P258,RR1+,RGU01 diff --git a/codes/code_conv_lists/pkbsite_to_pkbmain.csv b/codes/code_conv_lists/pkbsite_to_pkbmain.csv deleted file mode 100644 index 88d4e5e..0000000 --- a/codes/code_conv_lists/pkbsite_to_pkbmain.csv +++ /dev/null @@ -1,26 +0,0 @@ -PKB_SITE,2020,PKB_MAIN,11023 -PKB_SITE,48021,PKB_MAIN,45020 -PKB_SITE,45021,PKB_MAIN,45020 -PKB_SITE,RKGA1,PKB_MAIN,NHSWLS -PKB_SITE,RQHC7,PKB_MAIN,NHSWLS -PKB_SITE,RKHA4,PKB_MAIN,NHSWLS -PKB_SITE,RQBAU,PKB_MAIN,NHSWLS -PKB_SITE,RRBBV,PKB_MAIN,NHSWLS -PKB_SITE,RDDH0,PKB_MAIN,RAJ -PKB_SITE,RQ8L0,PKB_MAIN,RAJ -PKB_SITE,RAJ01,PKB_MAIN,RAJ -PKB_SITE,RBL20,PKB_MAIN,RBL14 -PKB_SITE,RDEE4,PKB_MAIN,RGQ02 -PKB_SITE,RW3RM,PKB_MAIN,RM574 -PKB_SITE,RQ601,PKB_MAIN,RQ617 -PKB_SITE,RW402,PKB_MAIN,RQ617 -PKB_SITE,RVY01,PKB_MAIN,RQ617 -PKB_SITE,RKC81,PKB_MAIN,RQ617 -PKB_SITE,REM26,PKB_MAIN,RQ617 -PKB_SITE,RBN63,PKB_MAIN,RQ617 -PKB_SITE,9RW402,PKB_MAIN,RQ617 -PKB_SITE,9RBN01,PKB_MAIN,RQ617 -PKB_SITE,99RQR13,PKB_MAIN,RQR13 -PKB_SITE,RL7,PKB_MAIN,RRK02 -PKB_SITE,SGC02,PKB_MAIN,SGC04 -PKB_SITE,99RCSLB,PKB_MAIN,RCSLB diff --git a/codes/code_conv_lists/pv_facilities_to_rr1plus.csv b/codes/code_conv_lists/pv_facilities_to_rr1plus.csv deleted file mode 100644 index bc1623b..0000000 --- a/codes/code_conv_lists/pv_facilities_to_rr1plus.csv +++ /dev/null @@ -1,9 +0,0 @@ -PV,RSC02,RR1+,SSC02 -PV,RX1CC,RR1+,RCSLB -PV,R1H00,RR1+,RNJ00 -PV,RJ100,RR1+,RJ121 -PV,RQR00,RR1+,RQR13 -PV,SYC01,RR1+,SYC02 -PV,SGC05,RR1+,SGC04 -PV,RCD37,RR1+,RD1 -PV,99RHM01,RR1+,RHM02 \ No newline at end of file diff --git a/codes/code_conv_lists/pv_testcodes_to_loinc.csv b/codes/code_conv_lists/pv_testcodes_to_loinc.csv deleted file mode 100644 index f4b272c..0000000 --- a/codes/code_conv_lists/pv_testcodes_to_loinc.csv +++ /dev/null @@ -1,82 +0,0 @@ -PV,acr,LOINC,32294-1 -PV,adjustedcalcium,LOINC,19072-8 -PV,albumin,LOINC,1751-7 -PV,albumin_post,LOINC,1751-7 -PV,alp,LOINC,6768-6 -PV,alt,LOINC,1742-6 -PV,amy,LOINC,1798-8 -PV,ast,LOINC,1920-8 -PV,bili,LOINC,14631-6 -PV,calcium,LOINC,1996-8 -PV,calcium_post,LOINC,59148-7 -PV,cholesterol,LOINC,14647-2 -PV,covid19antibody,LOINC,95542-7 -PV,covid19lflow,LOINC,95209-3 -PV,covid19pcr,LOINC,94500-6 -PV,creatinine,LOINC,14682-9 -PV,creatinine_post,LOINC,51620-3 -PV,crp,LOINC,1988-5 -PV,egfr,LOINC,69405-9 -PV,FaecalCalprotectin,LOINC,38445-3 -PV,ferritin,LOINC,2276-4 -PV,folate,LOINC,2284-8 -PV,ft3,LOINC,14928-6 -PV,ft4,LOINC,14920-3 -PV,ggt,LOINC,2324-2 -PV,glucose,LOINC,14749-6 -PV,hb,LOINC,718-7 -PV,hba1c,LOINC,59261-8 -PV,hbv,LOINC,13952-7 -PV,hco3,LOINC,1959-6 -PV,hco3_post,LOINC,48631-6 -PV,hct,LOINC,4544-3 -PV,hcv,LOINC,16128-1 -PV,hdl,LOINC,14646-4 -PV,inr,LOINC,6301-6 -PV,iron,LOINC,14798-3 -PV,ironsat,LOINC,2502-3 -PV,ktv,LOINC,70961-8 -PV,ktv_post,LOINC,70961-8 -PV,ldh,LOINC,2532-0 -PV,ldl,LOINC,39469-2 -PV,lhratio,LOINC,44915-7 -PV,lipase,LOINC,3040-3 -PV,lithium,LOINC,14334-7 -PV,magnesium,LOINC,2601-3 -PV,mmp,LOINC,90294-0 -PV,neutrophils,LOINC,751-8 -PV,pcr,LOINC,34366-5 -PV,phepku,LOINC, -PV,phosphate,LOINC,14879-1 -PV,phosphate_post,LOINC,55972-4 -PV,platelets,LOINC,777-3 -PV,potassium,LOINC,2823-3 -PV,potassium_post,LOINC,29349-8 -PV,psa,LOINC,2857-1 -PV,pth,LOINC,14866-8 -PV,ret-he,LOINC,42810-2 -PV,sirolimus,LOINC,29247-4 -PV,sodium,LOINC,2951-2 -PV,sodium_post,LOINC,74688-3 -PV,t4,LOINC,3024-7 -PV,tacrolimus,LOINC,11253-2 -PV,testosterone,LOINC,2986-8 -PV,tg,LOINC,2571-8 -PV,tgn,LOINC,34381-4 -PV,tpmt,LOINC,91141-2 -PV,transferrin,LOINC,3034-6 -PV,trop,LOINC,6598-7 -PV,tsh,LOINC,3016-3 -PV,ualbumin,LOINC,6942-7 -PV,ucreatinine,LOINC,14683-7 -PV,updipstick,LOINC,20454-5 -PV,uprotein,LOINC,2888-6 -PV,urate,LOINC,14933-6 -PV,urea,LOINC,14937-7 -PV,urea_post,LOINC,39776-0 -PV,urr,LOINC,54456-9 -PV,urr_post,LOINC,54456-9 -PV,vitb12,LOINC,2132-9 -PV,vitd,LOINC,46269-7 -PV,wbc,LOINC,6690-2 -PV,ciclosporin,LOINC,3520-4 diff --git a/codes/code_conv_lists/pv_testcodes_to_snomed.csv b/codes/code_conv_lists/pv_testcodes_to_snomed.csv deleted file mode 100644 index ddcb161..0000000 --- a/codes/code_conv_lists/pv_testcodes_to_snomed.csv +++ /dev/null @@ -1,7 +0,0 @@ -PV,weight,SNOMED,27113001 -PV,height,SNOMED,162755006 -PV,bmi,SNOMED,301331008 -PV,pulse,SNOMED,162986007 -PV,bpsys,SNOMED,163030003 -PV,bpdia,SNOMED,163031004 -PV,bp_header,SNOMED,75367002 \ No newline at end of file diff --git a/codes/code_conv_lists/pvmig_testcodes_to_pv.csv b/codes/code_conv_lists/pvmig_testcodes_to_pv.csv deleted file mode 100644 index ef902a0..0000000 --- a/codes/code_conv_lists/pvmig_testcodes_to_pv.csv +++ /dev/null @@ -1,83 +0,0 @@ -PVMIGRATE,acr,PV,acr -PVMIGRATE,Adjusted Calcium,PV,adjustedcalcium -PVMIGRATE,adjustedca,PV,adjustedcalcium -PVMIGRATE,adjustedcalcium,PV,adjustedcalcium -PVMIGRATE,albumin,PV,albumin -PVMIGRATE,Alkaline Phosphatase,PV,alp -PVMIGRATE,alp,PV,alp -PVMIGRATE,alt,PV,alt -PVMIGRATE,amy,PV,amy -PVMIGRATE,ast,PV,ast -PVMIGRATE,bili,PV,bili -PVMIGRATE,bmi,PV,bmi -PVMIGRATE,BodyTemperature,PV,BodyTemperature -PVMIGRATE,BP dia,PV,bpdia -PVMIGRATE,BP sys,PV,bpsys -PVMIGRATE,bpdia,PV,bpdia -PVMIGRATE,bpsys,PV,bpsys -PVMIGRATE,calcium,PV,calcium -PVMIGRATE,cholestero,PV,cholesterol -PVMIGRATE,cholesterol,PV,cholesterol -PVMIGRATE,ciclospori,PV,ciclosporin -PVMIGRATE,ciclosporin,PV,ciclosporin -PVMIGRATE,creatinine,PV,creatinine -PVMIGRATE,crp,PV,crp -PVMIGRATE,egfr,PV,egfr -PVMIGRATE,FaecalCalprotectin,PV,FaecalCalprotectin -PVMIGRATE,ferr,PV,ferritin -PVMIGRATE,ferritin,PV,ferritin -PVMIGRATE,folate,PV,folate -PVMIGRATE,ft3,PV,ft3 -PVMIGRATE,ft4,PV,ft4 -PVMIGRATE,ggt,PV,ggt -PVMIGRATE,glucose,PV,glucose -PVMIGRATE,hb,PV,hb -PVMIGRATE,hba1c,PV,hba1c -PVMIGRATE,HbA1c (IFCC),PV,hba1c -PVMIGRATE,hco3,PV,hco3 -PVMIGRATE,hct,PV,hct -PVMIGRATE,hdl,PV,hdl -PVMIGRATE,height,PV,height -PVMIGRATE,hypotension,PV,hypotension -PVMIGRATE,inr,PV,inr -PVMIGRATE,iron,PV,iron -PVMIGRATE,ironsat,PV,ironsat -PVMIGRATE,KT/V,PV,ktv -PVMIGRATE,ktv,PV,ktv -PVMIGRATE,ldh,PV,ldh -PVMIGRATE,ldl,PV,ldl -PVMIGRATE,lhratio,PV,lhratio -PVMIGRATE,lipase,PV,lipase -PVMIGRATE,lithium,PV,lithium -PVMIGRATE,magnesium,PV,magnesium -PVMIGRATE,neutrophils,PV,neutrophils -PVMIGRATE,pcr,PV,pcr -PVMIGRATE,phepku,PV,phepku -PVMIGRATE,phosphate,PV,phosphate -PVMIGRATE,platelets,PV,platelets -PVMIGRATE,potassium,PV,potassium -PVMIGRATE,psa,PV,psa -PVMIGRATE,pth,PV,pth -PVMIGRATE,pulse,PV,pulse -PVMIGRATE,Random plasma glucose:,PV,glucose -PVMIGRATE,Serum Creatinine,PV,creatinine -PVMIGRATE,Serum Urea,PV,urea -PVMIGRATE,sirolimus,PV,sirolimus -PVMIGRATE,sirolimus (rapamycin),PV,sirolimus -PVMIGRATE,sodium,PV,sodium -PVMIGRATE,t4,PV,t4 -PVMIGRATE,tacrolimus,PV,tacrolimus -PVMIGRATE,testosterone,PV,testosterone -PVMIGRATE,tg,PV,tg -PVMIGRATE,tpmt,PV,tpmt -PVMIGRATE,transferri,PV,transferrin -PVMIGRATE,transferrin,PV,transferrin -PVMIGRATE,tsh,PV,tsh -PVMIGRATE,ualbumin,PV,ualbumin -PVMIGRATE,urate,PV,urate -PVMIGRATE,urea,PV,urea -PVMIGRATE,urr,PV,urr -PVMIGRATE,vitb12,PV,vitb12 -PVMIGRATE,vitd,PV,vitd -PVMIGRATE,wbc,PV,wbc -PVMIGRATE,weight,PV,weight diff --git a/codes/code_conv_lists/pvmig_testunits_to_pv.csv b/codes/code_conv_lists/pvmig_testunits_to_pv.csv deleted file mode 100644 index da3dcae..0000000 --- a/codes/code_conv_lists/pvmig_testunits_to_pv.csv +++ /dev/null @@ -1,53 +0,0 @@ -PVMIGRATION,#G ( )/L,PV,ml/min/1.73m2 -PVMIGRATION,*10^9/cumm,PV,x10^9/L -PVMIGRATION,/mL,PV,ml/min/1.73m2 -PVMIGRATION,10**9/L,PV,x10^9/L -PVMIGRATION,10*9 cells/L,PV,x10^9/L -PVMIGRATION,10*9/L,PV,x10^9/L -PVMIGRATION,10^9/l,PV,x10^9/L -PVMIGRATION,IU/L,PV,IU/L -PVMIGRATION,IU/l,PV,IU/L -PVMIGRATION,Kg,PV,kg -PVMIGRATION,MCMOL/L,PV,micromol/L -PVMIGRATION,MMOL/L,PV,mmol/L -PVMIGRATION,None,PV,ml/min/1.73m2 -PVMIGRATION,U/L,PV,IU/L -PVMIGRATION,Ug/L,PV,microg/L -PVMIGRATION,Ug/L,PV,ng/mL -PVMIGRATION,bpm,PV,bpm -PVMIGRATION,cm,PV,cm -PVMIGRATION,g/L,PV,g/L -PVMIGRATION,g/l,PV,g/L -PVMIGRATION,g/mol,PV,mg/mmol -PVMIGRATION,gm/l,PV,g/L -PVMIGRATION,kg,PV,kg -PVMIGRATION,mL/24h/1.73m*2,PV,ml/min/1.73m2 -PVMIGRATION,mL/min,PV,ml/min/1.73m2 -PVMIGRATION,mL/min/1.73m*2,PV,ml/min/1.73m2 -PVMIGRATION,mL/min/1.73m2,PV,ml/min/1.73m2 -PVMIGRATION,mL/min/1.73m^2,PV,ml/min/1.73m2 -PVMIGRATION,mU/L,PV,mIU/L -PVMIGRATION,mg/L,PV,mg/L -PVMIGRATION,mg/mmol,PV,mg/mmol -PVMIGRATION,mg/mmol(creat),PV,mg/mmol -PVMIGRATION,micmol/l,PV,micromol/L -PVMIGRATION,micromol/l,PV,micromol/L -PVMIGRATION,ml/min/1.73m,PV,ml/min/1.73m2 -PVMIGRATION,ml/min/1.73m*2,PV,ml/min/1.73m2 -PVMIGRATION,ml/min/1.73m2,PV,ml/min/1.73m2 -PVMIGRATION,mm Hg,PV,mmHg -PVMIGRATION,mmHg,PV,mmHg -PVMIGRATION,mm[Hg],PV,mmHg -PVMIGRATION,mmo/L,PV,mmol/L -PVMIGRATION,mmol/L,PV,mmol/L -PVMIGRATION,mmol/l,PV,mmol/L -PVMIGRATION,mmol/mol,PV,mmol/mol -PVMIGRATION,mu/L,PV,mIU/L -PVMIGRATION,ng/L,PV,ng/L -PVMIGRATION,ng/mL,PV,ng/mL -PVMIGRATION,pmol/L,PV,pmol/L -PVMIGRATION,u/L,PV,IU/L -PVMIGRATION,ug/l,PV,microg/L -PVMIGRATION,umol/L,PV,micromol/L -PVMIGRATION,x10^9/L,PV,x10^9/L -PVMIGRATION,x10^9/l,PV,x10^9/L diff --git a/codes/code_conv_lists/pvraw_testcodes_to_pv.csv b/codes/code_conv_lists/pvraw_testcodes_to_pv.csv deleted file mode 100644 index c16e23e..0000000 --- a/codes/code_conv_lists/pvraw_testcodes_to_pv.csv +++ /dev/null @@ -1,3 +0,0 @@ -PV_RAW,mg,PV,magnesium -PV_RAW,faecalcalprotectin,PV,FaecalCalprotectin -PV_RAW,targetweight,PV,TargetWeight \ No newline at end of file diff --git a/codes/code_conv_lists/radar_facilities_to_rr1plus.csv b/codes/code_conv_lists/radar_facilities_to_rr1plus.csv deleted file mode 100644 index e4d832e..0000000 --- a/codes/code_conv_lists/radar_facilities_to_rr1plus.csv +++ /dev/null @@ -1,26 +0,0 @@ -RADAR,RCF22,RR1+,RQR13 -RADAR,RWY01,RR1+,RQR13 -RADAR,88RAZ,RR1+,RAZ -RADAR,RNXWC,RR1+,RNX02 -RADAR,RNU93,RR1+,RNX02 -RADAR,99RHM01,RR1+,RHM02 -RADAR,RWJ01,RR1+,RM574 -RADAR,RM327,RR1+,RM574 -RADAR,D1,RR1+,RJZ -RADAR,RM114,RR1+,RGT01 -RADAR,RH878,RR1+,RH8 -RADAR,RA901,RR1+,RH8 -RADAR,SGC05,RR1+,SGC04 -RADAR,NVH,RR1+,SGC04 -RADAR,RTD05,RR1+,RTD01 -RADAR,RJE55,RR1+,RFPFG -RADAR,RTG02,RR1+,RFPFG -RADAR,RR111,RR1+,RRK02 -RADAR,RLQ01,RR1+,RRK02 -RADAR,RLU01,RR1+,RRK02 -RADAR,RJ100,RR1+,RJ121 -RADAR,RSC02,RR1+,SSC02 -RADAR,RX1CC,RR1+,RCSLB -RADAR,RXP,RR1+,RCJAT -RADAR,RWP50,RR1+,RRK02 -RADAR,RWDDA,RR1+,RKZDA diff --git a/codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv b/codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv deleted file mode 100644 index 87e772e..0000000 --- a/codes/code_conv_lists/rawpvrrtstatus_to_pvrrtstatus.csv +++ /dev/null @@ -1,101 +0,0 @@ -PV_RAW_RRTSTATUS,AAPD,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,ACUTE ITU,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,ACUTE,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,ALD,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,APD,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,CAPD,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,CK,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,CKD/TX,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,CLINIC,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,HD (HOME),PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,HD (HOSP),PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,HOME APD,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,HOME CAPD,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,HOME HD NOCTURNAL,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,HOME HD,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,HOSPITAL HD,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,IN-CENTRE HD,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,LOST,PV_RRTSTATUS,XFER -PV_RAW_RRTSTATUS,LRD,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,MOVED OUT,PV_RRTSTATUS,XFER -PV_RAW_RRTSTATUS,PR,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,PRE,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,REC,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,T/P RENAL(C),PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,T/P RENAL(L),PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,TRANSPLANT,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,TX (KL),PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,TX (PAK),PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,TX (PAT),PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,TX (SPK),PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,0,PV_RRTSTATUS,GEN -PV_RAW_RRTSTATUS,1,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,2,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,3,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,4,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,5,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,9,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,10,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,11,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,12,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,13,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,14,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,15,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,16,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,17,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,19,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,20,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,21,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,22,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,23,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,24,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,25,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,26,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,27,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,28,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,29,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,41,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,42,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,43,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,44,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,45,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,49,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,50,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,51,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,52,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,53,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,54,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,55,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,56,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,57,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,59,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,60,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,61,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,62,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,63,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,64,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,65,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,66,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,68,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,69,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,74,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,75,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,77,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,81,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,82,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,83,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,111,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,114,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,115,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,117,PV_RRTSTATUS,TP -PV_RAW_RRTSTATUS,121,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,162,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,181,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,182,PV_RRTSTATUS,HD -PV_RAW_RRTSTATUS,183,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,201,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,202,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,203,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,241,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,242,PV_RRTSTATUS,PD -PV_RAW_RRTSTATUS,243,PV_RRTSTATUS,PD \ No newline at end of file diff --git a/codes/code_conv_lists/rr1plus_facilities_to_pv.csv b/codes/code_conv_lists/rr1plus_facilities_to_pv.csv deleted file mode 100644 index 8bfadc3..0000000 --- a/codes/code_conv_lists/rr1plus_facilities_to_pv.csv +++ /dev/null @@ -1,7 +0,0 @@ -RR1+,SSC02,PV,RSC02 -RR1+,RCSLB,PV,RX1CC -RR1+,RNJ00,PV,R1H00 -RR1+,RJ121,PV,RJ100 -RR1+,RQR13,PV,RQR00 -RR1+,SYC02,PV,SYC01 -RR1+,SGC04,PV,SGC05 \ No newline at end of file diff --git a/codes/code_conv_lists/rr1plus_facilities_to_radar.csv b/codes/code_conv_lists/rr1plus_facilities_to_radar.csv deleted file mode 100644 index 4801101..0000000 --- a/codes/code_conv_lists/rr1plus_facilities_to_radar.csv +++ /dev/null @@ -1,4 +0,0 @@ -RR1+,RJ121,RADAR,RJ100 -RR1+,SSC02,RADAR,RSC02 -RR1+,RCSLB,RADAR,RX1CC -RR1+,RBN63,RADAR,RQ617 diff --git a/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv b/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv deleted file mode 100644 index 30ca493..0000000 --- a/codes/code_conv_lists/rr1plus_facilities_to_statistician_code.csv +++ /dev/null @@ -1,82 +0,0 @@ -RR1+,2020,STATISTICIAN_CODE,Belfast -RR1+,7021,STATISTICIAN_CODE,Ulster -RR1+,24027,STATISTICIAN_CODE,Antrim -RR1+,33020,STATISTICIAN_CODE,Newry -RR1+,45021,STATISTICIAN_CODE,West NI -RR1+,RAE05,STATISTICIAN_CODE,Bradfd -RR1+,RAJ,STATISTICIAN_CODE,EssexMS -RR1+,RAL01,STATISTICIAN_CODE,L Rfree -RR1+,RAQ01,STATISTICIAN_CODE,Stevng -RR1+,RAZ,STATISTICIAN_CODE,Carsh -RR1+,RBD01,STATISTICIAN_CODE,Dorset -RR1+,RBL14,STATISTICIAN_CODE,Wirral -RR1+,RCB55,STATISTICIAN_CODE,York -RR1+,RCJAT,STATISTICIAN_CODE,Middlbr -RR1+,RCSLB,STATISTICIAN_CODE,Nottm -RR1+,RDEE4,STATISTICIAN_CODE,Colchr -RR1+,REE01,STATISTICIAN_CODE,Bristol -RR1+,REF12,STATISTICIAN_CODE,Truro -RR1+,RF201,STATISTICIAN_CODE,Hull -RR1+,RFBAK,STATISTICIAN_CODE,Leic -RR1+,RFPFG,STATISTICIAN_CODE,Derby -RR1+,RGQ02,STATISTICIAN_CODE,Ipswi -RR1+,RGT01,STATISTICIAN_CODE,Camb -RR1+,RGU01,STATISTICIAN_CODE,Brightn -RR1+,RH641,STATISTICIAN_CODE,Glouc -RR1+,RH8,STATISTICIAN_CODE,Exeter -RR1+,RHU02,STATISTICIAN_CODE,Ports -RR1+,RHW01,STATISTICIAN_CODE,Redng -RR1+,RJ121,STATISTICIAN_CODE,L Guys -RR1+,RQN02,STATISTICIAN_CODE,L West -RR1+,RJ701,STATISTICIAN_CODE,L St.G -RR1+,RJE01,STATISTICIAN_CODE,Stoke -RR1+,RJZ,STATISTICIAN_CODE,L Kings -RR1+,RK7CC,STATISTICIAN_CODE,Sheff -RR1+,RK950,STATISTICIAN_CODE,Plymth -RR1+,RKB01,STATISTICIAN_CODE,Covnt -RR1+,RKGA1,STATISTICIAN_CODE,Clwyd -RR1+,RKHA4,STATISTICIAN_CODE,Wrexm -RR1+,RL403,STATISTICIAN_CODE,Wolve -RR1+,RL7,STATISTICIAN_CODE,Bham -RR1+,RLGAY,STATISTICIAN_CODE,Carlis -RR1+,RLNGH,STATISTICIAN_CODE,Sund -RR1+,RLZ01,STATISTICIAN_CODE,Shrew -RR1+,RM102,STATISTICIAN_CODE,Norwch -RR1+,RM301,STATISTICIAN_CODE,Salford -RR1+,RM574,STATISTICIAN_CODE,M RI -RR1+,RMF01,STATISTICIAN_CODE,Prestn -RR1+,RNA03,STATISTICIAN_CODE,Dudley -RR1+,RNJ00,STATISTICIAN_CODE,L Barts -RR1+,RNX02,STATISTICIAN_CODE,Oxford -RR1+,RP5,STATISTICIAN_CODE,Donc -RR1+,RQR13,STATISTICIAN_CODE,Leeds -RR1+,RQ617,STATISTICIAN_CODE,Liv UH -RR1+,RQBAU,STATISTICIAN_CODE,Bangor -RR1+,RQHC7,STATISTICIAN_CODE,Swanse -RR1+,RRBBV,STATISTICIAN_CODE,Cardff -RR1+,RRK02,STATISTICIAN_CODE,Bham -RR1+,RTD01,STATISTICIAN_CODE,Newc -RR1+,RVVKC,STATISTICIAN_CODE,Kent -RR1+,RW402,STATISTICIAN_CODE,Liv UH -RR1+,SAC02,STATISTICIAN_CODE,Klmarnk -RR1+,SFC01,STATISTICIAN_CODE,Krkcldy -RR1+,SGC04,STATISTICIAN_CODE,Glasgw -RR1+,SHC01,STATISTICIAN_CODE,Inverns -RR1+,SLC01,STATISTICIAN_CODE,Airdrie -RR1+,SNC01,STATISTICIAN_CODE,Abrdn -RR1+,SSC02,STATISTICIAN_CODE,Edinb -RR1+,STC01,STATISTICIAN_CODE,Dundee -RR1+,SYC02,STATISTICIAN_CODE,D&Gall -RR1+,11023,STATISTICIAN_CODE,Blfst_P -RR1+,99RCSLB,STATISTICIAN_CODE,Nottm_P -RR1+,99RHM01,STATISTICIAN_CODE,Soton_P -RR1+,99RQR13,STATISTICIAN_CODE,Leeds_P -RR1+,RA723,STATISTICIAN_CODE,Brstl_P -RR1+,RBS25,STATISTICIAN_CODE,Livpl_P -RR1+,RJ122,STATISTICIAN_CODE,L Eve_P -RR1+,RP4,STATISTICIAN_CODE,L GOSH_P -RR1+,RQ3,STATISTICIAN_CODE,Bham_P -RR1+,RTD02,STATISTICIAN_CODE,Newc_P -RR1+,RW3RM,STATISTICIAN_CODE,Manch_P -RR1+,RWM51,STATISTICIAN_CODE,Cardf_P -RR1+,SGC02,STATISTICIAN_CODE,Glasg_P diff --git a/codes/code_conv_lists/simplified_to_rr1plus_facilities.csv b/codes/code_conv_lists/simplified_to_rr1plus_facilities.csv deleted file mode 100644 index eff9da9..0000000 --- a/codes/code_conv_lists/simplified_to_rr1plus_facilities.csv +++ /dev/null @@ -1,55 +0,0 @@ -SIMPLIFIED_UNIT,S001,RR1+,RGT01 -SIMPLIFIED_UNIT,S002,RR1+,RQN02 -SIMPLIFIED_UNIT,S003,RR1+,RNJ00 -SIMPLIFIED_UNIT,S004,RR1+,RAE05 -SIMPLIFIED_UNIT,S005,RR1+,RAJ -SIMPLIFIED_UNIT,S006,RR1+,RP5 -SIMPLIFIED_UNIT,S007,RR1+,RVVKC -SIMPLIFIED_UNIT,S008,RR1+,RTD01 -SIMPLIFIED_UNIT,S009,RR1+,SGC04 -SIMPLIFIED_UNIT,S010,RR1+,RH641 -SIMPLIFIED_UNIT,S011,RR1+,RJ121 -SIMPLIFIED_UNIT,S014,RR1+,RJZ -SIMPLIFIED_UNIT,S015,RR1+,RFBAK -SIMPLIFIED_UNIT,S016,RR1+,RM574 -SIMPLIFIED_UNIT,S017,RR1+,RM102 -SIMPLIFIED_UNIT,S018,RR1+,RK7CC -SIMPLIFIED_UNIT,S019,RR1+,RCSLB -SIMPLIFIED_UNIT,S020,RR1+,RAL01 -SIMPLIFIED_UNIT,S021,RR1+,RQ617 -SIMPLIFIED_UNIT,S022,RR1+,RLZ01 -SIMPLIFIED_UNIT,S023,RR1+,RGU01 -SIMPLIFIED_UNIT,S024,RR1+,RM301 -SIMPLIFIED_UNIT,S025,RR1+,RAJ -SIMPLIFIED_UNIT,S026,RR1+,REE01 -SIMPLIFIED_UNIT,S027,RR1+,RJ701 -SIMPLIFIED_UNIT,S029,RR1+,RAQ01 -SIMPLIFIED_UNIT,S030,RR1+,RLNGH -SIMPLIFIED_UNIT,S031,RR1+,RW402 -SIMPLIFIED_UNIT,S032,RR1+,RRBBV -SIMPLIFIED_UNIT,S033,RR1+,RAJ -SIMPLIFIED_UNIT,S035,RR1+,RMF01 -SIMPLIFIED_UNIT,S036,RR1+,RH8 -SIMPLIFIED_UNIT,S037,RR1+,RJE01 -SIMPLIFIED_UNIT,S038,RR1+,RK950 -SIMPLIFIED_UNIT,S039,RR1+,RFPFG -SIMPLIFIED_UNIT,S040,RR1+,RQHC7 -SIMPLIFIED_UNIT,S041,RR1+,RBL14 -SIMPLIFIED_UNIT,S042,RR1+,RAZ -SIMPLIFIED_UNIT,S043,RR1+,STC01 -SIMPLIFIED_UNIT,S044,RR1+,SHC01 -SIMPLIFIED_UNIT,S045,RR1+,RGT01 -SIMPLIFIED_UNIT,S046,RR1+,RL7 -SIMPLIFIED_UNIT,S047,RR1+,RHW01 -SIMPLIFIED_UNIT,S048,RR1+,SAC02 -SIMPLIFIED_UNIT,S049,RR1+,RH8 -SIMPLIFIED_UNIT,S050,RR1+,RHU02 -SIMPLIFIED_UNIT,S051,RR1+,SLC01 -SIMPLIFIED_UNIT,S052,RR1+,RL403 -SIMPLIFIED_UNIT,S053,RR1+,RM102 -SIMPLIFIED_UNIT,S054,RR1+,RCJAT -SIMPLIFIED_UNIT,S146,RR1+,RLGAY -SIMPLIFIED_UNIT,S207,RR1+,RNA03 -SIMPLIFIED_UNIT,S238,RR1+, -SIMPLIFIED_UNIT,S249,RR1+,SFC01 -SIMPLIFIED_UNIT,S252,RR1+,SSC02 diff --git a/codes/code_conv_lists/snomed_testcodes_to_pv.csv b/codes/code_conv_lists/snomed_testcodes_to_pv.csv deleted file mode 100644 index dea599d..0000000 --- a/codes/code_conv_lists/snomed_testcodes_to_pv.csv +++ /dev/null @@ -1 +0,0 @@ -SNOMED,75367002,PV,bp_header \ No newline at end of file diff --git a/codes/code_conv_lists/snomed_to_edta2.csv b/codes/code_conv_lists/snomed_to_edta2.csv deleted file mode 100644 index e43e619..0000000 --- a/codes/code_conv_lists/snomed_to_edta2.csv +++ /dev/null @@ -1,234 +0,0 @@ -SNOMED,52254009,EDTA2,1003 -SNOMED,445119005,EDTA2,1019 -SNOMED,48796009,EDTA2,1026 -SNOMED,197601003,EDTA2,1035 -SNOMED,722369003,EDTA2,1057 -SNOMED,236384008,EDTA2,1061 -SNOMED,236385009,EDTA2,1074 -SNOMED,722118005,EDTA2,1088 -SNOMED,44785005,EDTA2,1090 -SNOMED,236407003,EDTA2,1116 -SNOMED,445404003,EDTA2,1137 -SNOMED,282364005,EDTA2,1159 -SNOMED,236411009,EDTA2,1171 -SNOMED,722119002,EDTA2,1185 -SNOMED,722086002,EDTA2,1192 -SNOMED,722120008,EDTA2,1205 -SNOMED,722168002,EDTA2,1214 -SNOMED,75888001,EDTA2,1222 -SNOMED,722760002,EDTA2,1233 -SNOMED,236409000,EDTA2,1246 -SNOMED,197697005,EDTA2,1251 -SNOMED,236404005,EDTA2,1267 -SNOMED,445388002,EDTA2,1279 -SNOMED,444977005,EDTA2,1298 -SNOMED,1269761000000101,EDTA2,1312 -SNOMED,3704008,EDTA2,1331 -SNOMED,35546006,EDTA2,1349 -SNOMED,83866005,EDTA2,1354 -SNOMED, 36171008,EDTA2,1377 -SNOMED, 724599009,EDTA2,1383 -SNOMED,722191003,EDTA2,1396 -SNOMED,195353004,EDTA2,1401 -SNOMED,1144805008,EDTA2,1429 -SNOMED,82275008,EDTA2,1438 -SNOMED,155441006,EDTA2,1455 -SNOMED,50581000,EDTA2,1464 -SNOMED,68815009,EDTA2,1486 -SNOMED,191306005,EDTA2,1504 -SNOMED,236502006,EDTA2,1527 -SNOMED,239947001,EDTA2,1543 -SNOMED,128971000119101,EDTA2,1562 -SNOMED,30911005,EDTA2,1589 -SNOMED,197764002,EDTA2,1602 -SNOMED,707208009,EDTA2,1618 -SNOMED,204949001,EDTA2,1625 -SNOMED,737562008,EDTA2,1639 -SNOMED,710571007,EDTA2,1641 -SNOMED,253864004,EDTA2,1656 -SNOMED,373584008,EDTA2,1660 -SNOMED,373585009,EDTA2,1673 -SNOMED,253900005,EDTA2,1687 -SNOMED,5187006,EDTA2,1694 -SNOMED,445387007,EDTA2,1706 -SNOMED,61758007,EDTA2,1710 -SNOMED,253904001,EDTA2,1723 -SNOMED,18417009,EDTA2,1734 -SNOMED,90241004,EDTA2,1747 -SNOMED,86249007,EDTA2,1752 -SNOMED,722078002,EDTA2,1768 -SNOMED,722082000,EDTA2,1775 -SNOMED,722081007,EDTA2,1781 -SNOMED,722089009,EDTA2,1799 -SNOMED,722088001,EDTA2,1809 -SNOMED,197808006,EDTA2,1813 -SNOMED,236017004,EDTA2,1821 -SNOMED,95566004,EDTA2,1832 -SNOMED,444717006,EDTA2,1845 -SNOMED,37497004,EDTA2,1850 -SNOMED,444690001,EDTA2,1866 -SNOMED,267441009,EDTA2,1878 -SNOMED,428255004,EDTA2,1884 -SNOMED,83923004,EDTA2,1907 -SNOMED,45927004,EDTA2,1924 -SNOMED,418839003,EDTA2,1948 -SNOMED,37061001,EDTA2,1969 -SNOMED,717770008,EDTA2,1982 -SNOMED,439990003,EDTA2,2005 -SNOMED,59400006,EDTA2,2022 -SNOMED,704203009,EDTA2,2046 -SNOMED,704205002,EDTA2,2067 -SNOMED,704206001,EDTA2,2080 -SNOMED,704055002,EDTA2,2108 -SNOMED,53556002,EDTA2,2120 -SNOMED,4390004,EDTA2,2149 -SNOMED,704204003,EDTA2,2165 -SNOMED,236496000,EDTA2,2183 -SNOMED,7725007,EDTA2,2219 -SNOMED,197772000,EDTA2,2226 -SNOMED,44323002,EDTA2,2235 -SNOMED,77377001,EDTA2,2242 -SNOMED,716864001,EDTA2,2257 -SNOMED,38898003,EDTA2,2261 -SNOMED,713504001,EDTA2,2274 -SNOMED,236706006,EDTA2,2290 -SNOMED,40733004,EDTA2,2300 -SNOMED,96441000119101,EDTA2,2316 -SNOMED,771000119108,EDTA2,2337 -SNOMED,38481006,EDTA2,2359 -SNOMED,65443008,EDTA2,2371 -SNOMED,445108007,EDTA2,2392 -SNOMED,710565001,EDTA2,2407 -SNOMED,302233006,EDTA2,2424 -SNOMED,51677000,EDTA2,2430 -SNOMED,783730009,EDTA2,2453 -SNOMED,236488005,EDTA2,2469 -SNOMED,15842009,EDTA2,2476 -SNOMED,445236007,EDTA2,2482 -SNOMED,51292008,EDTA2,2495 -SNOMED,48713002,EDTA2,2509 -SNOMED,274945004,EDTA2,2513 -SNOMED,23132008,EDTA2,2521 -SNOMED,66451004,EDTA2,2532 -SNOMED,367528006,EDTA2,2550 -SNOMED,32278006,EDTA2,2578 -SNOMED,373604002,EDTA2,2597 -SNOMED,73305009,EDTA2,2606 -SNOMED,373421000,EDTA2,2610 -SNOMED,373422007,EDTA2,2623 -SNOMED,78129009,EDTA2,2634 -SNOMED, 111407006,EDTA2,2647 -SNOMED,444976001,EDTA2,2652 -SNOMED,722721004,EDTA2,2668 -SNOMED,373420004,EDTA2,2675 -SNOMED,736993008,EDTA2,2681 -SNOMED,13886001,EDTA2,2699 -SNOMED,765330003,EDTA2,2718 -SNOMED,253878003,EDTA2,2725 -SNOMED,253879006,EDTA2,2739 -SNOMED,28770003,EDTA2,2741 -SNOMED,770414008,EDTA2,2756 -SNOMED,236418003,EDTA2,2787 -SNOMED, 722223000,EDTA2,2794 -SNOMED,726017001,EDTA2,2804 -SNOMED,723373006,EDTA2,2815 -SNOMED,46785007,EDTA2,2827 -SNOMED,204958008,EDTA2,2836 -SNOMED,444830001,EDTA2,2843 -SNOMED,444558002,EDTA2,2858 -SNOMED,444749006,EDTA2,2862 -SNOMED,446989009,EDTA2,2870 -SNOMED,446991001,EDTA2,2889 -SNOMED,447335007,EDTA2,2891 -SNOMED,236466005,EDTA2,2901 -SNOMED,197744007,EDTA2,2917 -SNOMED,444645005,EDTA2,2929 -SNOMED,79385002,EDTA2,2938 -SNOMED,698953004,EDTA2,2940 -SNOMED,85020001,EDTA2,2955 -SNOMED,190681003,EDTA2,2964 -SNOMED,226309007,EDTA2,2972 -SNOMED,82236004,EDTA2,2986 -SNOMED,726080006,EDTA2,2993 -SNOMED,1776003,EDTA2,3000 -SNOMED,24790002,EDTA2,3016 -SNOMED,236461000,EDTA2,3028 -SNOMED,722468005,EDTA2,3037 -SNOMED,111395007,EDTA2,3044 -SNOMED,10406007,EDTA2,3059 -SNOMED,35759001,EDTA2,3063 -SNOMED,31742004,EDTA2,3071 -SNOMED,707742001,EDTA2,3085 -SNOMED,707756004,EDTA2,3092 -SNOMED,707747007,EDTA2,3102 -SNOMED,237770005,EDTA2,3118 -SNOMED,237743003,EDTA2,3125 -SNOMED,237604008,EDTA2,3139 -SNOMED,43941006,EDTA2,3141 -SNOMED,15689008,EDTA2,3156 -SNOMED,237885008,EDTA2,3160 -SNOMED,711152006,EDTA2,3173 -SNOMED,48655003,EDTA2,3187 -SNOMED,17901006,EDTA2,3194 -SNOMED,65520001,EDTA2,3207 -SNOMED,40951006,EDTA2,3211 -SNOMED,16652001,EDTA2,3224 -SNOMED,190919008,EDTA2,3248 -SNOMED,22199006,EDTA2,3253 -SNOMED,45582004,EDTA2,3269 -SNOMED,7199000,EDTA2,3276 -SNOMED,46659004,EDTA2,3282 -SNOMED,236443009,EDTA2,3295 -SNOMED,41729002,EDTA2,3305 -SNOMED,445431000,EDTA2,3314 -SNOMED,290006,EDTA2,3322 -SNOMED,63247009,EDTA2,3333 -SNOMED,24750000,EDTA2,3346 -SNOMED,5619004,EDTA2,3351 -SNOMED,240096000,EDTA2,3367 -SNOMED,236419006,EDTA2,3379 -SNOMED,14669001,EDTA2,3380 -SNOMED,1048451000000103,EDTA2,3398 -SNOMED,1048481000000109,EDTA2,3403 -SNOMED,1048491000000106,EDTA2,3419 -SNOMED,23697004,EDTA2,3426 -SNOMED,236428007,EDTA2,3435 -SNOMED,444794000,EDTA2,3442 -SNOMED,36689008,EDTA2,3457 -SNOMED,126880001,EDTA2,3461 -SNOMED,702391001,EDTA2,3474 -SNOMED,408642003,EDTA2,3488 -SNOMED,302849000,EDTA2,3490 -SNOMED,307604008,EDTA2,3501 -SNOMED,824131000000108,EDTA2,3517 -SNOMED,722149000,EDTA2,3529 -SNOMED,722467000,EDTA2,3538 -SNOMED,722098007,EDTA2,3540 -SNOMED,709044004,EDTA2,3555 -SNOMED,34436003,EDTA2,3572 -SNOMED,29738008,EDTA2,3572 -SNOMED,449820008,EDTA2,3604 -SNOMED,705065000,EDTA2,3615 -SNOMED,609572000,EDTA2,3627 -SNOMED,190829000,EDTA2,3636 -SNOMED,722150000,EDTA2,3643 -SNOMED,446449009,EDTA2,3658 -SNOMED,33763006,EDTA2,3662 -SNOMED,49120005,EDTA2,3670 -SNOMED,236015007,EDTA2,3689 -SNOMED,42399005,EDTA2,3691 -SNOMED,90688005,EDTA2,3708 -SNOMED,53298000,EDTA2,3712 -SNOMED,12491000132101,EDTA2,3720 -SNOMED,734990008,EDTA2,3731 -SNOMED,36171008,EDTA2,3749 -SNOMED, 713887002,EDTA2,3754 -SNOMED, 722139003,EDTA2,3765 -SNOMED,722147003,EDTA2,3777 -SNOMED,723074006,EDTA2,3783 -SNOMED,722077007,EDTA2,3796 -SNOMED, 722085003,EDTA2,3806 -SNOMED, 95570007,EDTA2,3810 -SNOMED,118600007,EDTA2,3823 -SNOMED,736992003,EDTA2,3834 -SNOMED,6956008,EDTA2,3847 diff --git a/codes/code_conv_lists/snomed_to_survey_types.csv b/codes/code_conv_lists/snomed_to_survey_types.csv deleted file mode 100644 index dafa9c7..0000000 --- a/codes/code_conv_lists/snomed_to_survey_types.csv +++ /dev/null @@ -1,5 +0,0 @@ -SNOMED,821531000000101,SURVEY,EQ5D -SNOMED,925401000000103,SURVEY,PAM -SNOMED,761865002,SURVEY,PROM -SNOMED,925431000000109,SURVEY,PAM13_SCORE -SNOMED,962851000000103,SURVEY,PAM13_LEVEL diff --git a/codes/code_conv_lists/survey_types_to_snomed.csv b/codes/code_conv_lists/survey_types_to_snomed.csv deleted file mode 100644 index 2e8e857..0000000 --- a/codes/code_conv_lists/survey_types_to_snomed.csv +++ /dev/null @@ -1,5 +0,0 @@ -SURVEY,EQ5D,SNOMED,821531000000101 -SURVEY,PAM,SNOMED,925401000000103 -SURVEY,PROM,SNOMED,761865002 -SURVEY,PAM13_SCORE,SNOMED,925431000000109 -SURVEY,PAM13_LEVEL,SNOMED,962851000000103 diff --git a/codes/code_conv_lists/survey_units_to_rr1plus.csv b/codes/code_conv_lists/survey_units_to_rr1plus.csv deleted file mode 100644 index bc93256..0000000 --- a/codes/code_conv_lists/survey_units_to_rr1plus.csv +++ /dev/null @@ -1,72 +0,0 @@ -"source_coding_standard","source_code","destination_coding_standard","destination_code" -"YOURHEALTH_UNITNAME","ALTRINCHAM - SHARED CARE","RR1+","RM403" -"YOURHEALTH_UNITNAME","ALTRINCHAM DIALYSIS UNIT","RR1+","RM403" -"YOURHEALTH_UNITNAME","ALTRINCHAM","RR1+","RM403" -"YOURHEALTH_UNITNAME","BATH","RR1+","RD1" -"YOURHEALTH_UNITNAME","BEDFORD","RR1+","9RFU" -"YOURHEALTH_UNITNAME","BELFAST CITY HOSPITAL","RR1+","2020" -"YOURHEALTH_UNITNAME","BIRMINGHAM HEARTLANDS HOSPITAL","RR1+","RL7" -"YOURHEALTH_UNITNAME","CANNOCK","RR1+","RRE14" -"YOURHEALTH_UNITNAME","CASTLE VALE","RR1+","9RJH01" -"YOURHEALTH_UNITNAME","CENTENARY WING","RR1+","9RCSLB" -"YOURHEALTH_UNITNAME","CITY HOSPITAL","RR1+","RCSLB" -"YOURHEALTH_UNITNAME","COSSHAM","RR1+","9RVJ21" -"YOURHEALTH_UNITNAME","COVENTRY","RR1+","RKB01" -"YOURHEALTH_UNITNAME","DERBY","RR1+","RFPFG" -"YOURHEALTH_UNITNAME","DERRIFORD HOSPITAL","RR1+","RK950" -"YOURHEALTH_UNITNAME","DEWSBURY","RR1+","RMW10" -"YOURHEALTH_UNITNAME","DURHAM DRYBURN","RR1+","RR9" -"YOURHEALTH_UNITNAME","EASINGWOLD","RR1+","RCB23" -"YOURHEALTH_UNITNAME","FREEMAN HOSPITAL","RR1+","RTD01" -"YOURHEALTH_UNITNAME","GUY'S AND ST THOMAS'S HOSPITAL","RR1+","RJ121" -"YOURHEALTH_UNITNAME","HAMMERSMITH HOSPITAL","RR1+","RQN02" -"YOURHEALTH_UNITNAME","HARLOW","RR1+","RQW" -"YOURHEALTH_UNITNAME","HARROGATE","RR1+","RCD35" -"YOURHEALTH_UNITNAME","HEARTLANDS HOSPITAL (SOLIHULL DISTRICT GENERAL)","RR1+","RL301" -"YOURHEALTH_UNITNAME","HEELEY","RR1+","9RK7CC" -"YOURHEALTH_UNITNAME","HUDDERSFIELD","RR1+","RGB04" -"YOURHEALTH_UNITNAME","ILKESTON","RR1+","RXM56" -"YOURHEALTH_UNITNAME","JAMES COOK UNIVERSITY HOSPITAL","RR1+","RCJAT" -"YOURHEALTH_UNITNAME","KING'S COLLEGE HOSPITAL","RR1+","RJZ" -"YOURHEALTH_UNITNAME","KING'S LONDON","RR1+","RJZ" -"YOURHEALTH_UNITNAME","KINGS MILL","RR1+","RFJBC" -"YOURHEALTH_UNITNAME","LEEDS GENERAL INFIRMARY","RR1+","RQS01" -"YOURHEALTH_UNITNAME","LICHFIELD - HEARTLANDS","RR1+","RNG10" -"YOURHEALTH_UNITNAME","LISTER HOSPITAL","RR1+","RAQ01" -"YOURHEALTH_UNITNAME","LUTON & DUNSTABLE","RR1+","RC971" -"YOURHEALTH_UNITNAME","MANCHESTER ROYAL INFIRMARY","RR1+","RM574" -"YOURHEALTH_UNITNAME","NEW CROSS GATE","RR1+","8RJ121" -"YOURHEALTH_UNITNAME","NEW CROSS HOSPITAL","RR1+","RL403" -"YOURHEALTH_UNITNAME","NORTHERN GENERAL HOSPITAL","RR1+","RK7CC" -"YOURHEALTH_UNITNAME","NORTHERN TRUST - ANTRIM AREA HOSPITAL","RR1+","24027" -"YOURHEALTH_UNITNAME","NOTTINGHAM CITY HOSPITAL","RR1+","RCSLB" -"YOURHEALTH_UNITNAME","PONTEFRACT","RR1+","RXF03" -"YOURHEALTH_UNITNAME","QUEEN ELIZABETH HOSPITAL - BIRMINGHAM","RR1+","RRK02" -"YOURHEALTH_UNITNAME","QUEEN ELIZABETH HOSPITAL BIRMINGHAM","RR1+","RRK02" -"YOURHEALTH_UNITNAME","ROTHERHAM","RR1+","RFRPA" -"YOURHEALTH_UNITNAME","ROYAL DERBY HOSPITAL","RR1+","RFPFG" -"YOURHEALTH_UNITNAME","ROYAL LIVERPOOL HOSPITAL","RR1+","RQ617" -"YOURHEALTH_UNITNAME","ROYAL LIVERPOOL UNIVERSITY HOSPITAL","RR1+","RQ617" -"YOURHEALTH_UNITNAME","ROYAL PRESTON HOSPITAL","RR1+","RMF01" -"YOURHEALTH_UNITNAME","ROYAL SUSSEX COUNTY HOSPITAL","RR1+","RGU01" -"YOURHEALTH_UNITNAME","SALFORD ROYAL HOSPITAL","RR1+","RM301" -"YOURHEALTH_UNITNAME","SEACROFT - R & S","RR1+","9RQR14" -"YOURHEALTH_UNITNAME","SOLIHULL DISTRICT GENERAL","RR1+","RL301" -"YOURHEALTH_UNITNAME","SOUTHMEAD HOSPITAL","RR1+","REE01" -"YOURHEALTH_UNITNAME","ST HELIER HOSPITAL","RR1+","RAZ" -"YOURHEALTH_UNITNAME","ST JAMES HOSPITAL","RR1+","RQR13" -"YOURHEALTH_UNITNAME","ST JAMES'S HOSPITAL","RR1+","RQR13" -"YOURHEALTH_UNITNAME","ST JAMES'S UNIVERSITY HOSPITAL","RR1+","RQR13" -"YOURHEALTH_UNITNAME","ST LUKE'S HOSPITAL","RR1+","RAE05" -"YOURHEALTH_UNITNAME","ST LUKES HOSPITAL","RR1+","RAE05" -"YOURHEALTH_UNITNAME","STOCKPORT","RR1+","9RWJ" -"YOURHEALTH_UNITNAME","SUNDERLAND ROYAL HOSPITAL","RR1+","RLNGH" -"YOURHEALTH_UNITNAME","TAMESIDE","RR1+","RMP01" -"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL COVENTRY AND WARWICKSHIRE","RR1+","RKB01" -"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL CROSSHOUSE","RR1+","SAC02" -"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL OF NORTH MIDLANDS","RR1+","RJE01" -"YOURHEALTH_UNITNAME","UNIVERSITY HOSPITAL OF NORTH STAFFORDSHIRE","RR1+","RJE01" -"YOURHEALTH_UNITNAME","WASHINGTON","RR1+","9RLNGH" -"YOURHEALTH_UNITNAME","WESTERN TRUST - ALTNAGELVIN HOSPITAL","RR1+","45020" -"YOURHEALTH_UNITNAME","WOLVERHAMPTON","RR1+","RL403" -"YOURHEALTH_UNITNAME","YORK HOSPITAL","RR1+","RCB55" \ No newline at end of file diff --git a/codes/code_conv_lists/ukrr_testcodes_to_loinc.csv b/codes/code_conv_lists/ukrr_testcodes_to_loinc.csv deleted file mode 100644 index 0fdfa33..0000000 --- a/codes/code_conv_lists/ukrr_testcodes_to_loinc.csv +++ /dev/null @@ -1,50 +0,0 @@ -UKRR,QBLA1,LOINC,14682-9 -UKRR,QBLA3,LOINC,14937-7 -UKRR,QBLA4,LOINC,1959-6 -UKRR,QBLA6,LOINC,2951-2 -UKRR,QBLA9,LOINC,2823-3 -UKRR,QBLAB,LOINC,69405-9 -UKRR,QBLAC,LOINC,14933-6 -UKRR,QBLAL,LOINC,33914-3 -UKRR,QBLB1,LOINC,14879-1 -UKRR,QBLB3,LOINC,1996-8 -UKRR,QBLB4,LOINC,29265-6 -UKRR,QBLB5,LOINC,6768-6 -UKRR,QBLB7,LOINC,1751-7 -UKRR,QBLB9,LOINC,14866-8 -UKRR,QBLC1,LOINC,34366-5 -UKRR,QBLC3,LOINC,32294-1 -UKRR,QBLD1,LOINC,14647-2 -UKRR,QBLD3,LOINC,14646-4 -UKRR,QBLD4,LOINC,39469-2 -UKRR,QBLD5,LOINC,2571-8 -UKRR,QBLD6,LOINC,1988-5 -UKRR,QBLD8,LOINC,4548-4 -UKRR,QBLDA,LOINC,59261-8 -UKRR,QBLE1,LOINC,718-7 -UKRR,QBLE3,LOINC,59467-1 -UKRR,QBLE4,LOINC,777-3 -UKRR,QBLE5,LOINC,6690-2 -UKRR,QBLEB,LOINC,718-7 -UKRR,QBLF1,LOINC,2276-4 -UKRR,QBLF3,LOINC,3034-6 -UKRR,QBLF5,LOINC,76069-4 -UKRR,QBLF7,LOINC,2132-9 -UKRR,QBLF9,LOINC,2284-8 -UKRR,QBLFB,LOINC,2283-0 -UKRR,QBLFD,LOINC,14593-8 -UKRR,QBLFF,LOINC,11253-2 -UKRR,QBLFH,LOINC,29247-4 -UKRR,QBLG9,LOINC,54456-9 -UKRR,QBLGG,LOINC,70961-8 -UKRR,QBLHA,LOINC,13952-7 -UKRR,QBLHC,LOINC,13952-7 -UKRR,QBLHE,LOINC,16128-1 -UKRR,QBLHK,LOINC,30247-1 -UKRR,QBLHM,LOINC,56888-1 -UKRR,QBLHN,LOINC,21594-7 -UKRR,QBLHR,LOINC,69949-6 -UKRR,QBLHX,LOINC,14683-7 -UKRR,QBLPC,LOINC,1742-6 -UKRR,QBLPD,LOINC,751-8 -UKRR,QBLPE,LOINC,732-8 diff --git a/codes/code_conv_lists/ukrr_testcodes_to_pv.csv b/codes/code_conv_lists/ukrr_testcodes_to_pv.csv deleted file mode 100644 index a49b14e..0000000 --- a/codes/code_conv_lists/ukrr_testcodes_to_pv.csv +++ /dev/null @@ -1,46 +0,0 @@ -UKRR,QBLA1,PV,creatinine -UKRR,QBLA3,PV,urea -UKRR,QBLA4,PV,hco3 -UKRR,QBLA6,PV,sodium -UKRR,QBLA9,PV,potassium -UKRR,QBLAB,PV,egfr -UKRR,QBLAC,PV,urate -UKRR,QBLAL,PV,egfr -UKRR,QBLB1,PV,phosphate -UKRR,QBLB3,PV,calcium -UKRR,QBLB4,PV,adjustedcalcium -UKRR,QBLB5,PV,alp -UKRR,QBLB7,PV,albumin -UKRR,QBLB9,PV,pth -UKRR,QBLC1,PV,pcr -UKRR,QBLC3,PV,acr -UKRR,QBLD1,PV,cholesterol -UKRR,QBLD3,PV,hdl -UKRR,QBLD4,PV,ldl -UKRR,QBLD5,PV,tg -UKRR,QBLD6,PV,crp -UKRR,QBLD8,PV,hba1c -UKRR,QBLE1,PV,hb -UKRR,QBLE4,PV,platelets -UKRR,QBLE5,PV,wbc -UKRR,QBLEB,PV,hb -UKRR,QBLF1,PV,ferritin -UKRR,QBLF3,PV,transferrin -UKRR,QBLF7,PV,vitb12 -UKRR,QBLF9,PV,folate -UKRR,QBLFB,PV,folate -UKRR,QBLFF,PV,tacrolimus -UKRR,QBLFH,PV,sirolimus -UKRR,QBLFK,PV,ciclosporin -UKRR,QBLG1,PV,weight -UKRR,QBLG3,PV,bpsys -UKRR,QBLG4,PV,bpdia -UKRR,QBLG9,PV,urr -UKRR,QBLGG,PV,ktv -UKRR,QBLGB,PV,height -UKRR,QBLHA,PV,hbv -UKRR,QBLHC,PV,hbv -UKRR,QBLHE,PV,hcv -UKRR,QBLHX,PV,ucreatinine -UKRR,QBLPC,PV,alt -UKRR,QBLPD,PV,neutrophils diff --git a/codes/code_conv_lists/ukrr_testcodes_to_snomed.csv b/codes/code_conv_lists/ukrr_testcodes_to_snomed.csv deleted file mode 100644 index 53e37cc..0000000 --- a/codes/code_conv_lists/ukrr_testcodes_to_snomed.csv +++ /dev/null @@ -1,52 +0,0 @@ -UKRR,QBLA1,SNOMED,1107001000000108 -UKRR,QBLA3,SNOMED,1110281000000107 -UKRR,QBLA4,SNOMED,1106011000000107 -UKRR,QBLA6,SNOMED,1107871000000107 -UKRR,QBLA9,SNOMED,1107761000000109 -UKRR,QBLAB,SNOMED,1107411000000104 -UKRR,QBLAC,SNOMED,1109851000000106 -UKRR,QBLAL,SNOMED,857971000000104 -UKRR,QBLAL,SNOMED,1020291000000106 -UKRR,QBLB1,SNOMED,1107711000000107 -UKRR,QBLB3,SNOMED,1106621000000109 -UKRR,QBLB4,SNOMED,1107251000000104 -UKRR,QBLB5,SNOMED,1106051000000106 -UKRR,QBLB7,SNOMED,1105861000000106 -UKRR,QBLB9,SNOMED,1109581000000102 -UKRR,QBLC3,SNOMED,1023491000000104 -UKRR,QBLD1,SNOMED,1106541000000101 -UKRR,QBLD3,SNOMED,1107681000000108 -UKRR,QBLD4,SNOMED,1108551000000102 -UKRR,QBLD5,SNOMED,1109831000000104 -UKRR,QBLD6,SNOMED,1106741000000105 -UKRR,QBLDA,SNOMED,1107481000000106 -UKRR,QBLE3,SNOMED,1022471000000107 -UKRR,QBLE4,SNOMED,1108041000000107 -UKRR,QBLE5,SNOMED,1110441000000100 -UKRR,QBLF1,SNOMED,1108611000000102 -UKRR,QBLF5,SNOMED,1111581000000104 -UKRR,QBLF9,SNOMED,1108651000000103 -UKRR,QBLFB,SNOMED,1108641000000101 -UKRR,QBLFD,SNOMED,12711000237100 -UKRR,QBLFF,SNOMED,1111311000000103 -UKRR,QBLFH,SNOMED,1107851000000103 -UKRR,QBLFK,SNOMED,1107021000000104 -UKRR,QBLFM,SNOMED,1109271000000101 -UKRR,QBLFM,SNOMED,1109281000000104 -UKRR,QBLG1,SNOMED,27113001 -UKRR,QBLG9,SNOMED,1110411000000101 -UKRR,QBLGG,SNOMED,1110501000000104 -UKRR,QBLGG,SNOMED,1110511000000102 -UKRR,QBLHA,SNOMED,1111161000000103 -UKRR,QBLHC,SNOMED,1111171000000105 -UKRR,QBLHE,SNOMED,1111131000000108 -UKRR,QBLHG,SNOMED,1111211000000108 -UKRR,QBLHK,SNOMED,1107381000000101 -UKRR,QBLHM,SNOMED,1111341000000102 -UKRR,QBLHN,SNOMED,1111351000000104 -UKRR,QBLHR,SNOMED,1111041000000100 -UKRR,QBLHS,SNOMED,996101000000106 -UKRR,QBLHX,SNOMED,1107011000000105 -UKRR,QBLPC,SNOMED,1106081000000100 -UKRR,QBLPD,SNOMED,1108071000000101 -UKRR,QBLPE,SNOMED,1107961000000106 \ No newline at end of file diff --git a/codes/code_exclusions/pkb_observations.csv b/codes/code_exclusions/pkb_observations.csv deleted file mode 100644 index 7efd06e..0000000 --- a/codes/code_exclusions/pkb_observations.csv +++ /dev/null @@ -1,14 +0,0 @@ -LOINC,732-8,PKB -LOINC,76069-4,PKB -LOINC,59467-1,PKB -LOINC,2283-0,PKB -LOINC,69949-6,PKB -LOINC,56888-1,PKB -LOINC,55972-4,PKB -LOINC,59148-7,PKB -LOINC,21594-7,PKB -LOINC,30247-1,PKB -LOINC,14593-8,PKB -LOINC,95209-3,PKB -LOINC,95542-7,PKB -LOINC,94500-6,PKB diff --git a/codes/code_exclusions/pv_observations.csv b/codes/code_exclusions/pv_observations.csv deleted file mode 100644 index 4f3f41b..0000000 --- a/codes/code_exclusions/pv_observations.csv +++ /dev/null @@ -1,3 +0,0 @@ -PV,covid19pcr,RADAR -PV,covid19antibody,RADAR -PV,covid19lflow,RADAR diff --git a/codes/code_lists/RR22.csv b/codes/code_lists/RR22.csv deleted file mode 100644 index badf8f4..0000000 --- a/codes/code_lists/RR22.csv +++ /dev/null @@ -1,7 +0,0 @@ -RR22,1,Oral -RR22,2,Topical -RR22,3,Inhalation -RR22,4,Injection -RR22,5,Intra peritoneal -RR22,6,Rectal -RR22,9,Other - please specify in comments diff --git a/codes/code_lists/RR23.csv b/codes/code_lists/RR23.csv deleted file mode 100644 index 849e859..0000000 --- a/codes/code_lists/RR23.csv +++ /dev/null @@ -1,11 +0,0 @@ -CF_RR23,l,Litres -CF_RR23,dl,Decilitres -CF_RR23,ml,Mililitres -CF_RR23,g,Grams -CF_RR23,mg,Miligrams -CF_RR23,μg,Micrograms -CF_RR23,ng,Nanograms -CF_RR23,tab,Tablets -CF_RR23,units,Units (i.e. for Epoetins) -CF_RR23,mmol,Minimols -CF_RR23,other,Other \ No newline at end of file diff --git a/codes/code_lists/RR50.csv b/codes/code_lists/RR50.csv deleted file mode 100644 index b9baf89..0000000 --- a/codes/code_lists/RR50.csv +++ /dev/null @@ -1,3 +0,0 @@ -RR50,TPLTassess,Suitability for renal transplant -RR50,RRTassess,Shared future RRT choice -RR50,PPDassess,Preferred place of dying \ No newline at end of file diff --git a/codes/code_lists/RR51.csv b/codes/code_lists/RR51.csv deleted file mode 100644 index be6a661..0000000 --- a/codes/code_lists/RR51.csv +++ /dev/null @@ -1,12 +0,0 @@ -RR51,1,Unsuitable -RR51,2,Workup commenced -RR51,3,Suitable -RR51,4,Referred for assessment -RR51,5,Assessment in progress -RR51,6,Opts for transplant -RR51,7,Opts for ICHD -RR51,8,Opts for HHD -RR51,9,Opts for PD -RR51,10,Opts for supportive care -RR51,11,Current home -RR51,12,Nursing home \ No newline at end of file diff --git a/codes/code_lists/cf_rr7_discharge.csv b/codes/code_lists/cf_rr7_discharge.csv deleted file mode 100644 index 6b9730b..0000000 --- a/codes/code_lists/cf_rr7_discharge.csv +++ /dev/null @@ -1,9 +0,0 @@ -CF_RR7_DISCHARGE,30,Kidney Transplant Failure -CF_RR7_DISCHARGE,38,Patient Transferred Out -CF_RR7_DISCHARGE,84,ARF - Recovered -CF_RR7_DISCHARGE,85,ARF - Stopped Dialysis (without recovery of function) -CF_RR7_DISCHARGE,86,ARF - Transferred Out -CF_RR7_DISCHARGE,90,Treatment Stopped (Renal Function Recovered) -CF_RR7_DISCHARGE,91,Treatment Stopped (Without Recovery of Function) -CF_RR7_DISCHARGE,92,Conservative Management - Treatment stopped without recovery -CF_RR7_DISCHARGE,95,Patient - Lost to follow-up diff --git a/codes/code_lists/cf_rr7_treatment.csv b/codes/code_lists/cf_rr7_treatment.csv deleted file mode 100644 index 8e51611..0000000 --- a/codes/code_lists/cf_rr7_treatment.csv +++ /dev/null @@ -1,51 +0,0 @@ -CF_RR7_TREATMENT,1,Haemodialysis -CF_RR7_TREATMENT,2,Haemofiltration -CF_RR7_TREATMENT,3,Haemodiafiltration -CF_RR7_TREATMENT,4,Haemodialysis > 4 days per week / daily -CF_RR7_TREATMENT,5,Ultrafiltration -CF_RR7_TREATMENT,9,Haemodialysis - Type Unknown -CF_RR7_TREATMENT,10,CAPD Connect -CF_RR7_TREATMENT,11,CAPD Disconnect -CF_RR7_TREATMENT,12,Cycling PD >= 6 Nights/Week Dry -CF_RR7_TREATMENT,13,Cycling PD < 6 Nights/Week Dry -CF_RR7_TREATMENT,14,Cycling PD >= 6 Nights/Week Wet (Day Dwell) -CF_RR7_TREATMENT,15,Cycling PD < 6 Nights/Week Wet (Day Dwell) -CF_RR7_TREATMENT,16,Assisted Cycling PD >= 6 nights/Week Dry -CF_RR7_TREATMENT,17,Assisted Cycling PD >= 6 nights/Week Wet (Day Dwell) -CF_RR7_TREATMENT,19,Peritoneal Dialysis - Type Unknown -CF_RR7_TREATMENT,20,Transplant; Cadaver Donor -CF_RR7_TREATMENT,21,Transplant; Live Related - Sibling -CF_RR7_TREATMENT,22,Transplant; Live Related - Parent or Child -CF_RR7_TREATMENT,23,Transplant; Live Related - Other -CF_RR7_TREATMENT,24,Transplant; Live Genetically Unrelated -CF_RR7_TREATMENT,25,Transplant; Cadaver + Transp Other Organ -CF_RR7_TREATMENT,26,Transplant; Live Donor + Transp Other Organ -CF_RR7_TREATMENT,27,Transplant; Live Donor Non-UK Transplant -CF_RR7_TREATMENT,28,Transplant; Non-Heart Beating Donor -CF_RR7_TREATMENT,29,Transplant; Type Unknown -CF_RR7_TREATMENT,31,Graft Acute Rejection Episode - Biopsy Proven -CF_RR7_TREATMENT,32,Graft Acute Rejection Episode - No Biopsy -CF_RR7_TREATMENT,74,Transplant; Live Related - Father -CF_RR7_TREATMENT,75,Transplant; Live Related - Mother -CF_RR7_TREATMENT,77,Transplant; Live Related - Child -CF_RR7_TREATMENT,78,Transplant; Live Donor -CF_RR7_TREATMENT,80,Acute Renal Failure Not Dialysed -CF_RR7_TREATMENT,81,Acute Kidney Injury - Haemodialysis -CF_RR7_TREATMENT,82,Acute Kidney Injury - Haemofiltration -CF_RR7_TREATMENT,83,Acute Kidney Injury - Peritoneal Dialysis -CF_RR7_TREATMENT,88,Acute Kidney Injury receiving RRT not by renal service -CF_RR7_TREATMENT,93,Conservative Management - Mutual Decision not to offer RRT -CF_RR7_TREATMENT,94,Conservative Management - Clinical Decision not to offer RRT -CF_RR7_TREATMENT,101,First Assessment by Renal Service -CF_RR7_TREATMENT,110,Plasmapharesis / Plasma Exchange -CF_RR7_TREATMENT,111,Assisted CAPD -CF_RR7_TREATMENT,120,Transplant Clinic Followup -CF_RR7_TREATMENT,121,Assisted APD -CF_RR7_TREATMENT,201,Hybrid CAPD with HD -CF_RR7_TREATMENT,202,Hybrid APD with HD -CF_RR7_TREATMENT,203,Hybrid APD with CAPD -CF_RR7_TREATMENT,900,CKD (Not on RRT) -CF_RR7_TREATMENT,901,Patient - ESKD with no RRT -CF_RR7_TREATMENT,902,Patient - CKD-advanced MDT clinic -CF_RR7_TREATMENT,903,Patient - CKD-clinic follow-up -CF_RR7_TREATMENT,904,Patient - CKD-remote monitoring diff --git a/codes/code_lists/dose_units.csv b/codes/code_lists/dose_units.csv deleted file mode 100644 index 58ec28c..0000000 --- a/codes/code_lists/dose_units.csv +++ /dev/null @@ -1,20 +0,0 @@ -RADAR,l,litre,dose_unit -RADAR,dl,decilitre,dose_unit -RADAR,ml,millilitre,dose_unit -RADAR,g,gram,dose_unit -RADAR,mg,milligram,dose_unit -RADAR,ng,nanogram,dose_unit -RADAR,tab,tablet,dose_unit -RADAR,iu,international unit,dose_unit -RADAR,mmol,millimole,dose_unit -RADAR,puff,puff,dose_unit -RADAR,unit,unit,dose_unit -RADAR,ampoule,ampoule,dose_unit -RADAR,drop,drop,dose_unit -RADAR,capsule,capsule,dose_unit -RADAR,patch,patch,dose_unit -RADAR,sachet,sachet,dose_unit -RADAR,µg,microgram,dose_unit -RADAR,tbsp,table_spoon,dose_unit -RADAR,units,units,dose_unit -RADAR,other,other,dose_unit diff --git a/codes/code_lists/edta2.csv b/codes/code_lists/edta2.csv deleted file mode 100644 index d820aea..0000000 --- a/codes/code_lists/edta2.csv +++ /dev/null @@ -1,284 +0,0 @@ -EDTA2,1003,Adult nephrotic syndrome - no histology -EDTA2,1019,Nephrotic syndrome of childhood - steroid sensitive - no histology -EDTA2,1026,Congenital nephrotic syndrome (CNS) - no histology -EDTA2,1035,Congenital nephrotic syndrome (CNS) - Finnish type - no histology -EDTA2,1042,Congenital nephrotic syndrome (CNS) - Finnish type - histologically proven -EDTA2,1057,Congenital nephrotic syndrome (CNS) - diffuse mesangial sclerosis -EDTA2,1061,Congenital nephrotic syndrome (CNS) - focal segmental glomerulosclerosis (FSGS) -EDTA2,1074,Denys-Drash syndrome -EDTA2,1088,Congenital nephrotic syndrome (CNS) - congenital infection -EDTA2,1090,Minimal change nephropathy - no histology -EDTA2,1100,Minimal change nephropathy - histologically proven -EDTA2,1116,IgA nephropathy - no histology -EDTA2,1128,IgA nephropathy - histologically proven -EDTA2,1137,Familial IgA nephropathy - no histology -EDTA2,1144,Familial IgA nephropathy - histologically proven -EDTA2,1159,IgA nephropathy secondary to liver cirrhosis - no histology -EDTA2,1163,IgA nephropathy secondary to liver cirrhosis - histologically proven -EDTA2,1171,IgM - associated nephropathy -EDTA2,1185,Membranous nephropathy - idiopathic -EDTA2,1192,Membranous nephropathy - malignancy associated -EDTA2,1205,Membranous nephropathy - drug induced -EDTA2,1214,Membranous nephropathy - infection associated -EDTA2,1222,Mesangiocapillary glomerulonephritis type 1 -EDTA2,1233,Mesangiocapillary glomerulonephritis type 2 (dense deposit disease) -EDTA2,1246,Mesangiocapillary glomerulonephritis type 3 -EDTA2,1251,Idiopathic rapidly progressive (crescentic) glomerulonephritis -EDTA2,1267,Primary focal segmental glomerulosclerosis (FSGS) -EDTA2,1279,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - no histology -EDTA2,1280,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - histologically proven -EDTA2,1298,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - no histology -EDTA2,1308,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - histologically proven -EDTA2,1312,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - no histology -EDTA2,1320,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - histologically proven -EDTA2,1331,Diffuse endocapillary glomerulonephritis -EDTA2,1349,Mesangial proliferative glomerulonephritis -EDTA2,1354,Focal and segmental proliferative glomerulonephritis -EDTA2,1365,Glomerulonephritis - secondary to other systemic disease -EDTA2,1377,Glomerulonephritis - histologically indeterminate -EDTA2,1383,Systemic vasculitis - ANCA negative - histologically proven -EDTA2,1396,Systemic vasculitis - ANCA positive - no histology -EDTA2,1401,Granulomatosis with polyangiitis - no histology -EDTA2,1417,Granulomatosis with polyangiitis - histologically proven -EDTA2,1429,Microscopic polyangiitis - histologically proven -EDTA2,1438,Churg-Strauss syndrome - no histology -EDTA2,1440,Churg-Strauss syndrome - histologically proven -EDTA2,1455,Polyarteritis nodosa -EDTA2,1464,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - no histology -EDTA2,1472,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - histologically proven -EDTA2,1486,Systemic lupus erythematosus / nephritis - no histology -EDTA2,1493,Systemic lupus erythematosus / nephritis - histologically proven -EDTA2,1504,Henoch-Schönlein purpura / nephritis - no histology -EDTA2,1515,Henoch-Schönlein purpura / nephritis - histologically proven -EDTA2,1527,Renal scleroderma / systemic sclerosis - no histology -EDTA2,1536,Renal scleroderma / systemic sclerosis - histologically proven -EDTA2,1543,Essential mixed cryoglobulinaemia - no histology -EDTA2,1558,Essential mixed cryoglobulinaemia - histologically proven -EDTA2,1562,Cryoglobulinaemia secondary to hepatitis C - no histology -EDTA2,1570,Cryoglobulinaemia secondary to hepatitis C - histologically proven -EDTA2,1589,Cryoglobulinaemia secondary to systemic disease - no histology -EDTA2,1591,Cryoglobulinaemia secondary to systemic disease - histologically proven -EDTA2,1602,Primary reflux nephropathy - sporadic -EDTA2,1618,Familial reflux nephropathy -EDTA2,1625,Congenital dysplasia / hypoplasia -EDTA2,1639,Multicystic dysplastic kidneys -EDTA2,1641,Dysplasia due to fetal ACE-inhibitor exposure -EDTA2,1656,Glomerulocystic disease -EDTA2,1660,Congenital pelvi-ureteric junction obstruction -EDTA2,1673,Congenital vesico-ureteric junction obstruction -EDTA2,1687,Posterior urethral valves -EDTA2,1694,Syndrome of agenesis of abdominal muscles - prune belly syndrome -EDTA2,1706,Congenital neurogenic bladder -EDTA2,1710,Bladder exstrophy -EDTA2,1723,Megacystis-megaureter -EDTA2,1734,Oligomeganephronia -EDTA2,1747,Renal papillary necrosis -EDTA2,1752,Acquired obstructive uropathy / nephropathy -EDTA2,1768,Acquired obstructive nephropathy due to neurogenic bladder -EDTA2,1775,Obstructive nephropathy due to prostatic hypertrophy -EDTA2,1781,Obstructive nephropathy due to prostate cancer -EDTA2,1799,Obstructive nephropathy due to bladder cancer -EDTA2,1809,Obstructive nephropathy due to other malignancies -EDTA2,1813,Idiopathic retroperitoneal fibrosis -EDTA2,1821,Retroperitoneal fibrosis secondary to malignancies -EDTA2,1832,Calculus nephropathy / urolithiasis -EDTA2,1845,Calcium oxalate urolithiasis -EDTA2,1850,Enteric hyperoxaluria -EDTA2,1866,Magnesium ammonium phosphate (struvite) urolithiasis -EDTA2,1878,Uric acid urolithiasis -EDTA2,1884,Tubulointerstitial nephritis - no histology -EDTA2,1897,Tubulointerstitial nephritis - histologically proven -EDTA2,1907,Familial interstitial nephropathy - no histology -EDTA2,1911,Familial interstitial nephropathy - histologically proven -EDTA2,1924,Tubulointerstitial nephritis associated with autoimmune disease - no histology -EDTA2,1930,Tubulointerstitial nephritis associated with autoimmune disease - histologically proven -EDTA2,1948,Tubulointerstitial nephritis with uveitis (TINU) - no histology -EDTA2,1953,Tubulointerstitial nephritis with uveitis (TINU) - histologically proven -EDTA2,1969,Renal sarcoidosis - no histology -EDTA2,1976,Renal sarcoidosis - histologically proven -EDTA2,1982,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - no histology -EDTA2,1995,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - histologically proven -EDTA2,2005,Drug-induced tubulointerstitial nephritis - no histology -EDTA2,2014,Drug-induced tubulointerstitial nephritis - histologically proven -EDTA2,2022,Nephropathy due to analgesic drugs - no histology -EDTA2,2033,Nephropathy due to analgesic drugs - histologically proven -EDTA2,2046,Nephropathy due to ciclosporin - no histology -EDTA2,2051,Nephropathy due to ciclosporin - histologically proven -EDTA2,2067,Nephropathy due to tacrolimus - no histology -EDTA2,2079,Nephropathy due to tacrolimus - histologically proven -EDTA2,2080,Nephropathy due to aminoglycosides - no histology -EDTA2,2098,Nephropathy due to aminoglycosides - histologically proven -EDTA2,2108,Nephropathy due to amphotericin - no histology -EDTA2,2112,Nephropathy due to amphotericin - histologically proven -EDTA2,2120,Nephropathy due to cisplatin - no histology -EDTA2,2131,Nephropathy due to cisplatin - histologically proven -EDTA2,2149,Nephropathy due to lithium - no histology -EDTA2,2154,Nephropathy due to lithium - histologically proven -EDTA2,2165,Lead induced nephropathy - no histology -EDTA2,2177,Lead induced nephropathy - histologically proven -EDTA2,2183,Acute urate nephropathy - no histology -EDTA2,2196,Acute urate nephropathy - histologically proven -EDTA2,2203,Chronic urate nephropathy - histologically proven -EDTA2,2219,Radiation nephritis -EDTA2,2226,Renal / perinephric abscess -EDTA2,2235,Renal tuberculosis -EDTA2,2242,Leptospirosis -EDTA2,2257,Hantavirus nephropathy -EDTA2,2261,Xanthogranulomatous pyelonephritis -EDTA2,2274,Nephropathy related to HIV - no histology -EDTA2,2288,Nephropathy related to HIV - histologically proven -EDTA2,2290,Schistosomiasis -EDTA2,2300,Other specific infection -EDTA2,2316,Diabetic nephropathy in type I diabetes - no histology -EDTA2,2328,Diabetic nephropathy in type I diabetes - histologically proven -EDTA2,2337,Diabetic nephropathy in type II diabetes - no histology -EDTA2,2344,Diabetic nephropathy in type II diabetes - histologically proven -EDTA2,2359,Chronic hypertensive nephropathy - no histology -EDTA2,2363,Chronic hypertensive nephropathy - histologically proven -EDTA2,2371,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - no histology -EDTA2,2385,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - histologically proven -EDTA2,2392,Ageing kidney - no histology -EDTA2,2407,Ischaemic nephropathy - no histology -EDTA2,2411,Ischaemic nephropathy / microvascular disease - histologically proven -EDTA2,2424,Renal artery stenosis -EDTA2,2430,Atheroembolic renal disease - no histology -EDTA2,2448,Atheroembolic renal disease - histologically proven -EDTA2,2453,Fibromuscular dysplasia of renal artery -EDTA2,2469,Renal arterial thrombosis / occlusion -EDTA2,2476,Renal vein thrombosis -EDTA2,2482,Cardiorenal syndrome -EDTA2,2495,Hepatorenal syndrome -EDTA2,2509,Renal amyloidosis -EDTA2,2513,AA amyloid secondary to chronic inflammation -EDTA2,2521,AL amyloid secondary to plasma cell dyscrasia -EDTA2,2532,Familial amyloid secondary to protein mutations - no histology -EDTA2,2545,Familial amyloid secondary to protein mutations - histologically proven -EDTA2,2550,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - no histology -EDTA2,2566,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - histologically proven -EDTA2,2578,Myeloma kidney - no histology -EDTA2,2584,Myeloma cast nephropathy - histologically proven -EDTA2,2597,Light chain deposition disease -EDTA2,2606,Immunotactoid / fibrillary nephropathy -EDTA2,2610,Haemolytic uraemic syndrome (HUS) - diarrhoea associated -EDTA2,2623,Atypical haemolytic uraemic syndrome (HUS) - diarrhoea negative -EDTA2,2634,Thrombotic thrombocytopenic purpura (TTP) -EDTA2,2647,Haemolytic uraemic syndrome (HUS) secondary to systemic disease -EDTA2,2652,Congenital haemolytic uraemic syndrome (HUS) -EDTA2,2668,Familial haemolytic uraemic syndrome (HUS) -EDTA2,2675,Familial thrombotic thrombocytopenic purpura (TTP) -EDTA2,2681,Nephropathy due to eclampsia -EDTA2,2699,Sickle cell nephropathy - no histology -EDTA2,2702,Sickle cell nephropathy - histologically proven -EDTA2,2718,Autosomal dominant (AD) polycystic kidney disease -EDTA2,2725,Autosomal dominant (AD) polycystic kidney disease type I -EDTA2,2739,Autosomal dominant (AD) polycystic kidney disease type II -EDTA2,2741,Autosomal recessive (AR) polycystic kidney disease -EDTA2,2756,Alport syndrome - no histology -EDTA2,2760,Alport syndrome - histologically proven -EDTA2,2773,Benign familial haematuria -EDTA2,2787,Thin basement membrane disease -EDTA2,2794,Cystic kidney disease -EDTA2,2804,Medullary cystic kidney disease type I -EDTA2,2815,Medullary cystic kidney disease type II -EDTA2,2827,Uromodulin-associated nephropathy (familial juvenile hyperuricaemic nephropathy) -EDTA2,2836,Nephronophthisis -EDTA2,2843,Nephronophthisis - type 1 (juvenile type) -EDTA2,2858,Nephronophthisis - type 2 (infantile type) -EDTA2,2862,Nephronophthisis - type 3 (adolescent type) -EDTA2,2870,Nephronophthisis - type 4 (juvenile type) -EDTA2,2889,Nephronophthisis - type 5 -EDTA2,2891,Nephronophthisis - type 6 -EDTA2,2901,Primary Fanconi syndrome -EDTA2,2917,Tubular disorder as part of inherited metabolic diseases -EDTA2,2929,Dent disease -EDTA2,2938,Lowe syndrome (oculocerebrorenal syndrome) -EDTA2,2940,Inherited aminoaciduria -EDTA2,2955,Cystinuria -EDTA2,2964,Cystinosis -EDTA2,2972,Inherited renal glycosuria -EDTA2,2986,Hypophosphataemic rickets X-linked (XL) -EDTA2,2993,Hypophosphataemic rickets autosomal recessive (AR) -EDTA2,3000,Primary renal tubular acidosis (RTA) -EDTA2,3016,Proximal renal tubular acidosis (RTA) - type II -EDTA2,3028,Distal renal tubular acidosis (RTA) - type I -EDTA2,3037,Distal renal tubular acidosis with sensorineural deafness - gene mutations -EDTA2,3044,Nephrogenic diabetes insipidus -EDTA2,3059,Lesch Nyhan syndrome - hypoxanthine guanine phosphoribosyl transferase deficiency -EDTA2,3063,Phosphoribosyl pyrophosphate synthetase (PRPPS) superactivity -EDTA2,3071,Alagille syndrome -EDTA2,3085,Bartter syndrome -EDTA2,3092,Gitelman syndrome -EDTA2,3102,Liddle syndrome -EDTA2,3118,Apparent mineralocorticoid excess -EDTA2,3125,Glucocorticoid suppressible hyperaldosteronism -EDTA2,3139,Inherited / genetic diabetes mellitus type II -EDTA2,3141,Pseudohypoaldosteronism type 1 -EDTA2,3156,Pseudohypoaldosteronism type 2 (Gordon syndrome) -EDTA2,3160,Familial hypocalciuric hypercalcaemia -EDTA2,3173,Familial hypercalciuric hypocalcaemia -EDTA2,3187,Familial hypomagnesaemia -EDTA2,3194,Primary hyperoxaluria -EDTA2,3207,Primary hyperoxaluria type I -EDTA2,3211,Primary hyperoxaluria type II -EDTA2,3224,Fabry disease - no histology -EDTA2,3230,Fabry disease - histologically proven -EDTA2,3248,Xanthinuria -EDTA2,3253,Nail-patella syndrome -EDTA2,3269,Rubinstein-Taybi syndrome -EDTA2,3276,Tuberous sclerosis -EDTA2,3282,Von Hippel-Lindau disease -EDTA2,3295,Medullary sponge kidneys -EDTA2,3305,Horse-shoe kidney -EDTA2,3314,Frasier syndrome -EDTA2,3322,Branchio-oto-renal syndrome -EDTA2,3333,Williams syndrome -EDTA2,3346,Townes-Brocks syndrome -EDTA2,3351,Lawrence-Moon-Biedl / Bardet-Biedl syndrome -EDTA2,3367,Mitochondrial cytopathy -EDTA2,3379,Familial nephropathy -EDTA2,3380,Acute kidney injury -EDTA2,3398,Acute kidney injury due to hypovolaemia -EDTA2,3403,Acute kidney injury due to circulatory failure -EDTA2,3419,Acute kidney injury due to sepsis -EDTA2,3426,Acute kidney injury due to rhabdomyolysis -EDTA2,3435,Acute kidney injury due to nephrotoxicity -EDTA2,3442,Acute cortical necrosis -EDTA2,3457,Acute pyelonephritis -EDTA2,3461,Kidney tumour -EDTA2,3474,Renal cell carcinoma - histologically proven -EDTA2,3488,Transitional cell carcinoma - histologically proven -EDTA2,3490,Wilms tumour - histologically proven -EDTA2,3501,Mesoblastic nephroma - histologically proven -EDTA2,3517,Single kidney identified in adulthood -EDTA2,3529,Chronic kidney disease (CKD) / chronic renal failure (CRF) caused by tumour nephrectomy -EDTA2,3538,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to traumatic loss of kidney -EDTA2,3540,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to donor nephrectomy -EDTA2,3555,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - no histology -EDTA2,3564,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - histologically proven -EDTA2,3572,Haematuria and proteinuria - no histology -EDTA2,3604,Nephrotic syndrome of childhood - steroid resistant - no histology -EDTA2,3615,Nephrotic syndrome of childhood - no trial of steroids - no histology -EDTA2,3627,Renal cysts and diabetes syndrome -EDTA2,3636,Chronic urate nephropathy - no histology -EDTA2,3643,Chronic renal failure due to systemic infection -EDTA2,3658,Renal coloboma syndrome -EDTA2,3662,Hypercalcaemic nephropathy -EDTA2,3670,Retroperitoneal fibrosis secondary to peri-aortitis -EDTA2,3689,Retroperitoneal fibrosis secondary to drugs -EDTA2,3691,Renal failure -EDTA2,3708,Chronic renal failure -EDTA2,3712,Isolated haematuria - no histology -EDTA2,3720,Isolated proteinuria - no histology -EDTA2,3731,Primary hyperoxaluria type III -EDTA2,3749,Glomerulonephritis - no histology -EDTA2,3754,Focal segmental glomerulosclerosis (FSGS) secondary to HIV -EDTA2,3765,Focal segmental glomerulosclerosis (FSGS) secondary to lithium -EDTA2,3777,Focal segmental glomerulosclerosis (FSGS) secondary to sickle cell -EDTA2,3783,Renal papillary necrosis caused by diabetes -EDTA2,3796,Renal papillary necrosis caused by analgesics -EDTA2,3806,Renal papillary necrosis caused by sickle cell -EDTA2,3810,Kidney stones due to ARPT deficiency -EDTA2,3823,Infiltration by lymphoma - histologically proven -EDTA2,3834,Nephropathy due to pre- eclampsia -EDTA2,3847,Systemic vasculitis - ANCA negative - no histology -EDTA2,3852,Systemic vasculitis - ANCA positive - histologically proven diff --git a/codes/code_lists/edta_cod.csv b/codes/code_lists/edta_cod.csv deleted file mode 100644 index 2ad9ab3..0000000 --- a/codes/code_lists/edta_cod.csv +++ /dev/null @@ -1,65 +0,0 @@ -EDTA_COD,0,cause of death uncertain/not determined -EDTA_COD,11,myocardial ischaemia and infraction -EDTA_COD,12,hyperkalaemia -EDTA_COD,13,haemorrhagic pericarditis -EDTA_COD,14,other causes of cardiac failure -EDTA_COD,15,cardiac arrest/sudden death; other cause or unknown -EDTA_COD,16,hypertensive cardiac failure -EDTA_COD,17,hypokalaemia -EDTA_COD,18,fluid overload/pulmonary oedema -EDTA_COD,19,elevated pvr/pulmonary hypertension -EDTA_COD,21,pulmonary embolus -EDTA_COD,22,"cerebro-vascular accident, other cause or unspecified" -EDTA_COD,23,gastro-intestinal haemorrhage (digestive) -EDTA_COD,24,haemorrhage from graft site -EDTA_COD,25,haemorrhage from vascular access or dialysis circuit -EDTA_COD,26,cerebral haemorrhage from ruptured vascular aneurysm -EDTA_COD,27,haemorrhage from surgery (except digestive haemorrhage) -EDTA_COD,28,"other haemorrhage, other site and/or other cause" -EDTA_COD,29,mesenteric infarction -EDTA_COD,31,pulmonary infection (bacterial) -EDTA_COD,32,pulmonary infection (viral) -EDTA_COD,33,pulmonary infection (fungal or protozoal; parasitic) -EDTA_COD,34,infections elsewhere (except viral hepatitis) -EDTA_COD,35,septicaemia -EDTA_COD,36,tuberculosis (lung) -EDTA_COD,37,tuberculosis (elsewhere) -EDTA_COD,38,generalized viral infection -EDTA_COD,39,peritonitis (all causes except for peritoneal dialysis) -EDTA_COD,41,liver disease due to hepatitis b virus -EDTA_COD,42,liver disease due to other viral hepatitis -EDTA_COD,43,liver disease due to drug toxicity -EDTA_COD,44,cirrhosis - not viral (alcoholic or other cause) -EDTA_COD,45,cystic liver disease -EDTA_COD,46,liver failure - cause unknown -EDTA_COD,51,patient refused further treatment for erf -EDTA_COD,52,suicide -EDTA_COD,53,erf treatment ceased for any other reason -EDTA_COD,54,erf treatment withdrawn for medical reasons -EDTA_COD,61,ureamia caused by graft failure -EDTA_COD,62,pancreatitis -EDTA_COD,63,bone marrow depression (aplosia) -EDTA_COD,64,cachexia -EDTA_COD,66,malignant disease in patient treated by immunosuppressive therapy -EDTA_COD,67,malignant disease: solid tumors except those of 66 -EDTA_COD,68,malignant disease: lymphoproliferative disorders (except 66) -EDTA_COD,69,dementia -EDTA_COD,70,"peritonitis (sclerosing, with peritoneal dialysis)" -EDTA_COD,71,perforation of peptic ulcer -EDTA_COD,72,perforation of colon -EDTA_COD,73,chronic obstructive pulmonary disease -EDTA_COD,79,multi-system failure -EDTA_COD,81,accident related to erf treatment -EDTA_COD,82,accident unrelated to erf treatment -EDTA_COD,99,other identified cause of death -EDTA_COD,100,"peritonitis (bacterial, with peritoneal dialysis)" -EDTA_COD,101,"peritonitis (fungal, with peritoneal dialysis)" -EDTA_COD,102,"peritonitis (due to other cause, with peritoneal dialysis)" -EDTA_COD,103,peripheral vascular disease -EDTA_COD,104,calciphylaxis -EDTA_COD,105,ischaemic bowel -EDTA_COD,106,ruptured aaa -EDTA_COD,107,advanced ckd not on dialysis(conservative management) -EDTA_COD,108,acute kidney injury -EDTA_COD,109,c diff colitis -EDTA_COD,110,line related sepsis diff --git a/codes/code_lists/edta_prd.csv b/codes/code_lists/edta_prd.csv deleted file mode 100644 index 5363173..0000000 --- a/codes/code_lists/edta_prd.csv +++ /dev/null @@ -1,339 +0,0 @@ -EDTA,0,"CHRONIC RENAL FAILURE, AETIOLOGY UNCERTAIN" -EDTA,10,"GLOMERULONEPHRITIS, HISTOLOGICALLY NOT EXAMINED" -EDTA,11,SEVERE NEPHROTIC SYNDROME WITH FOCAL SCLEROSIS (PAEDIATRIC) -EDTA,12,IGA NEPHROPATHY PROVEN BY IMMUNOFLUORESCENCE -EDTA,13,"DENSE DEPOSIT DISEASE, MEMBRANO-PROLIF. GN TYPE II" -EDTA,14,MEMBRANOUS NEPHROPATHY -EDTA,15,MEMBRANO-PROLIFERATIVE GN TYPE I -EDTA,16,RAPIDLY PROGRESSIVE GN WITHOUT SYSTEMIC DISEASE (CRESCENTIC -EDTA,17,FOCAL SEGMENTAL GLOMERULOSCEROSIS WITH NEPHROTIC SYNDROME IN ADULTS -EDTA,19,"GLOMERULONEPHRITIS, HISTOLOGICALLY EXAMINED" -EDTA,199,UNAVAILABLE -EDTA,20,PYELO/INTERSTITIAL NEPHRITIS - CAUSE NOT SPECIFIED -EDTA,21,PYELO/INTERSTITIAL NEPHRITIS - WITH NEUROGENIC BLADDER -EDTA,22,PYELO/INTERSTITIAL NEPHRITIS - CONGEN. OBST. UROPATHY +/- REFLUX -EDTA,23,PYELO/INTERSTITIAL NEPHRITIS - ACQUIRED OBST. UROPATHY -EDTA,24,PYELO/INTERSTITIAL NEPHRITIS - VESICO-URETERIC REFLUX NO OBSTRUCTION -EDTA,25,PYELO/INTERSTITIAL NEPHRITIS - DUE TO UROLITHIASIS -EDTA,29,PYELO/INTERSTITIAL NEPHRITIS DUE TO OTHER CAUSE (PLEASE SPECIFY) -EDTA,30,TUBULO INTERSTITIAL NEPHRITIS (NOT PYELONEPHRITIS) -EDTA,31,NEPHROPATHY DUE TO ANALGESIC DRUGS -EDTA,32,NEPHROPATHY DUE TO CIS-PLATINUM -EDTA,33,NEPHROPATHY DUE TO CYCLOSPORIN A -EDTA,34,LEAD INDUCED NEPHROPATHY (INTERSTITIAL) -EDTA,39,NEPHROPATHY CAUSED BY OTHER SPECIFIC DRUG -EDTA,40,CYSTIC KIDNEY DISEASE - TYPE UNSPECIFIED -EDTA,41,POLYCYSTIC KIDNEYS - ADULT TYPE (DOMINANT) -EDTA,42,POLYCYSTIC KIDNEYS - INFANTILE (RECESSIVE) -EDTA,43,MEDULLARY CYSTIC DISEASE - INCLUDING NEPHRONOPHTHISIS -EDTA,49,CYSTIC KIDNEY DISEASE - OTHER SPECIFIED TYPE -EDTA,50,HEREDITARY/FAMILIAL NEPHROPATHY - TYPE UNSPECIFIED -EDTA,51,HEREDITARY NEPHRITIS WITH NERVE DEAFNESS (ALPORT'S) -EDTA,52,CYSTINOSIS -EDTA,53,PRIMARY OXALOSIS -EDTA,54,FABRY'S DISEASE -EDTA,59,HEREDITARY NEPHROPATHY - OTHER -EDTA,60,CONGENITAL RENAL HYPOPLASIA - TYPE UNSPECIFIED -EDTA,61,OLIGOMEGANEPHRONIC HYPOPLASIA -EDTA,63,CONGENITAL RENAL DYSPLASIA +/- URINARY TRACT MALFORMATION -EDTA,66,SYNDROME OF AGENESIS OF ABDO. MUSCLES - PRUNE BELLY SYNDROME -EDTA,70,RENAL VASCULAR DISEASE - TYPE UNSPECIFIED -EDTA,71,RENAL VASCULAR DISEASE DUE TO MALIGNANT HYPERTENSION -EDTA,72,RENAL VASCULAR DISEASE DUE TO HYPERTENSION -EDTA,73,RENAL VASCULAR DISEASE DUE TO POLYARTERITIS -EDTA,74,WEGENER'S GRANULOMATOSIS -EDTA,75,ISCHAEMIC RENAL DISEASE/CHOLESTEROL EMBOLISM -EDTA,76,GLOMERULONEPHRITIS RELATED TO LIVER CIRRHOSIS -EDTA,78,CRYOGLOBULINAEMIC GLOMERULONEPHRITIS -EDTA,79,RENAL VASCULAR DISEASE - CLASSIFIED (PLEASE SPECIFY) -EDTA,80,DIABETES TYPE 1 (INSULIN DEPENDENT) -EDTA,81,DIABETES TYPE 2 (NON-INSULIN DEPENDENT) -EDTA,82,MYELOMATOSIS -EDTA,83,AMYLOID -EDTA,84,SYSTEMIC LUPUS ERYTHEMATOSUS -EDTA,85,HENOCH-SCHONLEIN PURPURA -EDTA,86,GOODPASTURES SYNDROME -EDTA,87,SCLERODERMA -EDTA,88,HAEMOLYTIC URAEMIC SYNDROME -EDTA,89,MULTI-SYSTEM DISEASE - TYPE UNSPECIFIED -EDTA,90,CORTICAL OR TUBULAR NECROSIS -EDTA,91,TUBERCULOSIS -EDTA,92,GOUT -EDTA,93,NEPHROCALCINOSIS / HYPERCALCAEMIC NEPHROPATHY -EDTA,94,BALKAN NEPHROPATHY -EDTA,95,KIDNEY TUMOUR -EDTA,96,TRAUMATIC OR SURGICAL LOSS OF KIDNEY -EDTA,99,OTHER IDENTIFIED RENAL DISORDERS - PLEASE SPECIFY -EDTA2,1003,ADULT NEPHROTIC SYNDROME - NO HISTOLOGY -EDTA2,1019,NEPHROTIC SYNDROME OF CHILDHOOD - STEROID SENSITIVE - NO HISTOLOGY -EDTA2,1026,CONGENITAL NEPHROTIC SYNDROME (CNS) - NO HISTOLOGY -EDTA2,1035,CONGENITAL NEPHROTIC SYNDROME (CNS) - FINNISH TYPE - NO HISTOLOGY -EDTA2,1042,CONGENITAL NEPHROTIC SYNDROME (CNS) - FINNISH TYPE - HISTOLOGICALLY PROVEN -EDTA2,1057,CONGENITAL NEPHROTIC SYNDROME (CNS) - DIFFUSE MESANGIAL SCLEROSIS -EDTA2,1061,CONGENITAL NEPHROTIC SYNDROME (CNS) - FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) -EDTA2,1074,DENYS-DRASH SYNDROME -EDTA2,1088,CONGENITAL NEPHROTIC SYNDROME (CNS) - CONGENITAL INFECTION -EDTA2,1090,MINIMAL CHANGE NEPHROPATHY - NO HISTOLOGY -EDTA2,1100,MINIMAL CHANGE NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,1116,IGA NEPHROPATHY - NO HISTOLOGY -EDTA2,1128,IGA NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,1137,FAMILIAL IGA NEPHROPATHY - NO HISTOLOGY -EDTA2,1144,FAMILIAL IGA NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,1159,IGA NEPHROPATHY SECONDARY TO LIVER CIRRHOSIS - NO HISTOLOGY -EDTA2,1163,IGA NEPHROPATHY SECONDARY TO LIVER CIRRHOSIS - HISTOLOGICALLY PROVEN -EDTA2,1171,IGM - ASSOCIATED NEPHROPATHY -EDTA2,1185,MEMBRANOUS NEPHROPATHY - IDIOPATHIC -EDTA2,1192,MEMBRANOUS NEPHROPATHY - MALIGNANCY ASSOCIATED -EDTA2,1205,MEMBRANOUS NEPHROPATHY - DRUG INDUCED -EDTA2,1214,MEMBRANOUS NEPHROPATHY - INFECTION ASSOCIATED -EDTA2,1222,MESANGIOCAPILLARY GLOMERULONEPHRITIS TYPE 1 -EDTA2,1233,MESANGIOCAPILLARY GLOMERULONEPHRITIS TYPE 2 (DENSE DEPOSIT DISEASE) -EDTA2,1246,MESANGIOCAPILLARY GLOMERULONEPHRITIS TYPE 3 -EDTA2,1251,IDIOPATHIC RAPIDLY PROGRESSIVE (CRESCENTIC) GLOMERULONEPHRITIS -EDTA2,1267,PRIMARY FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) -EDTA2,1279,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL RECESSIVE - NO HISTOLOGY -EDTA2,1280,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL RECESSIVE - HISTOLOGICALLY PROVEN -EDTA2,1298,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL DOMINANT - NO HISTOLOGY -EDTA2,1308,FAMILIAL FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) - AUTOSOMAL DOMINANT - HISTOLOGICALLY PROVEN -EDTA2,1312,FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) SECONDARY TO OBESITY - NO HISTOLOGY -EDTA2,1320,FOCAL SEGMENTAL GLOMERULOSCLEROSIS (FSGS) SECONDARY TO OBESITY - HISTOLOGICALLY PROVEN -EDTA2,1331,DIFFUSE ENDOCAPILLARY GLOMERULONEPHRITIS -EDTA2,1349,MESANGIAL PROLIFERATIVE GLOMERULONEPHRITIS -EDTA2,1354,FOCAL AND SEGMENTAL PROLIFERATIVE GLOMERULONEPHRITIS -EDTA2,1365,GLOMERULONEPHRITIS - SECONDARY TO OTHER SYSTEMIC DISEASE -EDTA2,1377,GLOMERULONEPHRITIS - HISTOLOGICALLY INDETERMINATE -EDTA2,1383,SYSTEMIC VASCULITIS - ANCA NEGATIVE - HISTOLOGICALLY PROVEN -EDTA2,1396,SYSTEMIC VASCULITIS - ANCA POSITIVE - NO HISTOLOGY -EDTA2,1401,GRANULOMATOSIS WITH POLYANGIITIS - NO HISTOLOGY -EDTA2,1417,GRANULOMATOSIS WITH POLYANGIITIS - HISTOLOGICALLY PROVEN -EDTA2,1429,MICROSCOPIC POLYANGIITIS - HISTOLOGICALLY PROVEN -EDTA2,1438,CHURG-STRAUSS SYNDROME - NO HISTOLOGY -EDTA2,1440,CHURG-STRAUSS SYNDROME - HISTOLOGICALLY PROVEN -EDTA2,1455,POLYARTERITIS NODOSA -EDTA2,1464,ANTI-GLOMERULAR BASEMENT MEMBRANE (GBM) DISEASE / GOODPASTURE'S SYNDROME - NO HISTOLOGY -EDTA2,1472,ANTI-GLOMERULAR BASEMENT MEMBRANE (GBM) DISEASE / GOODPASTURE'S SYNDROME - HISTOLOGICALLY PROVEN -EDTA2,1486,SYSTEMIC LUPUS ERYTHEMATOSUS / NEPHRITIS - NO HISTOLOGY -EDTA2,1493,SYSTEMIC LUPUS ERYTHEMATOSUS / NEPHRITIS - HISTOLOGICALLY PROVEN -EDTA2,1504,HENOCH-SCHONLEIN PURPURA / NEPHRITIS - NO HISTOLOGY -EDTA2,1515,HENOCH-SCHONLEIN PURPURA / NEPHRITIS - HISTOLOGICALLY PROVEN -EDTA2,1527,RENAL SCLERODERMA / SYSTEMIC SCLEROSIS - NO HISTOLOGY -EDTA2,1536,RENAL SCLERODERMA / SYSTEMIC SCLEROSIS - HISTOLOGICALLY PROVEN -EDTA2,1543,ESSENTIAL MIXED CRYOGLOBULINAEMIA - NO HISTOLOGY -EDTA2,1558,ESSENTIAL MIXED CRYOGLOBULINAEMIA - HISTOLOGICALLY PROVEN -EDTA2,1562,CRYOGLOBULINAEMIA SECONDARY TO HEPATITIS C - NO HISTOLOGY -EDTA2,1570,CRYOGLOBULINAEMIA SECONDARY TO HEPATITIS C - HISTOLOGICALLY PROVEN -EDTA2,1589,CRYOGLOBULINAEMIA SECONDARY TO SYSTEMIC DISEASE - NO HISTOLOGY -EDTA2,1591,CRYOGLOBULINAEMIA SECONDARY TO SYSTEMIC DISEASE - HISTOLOGICALLY PROVEN -EDTA2,1602,PRIMARY REFLUX NEPHROPATHY - SPORADIC -EDTA2,1618,FAMILIAL REFLUX NEPHROPATHY -EDTA2,1625,CONGENITAL DYSPLASIA / HYPOPLASIA -EDTA2,1639,MULTICYSTIC DYSPLASTIC KIDNEYS -EDTA2,1641,DYSPLASIA DUE TO FETAL ACE-INHIBITOR EXPOSURE -EDTA2,1656,GLOMERULOCYSTIC DISEASE -EDTA2,1660,CONGENITAL PELVI-URETERIC JUNCTION OBSTRUCTION -EDTA2,1673,CONGENITAL VESICO-URETERIC JUNCTION OBSTRUCTION -EDTA2,1687,POSTERIOR URETHRAL VALVES -EDTA2,1694,SYNDROME OF AGENESIS OF ABDOMINAL MUSCLES - PRUNE BELLY SYNDROME -EDTA2,1706,CONGENITAL NEUROGENIC BLADDER -EDTA2,1710,BLADDER EXSTROPHY -EDTA2,1723,MEGACYSTIS-MEGAURETER -EDTA2,1734,OLIGOMEGANEPHRONIA -EDTA2,1747,RENAL PAPILLARY NECROSIS - CAUSE UNKNOWN -EDTA2,1752,ACQUIRED OBSTRUCTIVE UROPATHY / NEPHROPATHY -EDTA2,1768,ACQUIRED OBSTRUCTIVE NEPHROPATHY DUE TO NEUROGENIC BLADDER -EDTA2,1775,OBSTRUCTIVE NEPHROPATHY DUE TO PROSTATIC HYPERTROPHY -EDTA2,1781,OBSTRUCTIVE NEPHROPATHY DUE TO PROSTATE CANCER -EDTA2,1799,OBSTRUCTIVE NEPHROPATHY DUE TO BLADDER CANCER -EDTA2,1809,OBSTRUCTIVE NEPHROPATHY DUE TO OTHER MALIGNANCIES -EDTA2,1813,IDIOPATHIC RETROPERITONEAL FIBROSIS -EDTA2,1821,RETROPERITONEAL FIBROSIS SECONDARY TO MALIGNANCIES -EDTA2,1832,CALCULUS NEPHROPATHY / UROLITHIASIS -EDTA2,1845,CALCIUM OXALATE UROLITHIASIS -EDTA2,1850,ENTERIC HYPEROXALURIA -EDTA2,1866,MAGNESIUM AMMONIUM PHOSPHATE (STRUVITE) UROLITHIASIS -EDTA2,1878,URIC ACID UROLITHIASIS -EDTA2,1884,TUBULOINTERSTITIAL NEPHRITIS - NO HISTOLOGY -EDTA2,1897,TUBULOINTERSTITIAL NEPHRITIS - HISTOLOGICALLY PROVEN -EDTA2,1907,FAMILIAL INTERSTITIAL NEPHROPATHY - NO HISTOLOGY -EDTA2,1911,FAMILIAL INTERSTITIAL NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,1924,TUBULOINTERSTITIAL NEPHRITIS ASSOCIATED WITH AUTOIMMUNE DISEASE - NO HISTOLOGY -EDTA2,1930,TUBULOINTERSTITIAL NEPHRITIS ASSOCIATED WITH AUTOIMMUNE DISEASE - HISTOLOGICALLY PROVEN -EDTA2,1948,TUBULOINTERSTITIAL NEPHRITIS WITH UVEITIS (TINU) - NO HISTOLOGY -EDTA2,1953,TUBULOINTERSTITIAL NEPHRITIS WITH UVEITIS (TINU) - HISTOLOGICALLY PROVEN -EDTA2,1969,RENAL SARCOIDOSIS - NO HISTOLOGY -EDTA2,1976,RENAL SARCOIDOSIS - HISTOLOGICALLY PROVEN -EDTA2,1982,ARISTOLOCHIC ACID NEPHROPATHY (BALKAN / CHINESE HERB / ENDEMIC NEPHROPATHY) - NO HISTOLOGY -EDTA2,1995,ARISTOLOCHIC ACID NEPHROPATHY (BALKAN / CHINESE HERB / ENDEMIC NEPHROPATHY) - HISTOLOGICALLY PROVEN -EDTA2,2005,DRUG-INDUCED TUBULOINTERSTITIAL NEPHRITIS - NO HISTOLOGY -EDTA2,2014,DRUG-INDUCED TUBULOINTERSTITIAL NEPHRITIS - HISTOLOGICALLY PROVEN -EDTA2,2022,NEPHROPATHY DUE TO ANALGESIC DRUGS - NO HISTOLOGY -EDTA2,2033,NEPHROPATHY DUE TO ANALGESIC DRUGS - HISTOLOGICALLY PROVEN -EDTA2,2046,NEPHROPATHY DUE TO CICLOSPORIN - NO HISTOLOGY -EDTA2,2051,NEPHROPATHY DUE TO CICLOSPORIN - HISTOLOGICALLY PROVEN -EDTA2,2067,NEPHROPATHY DUE TO TACROLIMUS - NO HISTOLOGY -EDTA2,2079,NEPHROPATHY DUE TO TACROLIMUS - HISTOLOGICALLY PROVEN -EDTA2,2080,NEPHROPATHY DUE TO AMINOGLYCOSIDES - NO HISTOLOGY -EDTA2,2098,NEPHROPATHY DUE TO AMINOGLYCOSIDES - HISTOLOGICALLY PROVEN -EDTA2,2108,NEPHROPATHY DUE TO AMPHOTERICIN - NO HISTOLOGY -EDTA2,2112,NEPHROPATHY DUE TO AMPHOTERICIN - HISTOLOGICALLY PROVEN -EDTA2,2120,NEPHROPATHY DUE TO CISPLATIN - NO HISTOLOGY -EDTA2,2131,NEPHROPATHY DUE TO CISPLATIN - HISTOLOGICALLY PROVEN -EDTA2,2149,NEPHROPATHY DUE TO LITHIUM - NO HISTOLOGY -EDTA2,2154,NEPHROPATHY DUE TO LITHIUM - HISTOLOGICALLY PROVEN -EDTA2,2165,LEAD INDUCED NEPHROPATHY - NO HISTOLOGY -EDTA2,2177,LEAD INDUCED NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2183,ACUTE URATE NEPHROPATHY - NO HISTOLOGY -EDTA2,2196,ACUTE URATE NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2203,CHRONIC URATE NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2219,RADIATION NEPHRITIS -EDTA2,2226,RENAL / PERINEPHRIC ABSCESS -EDTA2,2235,RENAL TUBERCULOSIS -EDTA2,2242,LEPTOSPIROSIS -EDTA2,2257,HANTAVIRUS NEPHROPATHY -EDTA2,2261,XANTHOGRANULOMATOUS PYELONEPHRITIS -EDTA2,2274,NEPHROPATHY RELATED TO HIV - NO HISTOLOGY -EDTA2,2288,NEPHROPATHY RELATED TO HIV - HISTOLOGICALLY PROVEN -EDTA2,2290,SCHISTOSOMIASIS -EDTA2,2300,OTHER SPECIFIC INFECTION -EDTA2,2316,DIABETIC NEPHROPATHY IN TYPE I DIABETES - NO HISTOLOGY -EDTA2,2328,DIABETIC NEPHROPATHY IN TYPE I DIABETES - HISTOLOGICALLY PROVEN -EDTA2,2337,DIABETIC NEPHROPATHY IN TYPE II DIABETES - NO HISTOLOGY -EDTA2,2344,DIABETIC NEPHROPATHY IN TYPE II DIABETES - HISTOLOGICALLY PROVEN -EDTA2,2359,CHRONIC HYPERTENSIVE NEPHROPATHY - NO HISTOLOGY -EDTA2,2363,CHRONIC HYPERTENSIVE NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2371,MALIGNANT HYPERTENSIVE NEPHROPATHY / ACCELERATED HYPERTENSIVE NEPHROPATHY - NO HISTOLOGY -EDTA2,2385,MALIGNANT HYPERTENSIVE NEPHROPATHY / ACCELERATED HYPERTENSIVE NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2392,AGEING KIDNEY - NO HISTOLOGY -EDTA2,2407,ISCHAEMIC NEPHROPATHY - NO HISTOLOGY -EDTA2,2411,ISCHAEMIC NEPHROPATHY / MICROVASCULAR DISEASE - HISTOLOGICALLY PROVEN -EDTA2,2424,RENAL ARTERY STENOSIS -EDTA2,2430,ATHEROEMBOLIC RENAL DISEASE - NO HISTOLOGY -EDTA2,2448,ATHEROEMBOLIC RENAL DISEASE - HISTOLOGICALLY PROVEN -EDTA2,2453,FIBROMUSCULAR DYSPLASIA OF RENAL ARTERY -EDTA2,2469,RENAL ARTERIAL THROMBOSIS / OCCLUSION -EDTA2,2476,RENAL VEIN THROMBOSIS -EDTA2,2482,CARDIORENAL SYNDROME -EDTA2,2495,HEPATORENAL SYNDROME -EDTA2,2509,RENAL AMYLOIDOSIS -EDTA2,2513,AA AMYLOID SECONDARY TO CHRONIC INFLAMMATION -EDTA2,2521,AL AMYLOID SECONDARY TO PLASMA CELL DYSCRASIA -EDTA2,2532,FAMILIAL AMYLOID SECONDARY TO PROTEIN MUTATIONS - NO HISTOLOGY -EDTA2,2545,FAMILIAL AMYLOID SECONDARY TO PROTEIN MUTATIONS - HISTOLOGICALLY PROVEN -EDTA2,2550,FAMILIAL AA AMYLOID SECONDARY TO FAMILIAL MEDITERRANEAN FEVER / TRAPS (HIBERNIAN FEVER) - NO HISTOLOGY -EDTA2,2566,FAMILIAL AA AMYLOID SECONDARY TO FAMILIAL MEDITERRANEAN FEVER / TRAPS (HIBERNIAN FEVER) - HISTOLOGICALLY PROVEN -EDTA2,2578,MYELOMA KIDNEY - NO HISTOLOGY -EDTA2,2584,MYELOMA CAST NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2597,LIGHT CHAIN DEPOSITION DISEASE -EDTA2,2606,IMMUNOTACTOID / FIBRILLARY NEPHROPATHY -EDTA2,2610,HAEMOLYTIC URAEMIC SYNDROME (HUS) - DIARRHOEA ASSOCIATED -EDTA2,2623,ATYPICAL HAEMOLYTIC URAEMIC SYNDROME (HUS) - DIARRHOEA NEGATIVE -EDTA2,2634,THROMBOTIC THROMBOCYTOPENIC PURPURA (TTP) -EDTA2,2647,HAEMOLYTIC URAEMIC SYNDROME (HUS) SECONDARY TO SYSTEMIC DISEASE -EDTA2,2652,CONGENITAL HAEMOLYTIC URAEMIC SYNDROME (HUS) -EDTA2,2668,FAMILIAL HAEMOLYTIC URAEMIC SYNDROME (HUS) -EDTA2,2675,FAMILIAL THROMBOTIC THROMBOCYTOPENIC PURPURA (TTP) -EDTA2,2681,NEPHROPATHY DUE TO PRE-ECLAMPSIA / ECLAMPSIA -EDTA2,2699,SICKLE CELL NEPHROPATHY - NO HISTOLOGY -EDTA2,2702,SICKLE CELL NEPHROPATHY - HISTOLOGICALLY PROVEN -EDTA2,2718,AUTOSOMAL DOMINANT (AD) POLYCYSTIC KIDNEY DISEASE -EDTA2,2725,AUTOSOMAL DOMINANT (AD) POLYCYSTIC KIDNEY DISEASE TYPE I -EDTA2,2739,AUTOSOMAL DOMINANT (AD) POLYCYSTIC KIDNEY DISEASE TYPE II -EDTA2,2741,AUTOSOMAL RECESSIVE (AR) POLYCYSTIC KIDNEY DISEASE -EDTA2,2756,ALPORT SYNDROME - NO HISTOLOGY -EDTA2,2760,ALPORT SYNDROME - HISTOLOGICALLY PROVEN -EDTA2,2773,BENIGN FAMILIAL HAEMATURIA -EDTA2,2787,THIN BASEMENT MEMBRANE DISEASE -EDTA2,2794,CYSTIC KIDNEY DISEASE -EDTA2,2804,MEDULLARY CYSTIC KIDNEY DISEASE TYPE I -EDTA2,2815,MEDULLARY CYSTIC KIDNEY DISEASE TYPE II -EDTA2,2827,UROMODULIN-ASSOCIATED NEPHROPATHY (FAMILIAL JUVENILE HYPERURICAEMIC NEPHROPATHY) -EDTA2,2836,NEPHRONOPHTHISIS -EDTA2,2843,NEPHRONOPHTHISIS - TYPE 1 (JUVENILE TYPE) -EDTA2,2858,NEPHRONOPHTHISIS - TYPE 2 (INFANTILE TYPE) -EDTA2,2862,NEPHRONOPHTHISIS - TYPE 3 (ADOLESCENT TYPE) -EDTA2,2870,NEPHRONOPHTHISIS - TYPE 4 (JUVENILE TYPE) -EDTA2,2889,NEPHRONOPHTHISIS - TYPE 5 -EDTA2,2891,NEPHRONOPHTHISIS - TYPE 6 -EDTA2,2901,PRIMARY FANCONI SYNDROME -EDTA2,2917,TUBULAR DISORDER AS PART OF INHERITED METABOLIC DISEASES -EDTA2,2929,DENT DISEASE -EDTA2,2938,LOWE SYNDROME (OCULOCEREBRORENAL SYNDROME) -EDTA2,2940,INHERITED AMINOACIDURIA -EDTA2,2955,CYSTINURIA -EDTA2,2964,CYSTINOSIS -EDTA2,2972,INHERITED RENAL GLYCOSURIA -EDTA2,2986,HYPOPHOSPHATAEMIC RICKETS X-LINKED (XL) -EDTA2,2993,HYPOPHOSPHATAEMIC RICKETS AUTOSOMAL RECESSIVE (AR) -EDTA2,3000,PRIMARY RENAL TUBULAR ACIDOSIS (RTA) -EDTA2,3016,PROXIMAL RENAL TUBULAR ACIDOSIS (RTA) - TYPE II -EDTA2,3028,DISTAL RENAL TUBULAR ACIDOSIS (RTA) - TYPE I -EDTA2,3037,DISTAL RENAL TUBULAR ACIDOSIS WITH SENSORINEURAL DEAFNESS - GENE MUTATIONS -EDTA2,3044,NEPHROGENIC DIABETES INSIPIDUS -EDTA2,3059,LESCH NYHAN SYNDROME - HYPOXANTHINE GUANINE PHOSPHORIBOSYL TRANSFERASE DEFICIENCY -EDTA2,3063,PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE (PRPPS) SUPERACTIVITY -EDTA2,3071,ALAGILLE SYNDROME -EDTA2,3085,BARTTER SYNDROME -EDTA2,3092,GITELMAN SYNDROME -EDTA2,3102,LIDDLE SYNDROME -EDTA2,3118,APPARENT MINERALOCORTICOID EXCESS -EDTA2,3125,GLUCOCORTICOID SUPPRESSIBLE HYPERALDOSTERONISM -EDTA2,3139,INHERITED / GENETIC DIABETES MELLITUS TYPE II -EDTA2,3141,PSEUDOHYPOALDOSTERONISM TYPE 1 -EDTA2,3156,PSEUDOHYPOALDOSTERONISM TYPE 2 (GORDON SYNDROME) -EDTA2,3160,FAMILIAL HYPOCALCIURIC HYPERCALCAEMIA -EDTA2,3173,FAMILIAL HYPERCALCIURIC HYPOCALCAEMIA -EDTA2,3187,FAMILIAL HYPOMAGNESAEMIA -EDTA2,3194,PRIMARY HYPEROXALURIA -EDTA2,3207,PRIMARY HYPEROXALURIA TYPE I -EDTA2,3211,PRIMARY HYPEROXALURIA TYPE II -EDTA2,3224,FABRY DISEASE - NO HISTOLOGY -EDTA2,3230,FABRY DISEASE - HISTOLOGICALLY PROVEN -EDTA2,3248,XANTHINURIA -EDTA2,3253,NAIL-PATELLA SYNDROME -EDTA2,3269,RUBINSTEIN-TAYBI SYNDROME -EDTA2,3276,TUBEROUS SCLEROSIS -EDTA2,3282,VON HIPPEL-LINDAU DISEASE -EDTA2,3295,MEDULLARY SPONGE KIDNEYS -EDTA2,3305,HORSE-SHOE KIDNEY -EDTA2,3314,FRASIER SYNDROME -EDTA2,3322,BRANCHIO-OTO-RENAL SYNDROME -EDTA2,3333,WILLIAMS SYNDROME -EDTA2,3346,TOWNES-BROCKS SYNDROME -EDTA2,3351,LAWRENCE-MOON-BIEDL / BARDET-BIEDL SYNDROME -EDTA2,3367,MITOCHONDRIAL CYTOPATHY -EDTA2,3379,FAMILIAL NEPHROPATHY -EDTA2,3380,ACUTE KIDNEY INJURY -EDTA2,3398,ACUTE KIDNEY INJURY DUE TO HYPOVOLAEMIA -EDTA2,3403,ACUTE KIDNEY INJURY DUE TO CIRCULATORY FAILURE -EDTA2,3419,ACUTE KIDNEY INJURY DUE TO SEPSIS -EDTA2,3426,ACUTE KIDNEY INJURY DUE TO RHABDOMYOLYSIS -EDTA2,3435,ACUTE KIDNEY INJURY DUE TO NEPHROTOXICITY -EDTA2,3442,ACUTE CORTICAL NECROSIS -EDTA2,3457,ACUTE PYELONEPHRITIS -EDTA2,3461,KIDNEY TUMOUR -EDTA2,3474,RENAL CELL CARCINOMA - HISTOLOGICALLY PROVEN -EDTA2,3488,TRANSITIONAL CELL CARCINOMA - HISTOLOGICALLY PROVEN -EDTA2,3490,WILMS TUMOUR - HISTOLOGICALLY PROVEN -EDTA2,3501,MESOBLASTIC NEPHROMA - HISTOLOGICALLY PROVEN -EDTA2,3517,SINGLE KIDNEY IDENTIFIED IN ADULTHOOD -EDTA2,3529,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) CAUSED BY TUMOUR NEPHRECTOMY -EDTA2,3538,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) DUE TO TRAUMATIC LOSS OF KIDNEY -EDTA2,3540,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) DUE TO DONOR NEPHRECTOMY -EDTA2,3555,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) - AETIOLOGY UNCERTAIN / UNKNOWN - NO HISTOLOGY -EDTA2,3564,CHRONIC KIDNEY DISEASE (CKD) / CHRONIC RENAL FAILURE (CRF) - AETIOLOGY UNCERTAIN / UNKNOWN - HISTOLOGICALLY PROVEN -EDTA2,3572,HAEMATURIA AND PROTEINURIA - NO HISTOLOGY -EDTA2,3604,NEPHROTIC SYNDROME OF CHILDHOOD - STEROID RESISTANT - NO HISTOLOGY -EDTA2,3615,NEPHROTIC SYNDROME OF CHILDHOOD - NO TRIAL OF STEROIDS - NO HISTOLOGY -EDTA2,3627,RENAL CYSTS AND DIABETES SYNDROME -EDTA2,3636,CHRONIC URATE NEPHROPATHY - NO HISTOLOGY -EDTA2,3643,CHRONIC RENAL FAILURE DUE TO SYSTEMIC INFECTION -EDTA2,3658,RENAL COLOBOMA SYNDROME -EDTA2,3662,HYPERCALCAEMIC NEPHROPATHY -EDTA2,3670,RETROPERITONEAL FIBROSIS SECONDARY TO PERI-AORTITIS -EDTA2,3689,RETROPERITONEAL FIBROSIS SECONDARY TO DRUGS -EDTA2,3691,RENAL FAILURE -EDTA2,3708,CHRONIC RENAL FAILURE -EDTA2,3712,ISOLATED HAEMATURIA - NO HISTOLOGY -EDTA2,3720,ISOLATED PROTEINURIA - NO HISTOLOGY -EDTA2,3731,PRIMARY HYPEROXALURIA TYPE III -EDTA2,3749,GLOMERULONEPHRITIS - NO HISTOLOGY diff --git a/codes/code_lists/loinc_observations.csv b/codes/code_lists/loinc_observations.csv deleted file mode 100644 index 57933d3..0000000 --- a/codes/code_lists/loinc_observations.csv +++ /dev/null @@ -1,86 +0,0 @@ -LOINC,32294-1,Albumin:creatinine ratio,result,mg/mmol -LOINC,19072-8,Adjusted Calcium,result,mmol/L -LOINC,1751-7,Albumin,result,g/L -LOINC,6768-6,AlkP,result,U/L -LOINC,1742-6,ALT,result,U/L -LOINC,1798-8,Amylase,result,U/L -LOINC,1920-8,AST,result,U/L -LOINC,14631-6,Bilirubin,result,umol/L -LOINC,1996-8,Calcium,result,mmol/L -LOINC,14647-2,Cholesterol,result,mmol/L -LOINC,14682-9,Creatinine,result,umol/L -LOINC,1988-5,C-reactive Protein,result,mg/L -LOINC,69405-9,eGFR,result,mL/min/1.73m2 -LOINC,77147-7,eGFR (MDRD),result,mL/min/1.73m2 -LOINC,2276-4,Ferritin,result,ng/mL or ug/L -LOINC,14928-6,Free T3,result,pmol/L -LOINC,14920-3,Free T4,result,pmol/L -LOINC,2324-2,GGT,result,U/L -LOINC,14749-6,glucose,result,mmol/L -LOINC,718-7,hb,result,g/L -LOINC,59261-8,hba1c,result,mmol/mol -LOINC,13952-7,hbv,result, -LOINC,1959-6,hco3,result,mmol/L -LOINC,4544-3,hct,result,% -LOINC,16128-1,Hepatitis C Antibody,result, -LOINC,14646-4,HDL,result,mmol/L -LOINC,6301-6,INR,result, -LOINC,14798-3,Iron,result,umol/L -LOINC,2502-3,Iron Saturation,result,% -LOINC,70961-8,Kt/V,result, -LOINC,2532-0,LDH,result,U/L -LOINC,39469-2,LDL,result,mmol/L -LOINC,44915-7,LDL:HDL Ratio,result, -LOINC,3040-3,Lipase,result,U/L -LOINC,14334-7,Lithium Level,result,mmol/L -LOINC,2601-3,Magnesium,result,mmol/L -LOINC,751-8,Neutrophils,result,billion/L or 10^9/L -LOINC,34366-5,Protein Creatinine Ratio,result,mg/mmol -LOINC,14879-1,Phosphate,result,mmol/L -LOINC,777-3,Platelets,result,10^9/L -LOINC,2823-3,Potassium,result,mmol/L -LOINC,2857-1,Prostate Specific Antigen,result,ng/mL -LOINC,14866-8,Parathyroid Hormone,result,pmol/L -LOINC,42810-2,Reticulocyte Haemoglobin,result,pg -LOINC,2951-2,Sodium,result,mmol/L -LOINC,3024-7,Total Thyroxine,result,ng/L -LOINC,11253-2,Tacrolimus,result,ng/mL -LOINC,2986-8,Testosterone,result,ng/dL -LOINC,2571-8,Triglycerides,result,mg/dL -LOINC,91141-2,TPMT,result,mU/L -LOINC,3034-6,Transferrin,result,mg/dL -LOINC,6598-7,Troponin-T,result,ng/mL -LOINC,3016-3,Thyroid stimulating hormone,result,mU/L -LOINC,6942-7,Urine Albumin,result,mg/L -LOINC,14683-7,Urine Creatinine,result,mmol/L -LOINC,2888-6,Urine Protein,result,mmol/L -LOINC,14933-6,Urate,result,mmol/L -LOINC,14937-7,Urea,result,mmol/L -LOINC,54456-9,URR,result, -LOINC,2132-9,Vitamin B12,result,ng/L or pg/mL -LOINC,46269-7,Vitamin D,result,nmol/L -LOINC,6690-2,White Blood Cell Count,result,billion/L or 10^9/L -LOINC,29247-4,Sirolimus,result,ng/mL -LOINC,51620-3,Creatinine (Post-Dialysis),result,mmol/L -LOINC,39776-0,Urea (Post-Dialysis),result,mmol/L -LOINC,29349-8,Potassium (Post-Dialysis),result,mmol/L -LOINC,74688-3,Sodium (Post-Dialysis),result,mmol/L -LOINC,48631-6,hco3 (Post-Dialysis),result,mmol/L -LOINC,2284-8,Serum Folate,result,ng/mL -LOINC,34381-4,TGN,result,ng/mL -LOINC,90294-0,MMP,result,U/mL -LOINC,4548-4,hba1c,result,% -LOINC,38445-3,Faecal Calprotectin,result,ug/g -LOINC,95209-3,Covid-19 Lateral Flow Test,result, -LOINC,95542-7,Covid-19 Antibody Test,result, -LOINC,94500-6,Covid-19 PCR Test,result, -LOINC,732-8,ALC,result,10^3/uL -LOINC,76069-4,Hypochromic Red Cells,result,% -LOINC,59467-1,MCH,result,mmol/L -LOINC,2283-0,Red Cell Folate,result,ng/mL -LOINC,29265-6,Corrected Calcium,result,mmol/L -LOINC,69949-6,EBV Status,result, -LOINC,56888-1,HIV Antigen,result, -LOINC,55972-4,Phosphate (Post),result,mmol/L -LOINC,59148-7,Calcium (Post),result,mmol/L -LOINC,3520-4,Ciclosporin,result,ng/mL diff --git a/codes/code_lists/nhs_data_dictionary_employment_status.csv b/codes/code_lists/nhs_data_dictionary_employment_status.csv deleted file mode 100644 index 13dd608..0000000 --- a/codes/code_lists/nhs_data_dictionary_employment_status.csv +++ /dev/null @@ -1,9 +0,0 @@ -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,01,Employed -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,02,Unemployed and actively seeking work -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,03,Undertaking full (at least 16 hours per week) or part-time (less than 16 hours per week) education or training as a student and not working or actively seeking work -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,04,Long-term sick or disabled, those receiving government sickness and disability benefits -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,05,Looking after the family or home as a homemaker and not working or actively seeking work -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,06,Not receiving government sickness and disability benefits and not working or actively seeking work -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,07,Unpaid voluntary work and not working or actively seeking work -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,08,Retired -NHS_DATA_DICTIONARY_EMPLOYMENT_STATUS,ZZ,Not Stated (PERSON asked but declined to provide a response) diff --git a/codes/code_lists/nhs_data_dictionary_ethnicity.csv b/codes/code_lists/nhs_data_dictionary_ethnicity.csv deleted file mode 100644 index aa62e0f..0000000 --- a/codes/code_lists/nhs_data_dictionary_ethnicity.csv +++ /dev/null @@ -1,17 +0,0 @@ -NHS_DATA_DICTIONARY,A,British, -NHS_DATA_DICTIONARY,B,Irish, -NHS_DATA_DICTIONARY,C,Any other White Background, -NHS_DATA_DICTIONARY,D,White and Black Caribbean, -NHS_DATA_DICTIONARY,E,White and Black African, -NHS_DATA_DICTIONARY,F,White and Asian, -NHS_DATA_DICTIONARY,G,Any other mixed background, -NHS_DATA_DICTIONARY,H,Indian, -NHS_DATA_DICTIONARY,J,Pakistani, -NHS_DATA_DICTIONARY,K,Bangladeshi, -NHS_DATA_DICTIONARY,L,Any other Asian background, -NHS_DATA_DICTIONARY,M,Caribbean, -NHS_DATA_DICTIONARY,N,African, -NHS_DATA_DICTIONARY,P,Any other black background, -NHS_DATA_DICTIONARY,R,Chinese, -NHS_DATA_DICTIONARY,S,Any other ethnic group, -NHS_DATA_DICTIONARY,Z,Not stated, diff --git a/codes/code_lists/nhs_data_dictionary_language_code.csv b/codes/code_lists/nhs_data_dictionary_language_code.csv deleted file mode 100644 index 810b2a0..0000000 --- a/codes/code_lists/nhs_data_dictionary_language_code.csv +++ /dev/null @@ -1,189 +0,0 @@ -NHS_DATA_DICTIONARY_LANGUAGE_CODE,aa,Afar -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ab,Abkhazian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ae,Avestan -NHS_DATA_DICTIONARY_LANGUAGE_CODE,af,Afrikaans -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ak,Akan -NHS_DATA_DICTIONARY_LANGUAGE_CODE,am,Amharic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,an,Aragonese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ar,Arabic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,as,Assamese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,av,Avaric -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ay,Aymara -NHS_DATA_DICTIONARY_LANGUAGE_CODE,az,Azerbaijani -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ba,Bashkir -NHS_DATA_DICTIONARY_LANGUAGE_CODE,be,Belarusian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bg,Bulgarian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bh,Bihari languages -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bi,Bislama -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bm,Bambara -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bn,Bengali -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bo,Tibetan -NHS_DATA_DICTIONARY_LANGUAGE_CODE,br,Breton -NHS_DATA_DICTIONARY_LANGUAGE_CODE,bs,Bosnian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ca,Catalan; Valencian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ce,Chechen -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ch,Chamorro -NHS_DATA_DICTIONARY_LANGUAGE_CODE,co,Corsican -NHS_DATA_DICTIONARY_LANGUAGE_CODE,cr,Cree -NHS_DATA_DICTIONARY_LANGUAGE_CODE,cs,Czech -NHS_DATA_DICTIONARY_LANGUAGE_CODE,cu,Church Slavic; Old Slavonic; Church Slavonic; Old Bulgarian; Old Church Slavonic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,cv,Chuvash -NHS_DATA_DICTIONARY_LANGUAGE_CODE,cy,Welsh -NHS_DATA_DICTIONARY_LANGUAGE_CODE,da,Danish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,de,German -NHS_DATA_DICTIONARY_LANGUAGE_CODE,dv,Divehi; Dhivehi; Maldivian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,dz,Dzongkha -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ee,Ewe -NHS_DATA_DICTIONARY_LANGUAGE_CODE,el,"Greek, Modern (1453-)" -NHS_DATA_DICTIONARY_LANGUAGE_CODE,en,English -NHS_DATA_DICTIONARY_LANGUAGE_CODE,eo,Esperanto -NHS_DATA_DICTIONARY_LANGUAGE_CODE,es,Spanish; Castilian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,et,Estonian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,eu,Basque -NHS_DATA_DICTIONARY_LANGUAGE_CODE,fa,Persian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ff,Fulah -NHS_DATA_DICTIONARY_LANGUAGE_CODE,fi,Finnish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,fj,Fijian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,fo,Faroese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,fr,French -NHS_DATA_DICTIONARY_LANGUAGE_CODE,fy,Western Frisian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ga,Irish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,gd,Gaelic; Scottish Gaelic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,gl,Galician -NHS_DATA_DICTIONARY_LANGUAGE_CODE,gn,Guarani -NHS_DATA_DICTIONARY_LANGUAGE_CODE,gu,Gujarati -NHS_DATA_DICTIONARY_LANGUAGE_CODE,gv,Manx -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ha,Hausa -NHS_DATA_DICTIONARY_LANGUAGE_CODE,he,Hebrew -NHS_DATA_DICTIONARY_LANGUAGE_CODE,hi,Hindi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ho,Hiri Motu -NHS_DATA_DICTIONARY_LANGUAGE_CODE,hr,Croatian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ht,Haitian; Haitian Creole -NHS_DATA_DICTIONARY_LANGUAGE_CODE,hu,Hungarian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,hy,Armenian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,hz,Herero -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ia,Interlingua (International Auxiliary Language Association) -NHS_DATA_DICTIONARY_LANGUAGE_CODE,id,Indonesian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ie,Interlingue; Occidental -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ig,Igbo -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ii,Sichuan Yi; Nuosu -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ik,Inupiaq -NHS_DATA_DICTIONARY_LANGUAGE_CODE,io,Ido -NHS_DATA_DICTIONARY_LANGUAGE_CODE,is,Icelandic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,it,Italian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,iu,Inuktitut -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ja,Japanese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,jv,Javanese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ka,Georgian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kg,Kongo -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ki,Kikuyu; Gikuyu -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kj,Kuanyama; Kwanyama -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kk,Kazakh -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kl,Kalaallisut; Greenlandic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,km,Central Khmer -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kn,Kannada -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ko,Korean -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kr,Kanuri -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ks,Kashmiri -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ku,Kurdish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kv,Komi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,kw,Cornish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ky,Kirghiz; Kyrgyz -NHS_DATA_DICTIONARY_LANGUAGE_CODE,la,Latin -NHS_DATA_DICTIONARY_LANGUAGE_CODE,lb,Luxembourgish; Letzeburgesch -NHS_DATA_DICTIONARY_LANGUAGE_CODE,lg,Ganda -NHS_DATA_DICTIONARY_LANGUAGE_CODE,li,Limburgan; Limburger; Limburgish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ln,Lingala -NHS_DATA_DICTIONARY_LANGUAGE_CODE,lo,Lao -NHS_DATA_DICTIONARY_LANGUAGE_CODE,lt,Lithuanian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,lu,Luba-Katanga -NHS_DATA_DICTIONARY_LANGUAGE_CODE,lv,Latvian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mg,Malagasy -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mh,Marshallese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mi,Maori -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mk,Macedonian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ml,Malayalam -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mn,Mongolian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mr,Marathi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ms,Malay -NHS_DATA_DICTIONARY_LANGUAGE_CODE,mt,Maltese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,my,Burmese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,na,Nauru -NHS_DATA_DICTIONARY_LANGUAGE_CODE,nb,"Bokmål, Norwegian; Norwegian Bokmål" -NHS_DATA_DICTIONARY_LANGUAGE_CODE,nd,"Ndebele, North; North Ndebele" -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ne,Nepali -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ng,Ndonga -NHS_DATA_DICTIONARY_LANGUAGE_CODE,nl,Dutch; Flemish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,nn,"Norwegian Nynorsk; Nynorsk, Norwegian" -NHS_DATA_DICTIONARY_LANGUAGE_CODE,no,Norwegian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,nr,"Ndebele, South; South Ndebele" -NHS_DATA_DICTIONARY_LANGUAGE_CODE,nv,Navajo; Navaho -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ny,Chichewa; Chewa; Nyanja -NHS_DATA_DICTIONARY_LANGUAGE_CODE,oc,Occitan (post 1500) -NHS_DATA_DICTIONARY_LANGUAGE_CODE,oj,Ojibwa -NHS_DATA_DICTIONARY_LANGUAGE_CODE,om,Oromo -NHS_DATA_DICTIONARY_LANGUAGE_CODE,or,Oriya -NHS_DATA_DICTIONARY_LANGUAGE_CODE,os,Ossetian; Ossetic -NHS_DATA_DICTIONARY_LANGUAGE_CODE,pa,Panjabi; Punjabi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,pi,Pali -NHS_DATA_DICTIONARY_LANGUAGE_CODE,pl,Polish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ps,Pushto; Pashto -NHS_DATA_DICTIONARY_LANGUAGE_CODE,pt,Portuguese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,qu,Quechua -NHS_DATA_DICTIONARY_LANGUAGE_CODE,rm,Romansh -NHS_DATA_DICTIONARY_LANGUAGE_CODE,rn,Rundi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ro,Romanian; Moldavian; Moldovan -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ru,Russian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,rw,Kinyarwanda -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sa,Sanskrit -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sc,Sardinian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sd,Sindhi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,se,Northern Sami -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sg,Sango -NHS_DATA_DICTIONARY_LANGUAGE_CODE,si,Sinhala; Sinhalese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sk,Slovak -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sl,Slovenian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sm,Samoan -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sn,Shona -NHS_DATA_DICTIONARY_LANGUAGE_CODE,so,Somali -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sq,Albanian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sr,Serbian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ss,Swati -NHS_DATA_DICTIONARY_LANGUAGE_CODE,st,"Sotho, Southern" -NHS_DATA_DICTIONARY_LANGUAGE_CODE,su,Sundanese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sv,Swedish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,sw,Swahili -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ta,Tamil -NHS_DATA_DICTIONARY_LANGUAGE_CODE,te,Telugu -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tg,Tajik -NHS_DATA_DICTIONARY_LANGUAGE_CODE,th,Thai -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ti,Tigrinya -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tk,Turkmen -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tl,Tagalog -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tn,Tswana -NHS_DATA_DICTIONARY_LANGUAGE_CODE,to,Tonga (Tonga Islands) -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tr,Turkish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ts,Tsonga -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tt,Tatar -NHS_DATA_DICTIONARY_LANGUAGE_CODE,tw,Twi -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ty,Tahitian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ug,Uighur; Uyghur -NHS_DATA_DICTIONARY_LANGUAGE_CODE,uk,Ukrainian -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ur,Urdu -NHS_DATA_DICTIONARY_LANGUAGE_CODE,uz,Uzbek -NHS_DATA_DICTIONARY_LANGUAGE_CODE,ve,Venda -NHS_DATA_DICTIONARY_LANGUAGE_CODE,vi,Vietnamese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,vo,Volapük -NHS_DATA_DICTIONARY_LANGUAGE_CODE,wa,Walloon -NHS_DATA_DICTIONARY_LANGUAGE_CODE,wo,Wolof -NHS_DATA_DICTIONARY_LANGUAGE_CODE,xh,Xhosa -NHS_DATA_DICTIONARY_LANGUAGE_CODE,yi,Yiddish -NHS_DATA_DICTIONARY_LANGUAGE_CODE,yo,Yoruba -NHS_DATA_DICTIONARY_LANGUAGE_CODE,za,Zhuang; Chuang -NHS_DATA_DICTIONARY_LANGUAGE_CODE,zh,Chinese -NHS_DATA_DICTIONARY_LANGUAGE_CODE,zu,Zulu -NHS_DATA_DICTIONARY_LANGUAGE_CODE,q1,Braille - for people who are unable to see -NHS_DATA_DICTIONARY_LANGUAGE_CODE,q2,American Sign Language -NHS_DATA_DICTIONARY_LANGUAGE_CODE,q3,Australian Sign Language -NHS_DATA_DICTIONARY_LANGUAGE_CODE,q4,British Sign Language -NHS_DATA_DICTIONARY_LANGUAGE_CODE,q5,Makaton - devised for children and adults with a variety of communication and Learning Disabilities diff --git a/codes/code_lists/pkb_main.csv b/codes/code_lists/pkb_main.csv deleted file mode 100644 index e435fe5..0000000 --- a/codes/code_lists/pkb_main.csv +++ /dev/null @@ -1,12 +0,0 @@ -PKB_MAIN,11023 -PKB_MAIN,RCSLB -PKB_MAIN,RGQ02 -PKB_MAIN,RM574 -PKB_MAIN,RQ617 -PKB_MAIN,RQR13 -PKB_MAIN,RRK02 -PKB_MAIN,SGC04 -PKB_MAIN,RBL14 -PKB_MAIN,RAJ -PKB_MAIN,NHSWLS -PKB_MAIN,45020,Altnagelvin diff --git a/codes/code_lists/pv_admit_reason.csv b/codes/code_lists/pv_admit_reason.csv deleted file mode 100644 index a053310..0000000 --- a/codes/code_lists/pv_admit_reason.csv +++ /dev/null @@ -1,2 +0,0 @@ -PV,INS_HOSPITALISATION -PV,INS_RELAPSE \ No newline at end of file diff --git a/codes/code_lists/pv_groups.csv b/codes/code_lists/pv_groups.csv deleted file mode 100644 index 53a3699..0000000 --- a/codes/code_lists/pv_groups.csv +++ /dev/null @@ -1,175 +0,0 @@ -PV,AAHF1,A&A Heart,,,,,,,,,,,,,,, -PV,SNC01,Aberdeen Royal,,,,,,,,,,,,,,, -PV,AHUS,AHUS,,,,,,,,,,,,,,, -PV,RW402,Aintree Hospital,,,,,,,,,,,,,,, -PV,9RW402,Aintree-FDU,,,,,,,,,,,,,,, -PV,RW402H,Aintree-HomeD,,,,,,,,,,,,,,, -PV,SLC01,Airdrie,,,,,,,,,,,,,,, -PV,ALPORT,Alport,,,,,,,,,,,,,,, -PV,45020,Altnagelvin,,,,,,,,,,,,,,, -PV,RM403,Altrincham,,,,,,,,,,,,,,, -PV,24027,Antrim,,,,,,,,,,,,,,, -PV,APRT,APRT Def,,,,,,,,,,,,,,, -PV,ARPKD,ARPKD,,,,,,,,,,,,,,, -PV,RQBAU,Bangor,,,,,,,,,,,,,,, -PV,RFRAA,Barnsley,,,,,,,,,,,,,,, -PV,RDDH0,Basildon,,,,,,,,,,,,,,, -PV,RCD37,Bath,,,,,,,,,,,,,,, -PV,RD1,Bath - Royal United,,,,,,,,,,,,,,, -PV,9RFU,Bedford,,,,,,,,,,,,,,, -PV,9RQR13,Beeston,,,,,,,,,,,,,,, -PV,11023,Belfast - Paeds,,,,,,,,,,,,,,, -PV,2020,Belfast City,,,,,,,,,,,,,,, -PV,7021,Belfast-Ulster Hosp,,,,,,,,,,,,,,, -PV,RQ3,B'Ham - Paeds,,,,,,,,,,,,,,, -PV,RL7,B'Ham-Heartlands,,,,,,,,,,,,,,, -PV,RRK02,B'Ham-QEH,,,,,,,,,,,,,,, -PV,RBL14,Birkenhead-Arrowe Pk,,,,,,,,,,,,,,, -PV,RKGA1,Bodlewyddan - Glan C,,,,,,,,,,,,,,, -PV,RMC00,Bolton,,,,,,,,,,,,,,, -PV,RAE05,Bradford,,,,,,,,,,,,,,, -PV,RGU01,Brighton,,,,,,,,,,,,,,, -PV,REE01,Bristol,,,,,,,,,,,,,,, -PV,RA723,Bristol-Childrens,,,,,,,,,,,,,,, -PV,CAIRO,Cairo,,,,,,,,,,,,,,, -PV,RGT01,Cambridge,,,,,,,,,,,,,,, -PV,RRE14,Cannock,,,,,,,,,,,,,,, -PV,RRBBV,Cardiff,,,,,,,,,,,,,,, -PV,RLGAY,Carlisle,,,,,,,,,,,,,,, -PV,RAZ,Carshalton-St Helier,,,,,,,,,,,,,,, -PV,9RJH01,Castle Vale,,,,,,,,,,,,,,, -PV,CCL,CCL,,,,,,,,,,,,,,, -PV,9RCSLB,Centenary Wing Dialy,,,,,,,,,,,,,,, -PV,RQ8L0,Chelmsford,,,,,,,,,,,,,,, -PV,RJR05,Chester,,,,,,,,,,,,,,, -PV,CHI,CHI,,,,,,,,,,,,,,, -PV,RBL20,Clatterbridge-satell,,,,,,,,,,,,,,, -PV,RDEE4,Colchester,,,,,,,,,,,,,,, -PV,9RVJ21,Cossham,,,,,,,,,,,,,,, -PV,RKB01,Coventry,,,,,,,,,,,,,,, -PV,CYSTIN,CYSTIN,,,,,,,,,,,,,,, -PV,CYSURIA,Cysuria,,,,,,,,,,,,,,, -PV,DEMO,Demonstration,,,,,,,,,,,,,,, -PV,DENTLOWE,Dent and Lowe,,,,,,,,,,,,,,, -PV,RFPFG,Derby,,,,,,,,,,,,,,, -PV,RMW10,Dewsbury,,,,,,,,,,,,,,, -PV,Diabetes,Diabetes,,,,,,,,,,,,,,, -PV,RP5,Doncaster,,,,,,,,,,,,,,, -PV,RBD01,Dorchester,,,,,,,,,,,,,,, -PV,RR9,Dryburn,,,,,,,,,,,,,,, -PV,RNA03,Dudley,,,,,,,,,,,,,,, -PV,SYC01,Dumfries,,,,,,,,,,,,,,, -PV,DUMMY,Dummy,,,,,,,,,,,,,,, -PV,STC01,Dundee,,,,,,,,,,,,,,, -PV,RCB23,Easingwold,,,,,,,,,,,,,,, -PV,ECS,ECS,,,,,,,,,,,,,,, -PV,RSC02,Edin,,,,,,,,,,,,,,, -PV,EDINHF1,Edin Heart,,,,,,,,,,,,,,, -PV,RH8,Exeter,,,,,,,,,,,,,,, -PV,SFC01,Fife,,,,,,,,,,,,,,, -PV,FUAN,FUAN,,,,,,,,,,,,,,, -PV,Generic,Generic,,,,,,,,,,,,,,, -PV,GGCHF1,GG&C Heart,,,,,,,,,,,,,,, -PV,SGC02,Glasgow Children's,,,,,,,,,,,,,,, -PV,SGC05,Glasgow QEUH,,,,,,,,,,,,,,, -PV,SGC04,Glasgow Renal,,,,,,,,,,,,,,, -PV,RH641,Gloucester,,,,,,,,,,,,,,, -PV,RBN63,Halton_Satellite,,,,,,,,,,,,,,, -PV,RQW,Harlow,,,,,,,,,,,,,,, -PV,RCD35,Harogate,,,,,,,,,,,,,,, -PV,Cardiol,Heart failure,,,,,,,,,,,,,,, -PV,9RK7CC,Heely,,,,,,,,,,,,,,, -PV,HNF1B,HNF1B,,,,,,,,,,,,,,, -PV,RGB04,Huddersfield,,,,,,,,,,,,,,, -PV,RF201,Hull,,,,,,,,,,,,,,, -PV,HYPERRDG,HY_OXALURIA,,,,,,,,,,,,,,, -PV,IBD,IBD,,,,,,,,,,,,,,, -PV,RXM56,Ilkeston,,,,,,,,,,,,,,, -PV,NEWDEHLI,INDIA New Dehli,,,,,,,,,,,,,,, -PV,BANGALORE,INDIA-Bangalore,,,,,,,,,,,,,,, -PV,VELLORE,INDIA-Vellore,,,,,,,,,,,,,,, -PV,SHC01,Inverness,,,,,,,,,,,,,,, -PV,RGQ02,Ipswich,,,,,,,,,,,,,,, -PV,TEHRAN,IRAN-Tehran,,,,,,,,,,,,,,, -PV,GUNMA,Japan - GUNMA,,,,,,,,,,,,,,, -PV,RVVKC,Kent,,,,,,,,,,,,,,, -PV,SAC02,Kilmarnock,,,,,,,,,,,,,,, -PV,RFJBC,King's Mill,,,,,,,,,,,,,,, -PV,RQS01,Leeds Infirmary,,,,,,,,,,,,,,, -PV,99RQR13,Leeds -Paeds,,,,,,,,,,,,,,, -PV,RQR00,Leeds- St James's,,,,,,,,,,,,,,, -PV,RFBAK,Leicester,,,,,,,,,,,,,,, -PV,RNG10,Lichfield,,,,,,,,,,,,,,, -PV,RBS25,Liverpool-A Hey,,,,,,,,,,,,,,, -PV,RQ601,Liverpool-Broadgreen,,,,,,,,,,,,,,, -PV,RQ617,Liverpool-Royal,,,,,,,,,,,,,,, -PV,RJZ,London - Kings,,,,,,,,,,,,,,, -PV,R1H00,London-Barts,,,,,,,,,,,,,,, -PV,RP4,London-GOSH,,,,,,,,,,,,,,, -PV,RJ100,London-Guys+Tommys,,,,,,,,,,,,,,, -PV,RAL01,London-Royal Free,,,,,,,,,,,,,,, -PV,RJ701,London-St George's,,,,,,,,,,,,,,, -PV,RQN02,London-West,,,,,,,,,,,,,,, -PV,RC971,Luton & Dunstable,,,,,,,,,,,,,,, -PV,RW3RM,Manchester Childrens,,,,,,,,,,,,,,, -PV,RM574,Manchester Royal I,,,,,,,,,,,,,,, -PV,MEMRDG,MEMRDG,,,,,,,,,,,,,,, -PV,RCJAT,Middlesbrough-J-Cook,,,,,,,,,,,,,,, -PV,MPGN,MPGN,,,,,,,,,,,,,,, -PV,8RJ121,New Cross Gate,,,,,,,,,,,,,,, -PV,RTD01,Newcastle,,,,,,,,,,,,,,, -PV,33020,Newry-Daisy Hill,,,,,,,,,,,,,,, -PV,RM102,Norfolk Norwich,,,,,,,,,,,,,,, -PV,RX1CC,Nottingham,,,,,,,,,,,,,,, -PV,99RCSLB,Nottingham -Paeds,,,,,,,,,,,,,,, -PV,48021,Omagh-Tyrone,,,,,,,,,,,,,,, -PV,RNX02,Oxford,,,,,,,,,,,,,,, -PV,PATIENT_ENTERED,Patient Entered,,,,,,,,,,,,,,, -PV,PV_SUP,PatientView Support,,,,,,,,,,,,,,, -PV,RK950,Plymouth,,,,,,,,,,,,,,, -PV,RXF03,Pontefract,,,,,,,,,,,,,,, -PV,RHU02,Portsmouth-Q-Alex,,,,,,,,,,,,,,, -PV,OBS,Pregnancy,,,,,,,,,,,,,,, -PV,RMF01,Preston,,,,,,,,,,,,,,, -PV,PRESR1,PRESTON_RES_GP1,,,,,,,,,,,,,,, -PV,RHW01,Reading,,,,,,,,,,,,,,, -PV,REDCAPLASIA,RedCAplasia,,,,,,,,,,,,,,, -PV,Renal,Renal,,,,,,,,,,,,,,, -PV,RENALREG,Renal Registry,,,,,,,,,,,,,,, -PV,RFRPA,Rotherham,,,,,,,,,,,,,,, -PV,SALIBD,Salford IBD,,,,,,,,,,,,,,, -PV,RM301,Salford Royal,,,,,,,,,,,,,,, -PV,DSF01,Salford_Diabetes,,,,,,,,,,,,,,, -PV,HYPALK,Salt Wasting,,,,,,,,,,,,,,, -PV,9RQR14,Seacroft,,,,,,,,,,,,,,, -PV,RK7CC,Sheffield,,,,,,,,,,,,,,, -PV,RLZ01,Shrewsbury,,,,,,,,,,,,,,, -PV,RL301,Solihull,,,,,,,,,,,,,,, -PV,99RHM01,Southampton-Paed,,,,,,,,,,,,,,, -PV,RAJ01,Southend,,,,,,,,,,,,,,, -PV,RVY01,Southport,,,,,,,,,,,,,,, -PV,SRNS,SRNS,,,,,,,,,,,,,,, -PV,9RBN01,St Helens_Satellite,,,,,,,,,,,,,,, -PV,STAFF_ENTERED,Staff Entered,,,,,,,,,,,,,,, -PV,STECHUS,STECHUS,,,,,,,,,,,,,,, -PV,RAQ01,Stevenage-Lister,,,,,,,,,,,,,,, -PV,9RWJ,Stockport,,,,,,,,,,,,,,, -PV,RJE01,Stoke,,,,,,,,,,,,,,, -PV,RLNGH,Sunderland,,,,,,,,,,,,,,, -PV,RQHC7,Swansea,,,,,,,,,,,,,,, -PV,RMP01,Tameside,,,,,,,,,,,,,,, -PV,REF12,Truro -Treliske,,,,,,,,,,,,,,, -PV,UNKNOWNTESTGROUP,Unknown,,,,,,,,,,,,,,, -PV,VASRDG,VASRDG,,,,,,,,,,,,,,, -PV,9RBK,Walsall Renal Unit,,,,,,,,,,,,,,, -PV,RKC81,Warrington,,,,,,,,,,,,,,, -PV,9RLNGH,Washington,,,,,,,,,,,,,,, -PV,REM26,Waterloo_Satellite,,,,,,,,,,,,,,, -PV,9RM301,Wigan,,,,,,,,,,,,,,, -PV,RL403,Wolverhampton,,,,,,,,,,,,,,, -PV,RKHA4,Wrexham,,,,,,,,,,,,,,, -PV,RCB55,York,,,,,,,,,,,,,,, -PV,PV,PatientView System -PV,INS_WEB,INS Website -PV,INS_APP,INS App -PV,NHSWLS,NHS Wales \ No newline at end of file diff --git a/codes/code_lists/pv_observations.csv b/codes/code_lists/pv_observations.csv deleted file mode 100644 index f87327d..0000000 --- a/codes/code_lists/pv_observations.csv +++ /dev/null @@ -1,92 +0,0 @@ -PV,BodyTemperature,Body Temperature,obs, -PV,FaecalCalprotectin,Faecal Calprotectin,result,ug/g -PV,TargetWeight,Target Weight,obs, -PV,acr,ACR,result,mg/mmol -PV,adjustedcalcium,Adjusted Calcium,result,mmol/L -PV,albumin,Albumin,result,g/L -PV,albumin_post,Albumin (Post),result,g/L -PV,alp,AlkP,result,U/L -PV,alt,ALT,result,U/L -PV,amy,Amylase,result,U/L -PV,ast,AST,result,U/L -PV,bili,Bili,result,umol/L -PV,bmi,BMI,obs, -PV,bpdia,BP Diastolic,obs,mm Hg -PV,bpsys,BP Systolic,obs,mm Hg -PV,calcium,Calcium,result,mmol/l -PV,calcium_post,Calcium (Post),result, -PV,cholesterol,Cholesterol,result,mmol/l -PV,ciclosporin,Ciclosporin,result,ng/ml -PV,covid19antibody,Covid-19 Antibody,result, -PV,covid19lflow,Covid-19 Lateral Flow,result, -PV,covid19pcr,Covid-19 PCR,result, -PV,creatinine,Creatinine,result,umol/l -PV,creatinine_post,Creatinine (Post),result, -PV,crp,CRP,result,mg/l -PV,egfr,eGFR,result,mL/min/1.73m^2 -PV,egfr_post,eGFR (Post),result,mL/min/1.73m^2 -PV,ferritin,Ferritin,result,ug/l -PV,folate,Folate,result,ug/l -PV,ft3,Free T3,result,pmol/l -PV,ft4,Free T4,result,pmol/l -PV,ggt,GGT,result,U/l -PV,glucose,Glucose Random,result,mmol/l -PV,hb,Hb,result,g/l -PV,hba1c,HbA1c,result,mmol/mol -PV,hbv,Hep B,result, -PV,hco3,Bicarb,result,mmol/l -PV,hco3_post,HCO3 (Post),result, -PV,hct,HCT/PCV,result,I/l -PV,hcv,Hep C,result, -PV,hdl,HDL,result,mmol/l -PV,height,Height,obs,cm -PV,hypotension,Symptomatic Hypotension,obs, -PV,inr,INR,result,ratio -PV,iron,Iron,result,mmol/l -PV,ironsat,Fe Sat,result,% -PV,ktv,Kt/V,result,ratio -PV,ldh,LDH,result,U/l -PV,ldl,LDL,result,mmol/l -PV,lhratio,LDL:LDH Ratio,result,ratio -PV,lipase,Lipase,result,U/l -PV,lithium,Lithium,result,mEq/l -PV,magnesium,Mg,result,mmol/l -PV,mmp,MMP Level,result, -PV,neutrophils,Neutrophils,result,10^9/l -PV,odema,Odema,obs, -PV,pcr,PCR,result,mg/mmol -PV,phepku,Phenylalanine,result,mg/dl -PV,phosphate,Phosphate,result,mmol/l -PV,phosphate_post,Phosphate (Post),result,mmol/l -PV,platelets,Platelets,result,10^9/l -PV,potassium,Potassium,result,mmol/l -PV,potassium_post,Potassium (Post),result,mmol/l -PV,psa,PSA,result,ng/ml -PV,pth,PTH,result,pmol/l -PV,pulse,Pulse,obs,bpm -PV,ret-he,RET-HE,result,pg -PV,sirolimus,Sirolimus,result,ng/l -PV,sodium,Sodium,result,mmol/l -PV,sodium_post,Sodium (Post),result,mmol/l -PV,t4,Total T4,result,ng/l -PV,tacrolimus,Tacrolimus,result,ng/ml -PV,testosterone,Serum Testosterone,result,ng/dl -PV,tg,TG,result,mmol/l -PV,tgn,TGN Levels,result, -PV,tpmt,TPMT Levels,result,mU/l -PV,transferrin,Transferrin,result,% -PV,trop,Troponin-T,result,ng/ml -PV,tsh,TSH,result,mU/l -PV,ualbumin,Urine Albumin,result,mg/l -PV,ucreatinine,Urine Creatinine,result,mmol/l -PV,updipstick,Urine Protein Dipstick,obs, -PV,uprotein,Urine Protein,result,mmol/l -PV,urate,Urate,result,mmol/l -PV,urea,Urea,result,mmol/l -PV,urea_post,Urea (Post),result,mmol/l -PV,urr,URR,result,ratio -PV,urr_post,URR (Post),result, -PV,vitb12,Vitamin B12,result,ng/l -PV,vitd,Vitamin D,result,nmol/l -PV,wbc,WBC,result,10^9/l -PV,weight,Weight,obs,kg diff --git a/codes/code_lists/pv_rrtstatus.csv b/codes/code_lists/pv_rrtstatus.csv deleted file mode 100644 index c751833..0000000 --- a/codes/code_lists/pv_rrtstatus.csv +++ /dev/null @@ -1,5 +0,0 @@ -PV_RRTSTATUS,GEN,Kidney Care (not Dialysis or Transplant) -PV_RRTSTATUS,HD,Haemodialysis -PV_RRTSTATUS,PD,Peritoneal Dialysis -PV_RRTSTATUS,TP,Transplant Follow up -PV_RRTSTATUS,XFER,Transferred Out diff --git a/codes/code_lists/pv_tpstatus.csv b/codes/code_lists/pv_tpstatus.csv deleted file mode 100644 index 1910840..0000000 --- a/codes/code_lists/pv_tpstatus.csv +++ /dev/null @@ -1,7 +0,0 @@ -PV_TPSTATUS,A,Active -PV_TPSTATUS,S,Suspended -PV_TPSTATUS,T,Transplanted -PV_TPSTATUS,R,Not on List -PV_TPSTATUS,N,Not on List -PV_TPSTATUS,O,Not on List -PV_TPSTATUS,U,No Status Uploaded diff --git a/codes/code_lists/radar_facilities.csv b/codes/code_lists/radar_facilities.csv deleted file mode 100644 index d564fc2..0000000 --- a/codes/code_lists/radar_facilities.csv +++ /dev/null @@ -1 +0,0 @@ -RADAR,RWDDA,LINCOLN COUNTY HOSPITAL diff --git a/codes/code_lists/rawpvrrtstatus.csv b/codes/code_lists/rawpvrrtstatus.csv deleted file mode 100644 index 134db9c..0000000 --- a/codes/code_lists/rawpvrrtstatus.csv +++ /dev/null @@ -1,101 +0,0 @@ -PV_RAW_RRTSTATUS,AAPD -PV_RAW_RRTSTATUS,ACUTE ITU -PV_RAW_RRTSTATUS,ACUTE -PV_RAW_RRTSTATUS,ALD -PV_RAW_RRTSTATUS,APD -PV_RAW_RRTSTATUS,CAPD -PV_RAW_RRTSTATUS,CK -PV_RAW_RRTSTATUS,CKD/TX -PV_RAW_RRTSTATUS,CLINIC -PV_RAW_RRTSTATUS,HD (HOME) -PV_RAW_RRTSTATUS,HD (HOSP) -PV_RAW_RRTSTATUS,HOME APD -PV_RAW_RRTSTATUS,HOME CAPD -PV_RAW_RRTSTATUS,HOME HD NOCTURNAL -PV_RAW_RRTSTATUS,HOME HD -PV_RAW_RRTSTATUS,HOSPITAL HD -PV_RAW_RRTSTATUS,IN-CENTRE HD -PV_RAW_RRTSTATUS,LOST -PV_RAW_RRTSTATUS,LRD -PV_RAW_RRTSTATUS,MOVED OUT -PV_RAW_RRTSTATUS,PR -PV_RAW_RRTSTATUS,PRE -PV_RAW_RRTSTATUS,REC -PV_RAW_RRTSTATUS,T/P RENAL(C) -PV_RAW_RRTSTATUS,T/P RENAL(L) -PV_RAW_RRTSTATUS,TRANSPLANT -PV_RAW_RRTSTATUS,TX (KL) -PV_RAW_RRTSTATUS,TX (PAK) -PV_RAW_RRTSTATUS,TX (PAT) -PV_RAW_RRTSTATUS,TX (SPK) -PV_RAW_RRTSTATUS,0 -PV_RAW_RRTSTATUS,1 -PV_RAW_RRTSTATUS,2 -PV_RAW_RRTSTATUS,3 -PV_RAW_RRTSTATUS,4 -PV_RAW_RRTSTATUS,5 -PV_RAW_RRTSTATUS,9 -PV_RAW_RRTSTATUS,10 -PV_RAW_RRTSTATUS,11 -PV_RAW_RRTSTATUS,12 -PV_RAW_RRTSTATUS,13 -PV_RAW_RRTSTATUS,14 -PV_RAW_RRTSTATUS,15 -PV_RAW_RRTSTATUS,16 -PV_RAW_RRTSTATUS,17 -PV_RAW_RRTSTATUS,19 -PV_RAW_RRTSTATUS,20 -PV_RAW_RRTSTATUS,21 -PV_RAW_RRTSTATUS,22 -PV_RAW_RRTSTATUS,23 -PV_RAW_RRTSTATUS,24 -PV_RAW_RRTSTATUS,25 -PV_RAW_RRTSTATUS,26 -PV_RAW_RRTSTATUS,27 -PV_RAW_RRTSTATUS,28 -PV_RAW_RRTSTATUS,29 -PV_RAW_RRTSTATUS,41 -PV_RAW_RRTSTATUS,42 -PV_RAW_RRTSTATUS,43 -PV_RAW_RRTSTATUS,44 -PV_RAW_RRTSTATUS,45 -PV_RAW_RRTSTATUS,49 -PV_RAW_RRTSTATUS,50 -PV_RAW_RRTSTATUS,51 -PV_RAW_RRTSTATUS,52 -PV_RAW_RRTSTATUS,53 -PV_RAW_RRTSTATUS,54 -PV_RAW_RRTSTATUS,55 -PV_RAW_RRTSTATUS,56 -PV_RAW_RRTSTATUS,57 -PV_RAW_RRTSTATUS,59 -PV_RAW_RRTSTATUS,60 -PV_RAW_RRTSTATUS,61 -PV_RAW_RRTSTATUS,62 -PV_RAW_RRTSTATUS,63 -PV_RAW_RRTSTATUS,64 -PV_RAW_RRTSTATUS,65 -PV_RAW_RRTSTATUS,66 -PV_RAW_RRTSTATUS,68 -PV_RAW_RRTSTATUS,69 -PV_RAW_RRTSTATUS,74 -PV_RAW_RRTSTATUS,75 -PV_RAW_RRTSTATUS,77 -PV_RAW_RRTSTATUS,81 -PV_RAW_RRTSTATUS,82 -PV_RAW_RRTSTATUS,83 -PV_RAW_RRTSTATUS,111 -PV_RAW_RRTSTATUS,114 -PV_RAW_RRTSTATUS,115 -PV_RAW_RRTSTATUS,117 -PV_RAW_RRTSTATUS,121 -PV_RAW_RRTSTATUS,162 -PV_RAW_RRTSTATUS,181 -PV_RAW_RRTSTATUS,182 -PV_RAW_RRTSTATUS,183 -PV_RAW_RRTSTATUS,201 -PV_RAW_RRTSTATUS,202 -PV_RAW_RRTSTATUS,203 -PV_RAW_RRTSTATUS,241 -PV_RAW_RRTSTATUS,242 -PV_RAW_RRTSTATUS,243 \ No newline at end of file diff --git a/codes/code_lists/rr1plus_facilities.csv b/codes/code_lists/rr1plus_facilities.csv deleted file mode 100644 index 64b5b32..0000000 --- a/codes/code_lists/rr1plus_facilities.csv +++ /dev/null @@ -1,437 +0,0 @@ -RR1+,11021,QUEEN VICTORIA -RR1+,11023,ROYAL BELFAST HOSPITAL FOR SICK CHILDREN -RR1+,2020,BELFAST HOSPITAL -RR1+,24027,ANTRIM HOSPITAL -RR1+,33020,DAISY HILL HOSPITAL -RR1+,45020,ALTNAGELVIN HOSPITAL -RR1+,45021,WESTERN TRUST -RR1+,48021,TYRONE COUNTY HOSPITAL -RR1+,7021,ULSTER HOSPITAL -RR1+,7RM301,OLDHAM RENAL UNIT -RR1+,88A713,ST JOHN AND ELIZABETH HOSPITAL -RR1+,8A713,ST. JOHN & ELIZABETH HOSPITAL -RR1+,8CJ06,LONDON BRIDGE HOSPITAL -RR1+,8RA911,SOUTH DEVON (TORQUAY) - DERRIFORD PATIENTS -RR1+,8RAL01,TOTTENHAM HALE -RR1+,8RJ121,NEW CROSS -RR1+,8TAF,CAMDEN -RR1+,96RRK02,REDDITCH SATELLITE UNIT -RR1+,97RRK02,SPARKHILL SATELLITE UNIT -RR1+,97TAF,MARY RANKIN -RR1+,98A713,ST JOHN & ELIZABETH HOSPITAL -RR1+,98CJ06,LONDON BRIDGE HOSPITAL -RR1+,98D917,PRIORY HOSPITAL -RR1+,98RAZ,WEST BYFLEET DIALYSIS CENTRE -RR1+,98RBK,WALSALL - QEH -RR1+,98RFBAK,HUMBERSTONE -RR1+,98RJ701,COLLIERS WOOD -RR1+,98RJZ,SYDENHAM -RR1+,98RQY,SUTTON SATELLITE UNIT -RR1+,98RRBBV,UHW - BAXTER UNIT -RR1+,98RRK02,WOODGATE VALLEY -RR1+,98TAF,ST PANCRAS -RR1+,990,N/A -RR1+,995,UNKNOWN -RR1+,999,NOT SUPPLIED -RR1+,99RAZ,WEST BYFLEET DIALYSIS CENTRE -RR1+,99RBK,WALSALL -RR1+,99RCSLB,NOTTINGHAM CITY HOSPITAL - PAEDIATRIC -RR1+,99RFBAK,CORBY -RR1+,99RHU02,HAVANT SATELLITE -RR1+,99RJ121,GUY'S HOSPITAL (SATELLITE) -RR1+,99RJ701,NORTH WANDSWORTH -RR1+,99RJZ,BROMLEY -RR1+,99RQR13,ST JAMES'S UNIVERSITY HOPSITAL - 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R & S -RR1+,9RQS1,SEACROFT LGI -RR1+,9RQY,SUTTON -RR1+,9RRBBV,UHW SATELLITE -RR1+,9RRK02,KINGS NORTON -RR1+,9RTP02,CRAWLEY -RR1+,9RTQ,FORREST OF DEAN -RR1+,9RVEB1,LLANTRISANT DIALYSIS CENTRE -RR1+,9RVJ21,COSSHAM (SOUTHMEAD SATELLITE) -RR1+,9RW,HAYLING ISLAND -RR1+,9RW402,FRESENIUS UNIT - AINTREE -RR1+,9RWD,GRANTHAM -RR1+,9RWDLB,SKEGNESS -RR1+,9RWJ,STOCKPORT SATELLITE UNIT -RR1+,9RWP31,KIDDERMINSTER -RR1+,9RWX,BRACKNELL -RR1+,9RXV06,PRESTWICH -RR1+,9RXX,PURLEY -RR1+,9TAF,CAMDEN -RR1+,ABROAD,CODE USED WHEN PATIENT HAS RECEIVED TXT ABROAD -RR1+,CEN1,Dummy -RR1+,GUERNSEY,GUERNSEY -RR1+,ISLEMAN,ISLEMAN -RR1+,JERSEY,JERSEY -RR1+,MV101,SOLIHULL HOSPITAL -RR1+,PRIVATE,PRIVATE -RR1+,R1G55,SOUTH HAMS HOSPITAL -RR1+,RA301,WESTON GENERAL HOSPITAL -RR1+,RA723,BRISTOL CHILDRENS HOSPITAL -RR1+,RA911,NEWTON ABBOT HOSPITAL -RR1+,RAE01,BRADFORD ROYAL INFIRMARY -RR1+,RAE05,ST LUKES HOSPITAL -RR1+,RAJ01,SOUTHEND HOSPITAL -RR1+,RAL01,THE ROYAL FREE HOSPITAL -RR1+,RAPNM,NORTH MIDDLESEX HOSPITAL -RR1+,RAQ01,LISTER HOSPITAL -RR1+,RAU31,CENTRAL MIDDLESEX HOSPITAL -RR1+,RAZ,ST HELIER NHS TRUST -RR1+,RBBP3,FROME -RR1+,RBD01,DORSET COUNTY HOSPITAL -RR1+,RBF33,HORTON GENERAL HOSPITAL -RR1+,RBH14,CANNOCK CHASE HOSPITAL -RR1+,RBK02,MANOR HOSPITAL -RR1+,RBL14,ARROWE PARK HOSPITAL -RR1+,RBL20,CLATTERBRIDGE HOSPITAL -RR1+,RBN01,WHISTON HOSPITAL -RR1+,RBN63,HALTON GENERAL HOSPITAL -RR1+,RBS25,ROYAL LIVERPOOL CHILDRENS HOSPITAL -RR1+,RBT20,LEIGHTON HOSPITAL -RR1+,RBZ16,HIGHFIELD DIALYSIS UNIT -RR1+,RBZ19,NEW SOUTH MOLTON HOSPITAL -RR1+,RC368,EALING HOSPITAL -RR1+,RC971,LUTON & DUNSTABLE HOSPITAL -RR1+,RCB23,ACORN COURT -RR1+,RCB55,YORK DISTRICT GENERAL HOSPITAL -RR1+,RCC25,SCARBOROUGH GENERAL HOSPITAL -RR1+,RCD35,HARROGATE DISTRICT HOSPITAL -RR1+,RCF31,SKIPTON GENERAL HOSPITAL -RR1+,RCJAT,SOUTH CLEVELAND HOSPITAL -RR1+,RCSLB,NOTTINGHAM CITY HOSPITAL -RR1+,RCX01,KINGS LYNN -RR1+,RCY03,ASHFORD HOSPITAL -RR1+,RD1,ROYAL UNITED HOSPITAL BATH NHS TRUST -RR1+,RD816,MILTON KEYNES GENERAL HOSPITAL -RR1+,RDA03,ST CHARLES HOSPITAL -RR1+,RDDH0,BASILDON HOSPITAL -RR1+,RDDH1,ORSETT HOSPITAL -RR1+,RDEE4,COLCHESTER GENERAL HOSPITAL -RR1+,RDM03,BEXHILL HOSPITAL -RR1+,RDZ00,ROYAL BOURNEMOUTH & CHRISTCHURCH NHS TRUST -RR1+,RDZ15,MILFORD-ON-SEA SATELLITE -RR1+,RE5BW,WESTMORLAND GENERAL HOSPITAL -RR1+,RE7CB,COCKERMOUTH COTTAGE HOSPITAL AND EYE CLINIC -RR1+,RE9GA,SOUTH TYNESIDE DISTRICT GENERAL HOSPITAL -RR1+,REE01,SOUTHMEAD HOSPITAL -RR1+,REF01,WEST CORNWALL HOSPITAL (PENZANCE) -RR1+,REF12,ROYAL CORNWALL HOSPITAL (TRELISKE) -RR1+,REFWW,LAUNCESTON HOSPITAL -RR1+,REM26,WATERLOO DAY HOSPITAL -RR1+,REP17,ROYAL LIVERPOOL UNIVERSITY HOSPITAL -RR1+,RES01,SEFTON GENERAL HOSPITAL -RR1+,RES05,MOSSLEY HILL HOSPITAL -RR1+,REZ02,BIRCH HILL HOSPITAL -RR1+,RF201,HULL ROYAL INFIRMARY -RR1+,RF4DG,KING GEORGE SATELLITE UNIT -RR1+,RF4HA,HAROLD WOOD HOSPITAL -RR1+,RF832,SCUNTHORPE GENERAL HOSPITAL -RR1+,RF8FC,BRIGG CLINIC -RR1+,RFBAK,LEICESTER GENERAL HOSPITAL -RR1+,RFBAT,Northampton -RR1+,RFHFG,DERBY CITY HOSPITALS MENTAL HEALTH UNIT -RR1+,RFJBC,KING'S MILL HOSPITAL -RR1+,RFPFG,ROYAL DERBY -RR1+,RFRAA,BARNSLEY DISTRICT GENERAL HOSPITAL -RR1+,RFRPA,ROTHERHAM DISTRICT GENERAL HOSPITAL -RR1+,RFSDA,CHESTERFIELD & NORTH DERBYSHIRE ROYAL HOSPITAL -RR1+,RFW01,WEST MIDDLESEX UNIVERSITY HOSPITAL -RR1+,RFZ20,NORTHWICK PARK HOSPITAL -RR1+,RG222,QUEEN ELIZABETH HOSPITAL -RR1+,RG303A,FARNBOROUGH DIALYSIS UNIT -RR1+,RGA02,ROYAL HALIFAX INFIRMARY -RR1+,RGB04,ST LUKES HOSPITAL -RR1+,RGCKH,WHIPPS CROSS -RR1+,RGCKJ,WANSTEAD HOSPITAL -RR1+,RGCNH,NEWHAM UNIVERSITY HOSPITAL -RR1+,RGE01,PINDERFIELDS GENERAL HOSPITAL -RR1+,RGN,PETERBOROUGH HOSPITALS NHS TRUST -RR1+,RGP75,JAMES PAGET HOSPITAL -RR1+,RGQ02,IPSWICH HOSPITAL -RR1+,RGQ03,ALDEBURGH COMMUNITY HOSPITAL -RR1+,RGR50,WEST SUFFOLK HOSPITAL -RR1+,RGT01,ADDENBROOKE'S HOSPITAL -RR1+,RGU01,ROYAL SUSSEX COUNTY HOSPITAL -RR1+,RH641,GLOUCESTERSHIRE ROYAL HOSPITAL -RR1+,RH8,ROYAL DEVON & EXETER HEALTHCARE NHS TRUST -RR1+,RH801,ROYAL DEVON & EXETER HEALTHCARE -RR1+,RH802,HEAVITREE HOSPITAL -RR1+,RH840,HONITON HOSPITAL -RR1+,RH8G3,BARNSTAPLE -RR1+,RHANN,LINGS BAR HOSPITAL -RR1+,RHBR6,MIDDLESEX HOSPITAL -RR1+,RHM01,SOUTHAMPTON GENERAL HOSPITAL -RR1+,RHM02,ROYAL SOUTH HANTS HOSPITAL -RR1+,RHS55,"TOTTON HEALTH CENTRE, TOTTON" -RR1+,RHU02,QUEEN ALEXANDRA HOSPITAL -RR1+,RHU03,PORTSMOUTH HOSPITALS NHS TRUST (QUEEN ALEXANDRA HO -RR1+,RHW01,ROYAL BERKSHIRE HOSPITAL -RR1+,RJ121,GUY'S HOSPITAL -RR1+,RJ122,ST THOMAS' HOSPITAL -RR1+,RJ2,LEWISHAM HOSPITAL NHS TRUST -RR1+,RJ224,LEWISHAM HOSPITAL -RR1+,RJ230,QUEEN MARYS HOSPITAL -RR1+,RJ501,PADD ST MARY'S HOSPITAL -RR1+,RJ50X,DUMMY CODE FOR ST. 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HOSPITAL NEWCASTLE -RR1+,RTD02,ROYAL VICTORIA HOSPITAL -RR1+,RTD03,Alnwick Dialysis Unit -RR1+,RTF67,NORTH SHIELDS SATELLITE UNIT -RR1+,RTJ,FARNHAM COMMUNITY HOSPITAL -RR1+,RTK02,ASHFORD -RR1+,RTP02,CRAWLEY -RR1+,RTRNT,UNIVERSITY HOSPITAL OF NORTH TEES -RR1+,RVL01,BARNET SATL UNIT -RR1+,RVL07,EDGEWARE HOSPITAL -RR1+,RVNCA,SWINDON -RR1+,RVV11,ALAN SQUIRELL (MARGATE) -RR1+,RVV20,WILLIAM HARVEY -RR1+,RVVKC,KENT AND CANTERBURY HOSPITAL -RR1+,RVVMA,ALAN SQUIRREL (MAIDSTONE) -RR1+,RVY01,SOUTHPORT -RR1+,RW3RM,MANCHESTER CHILDRENS HOSPITAL -RR1+,RW402,UNIVERSITY HOSPITAL AINTREE -RR1+,RW5CA,BURNLEY GENERAL HOSPITAL -RR1+,RW602,NORTH MANCHESTER -RR1+,RWG02,WATFORD GENERAL HOSPITAL -RR1+,RWL25,ASHTON -RR1+,RWM51,CARDIFF CHILDRENS HOSPITAL -RR1+,RWP31,KIDDERMINSTER -RR1+,RX1RA,QUEENS MEDICAL CENTRE -RR1+,RXC02,EASTBOURNE DIALYSIS UNIT -RR1+,RXF03,PONTEFRACT GENERAL INFIRMARY -RR1+,RXJ01,KINGS SATELLITE -RR1+,RXJ06,KINGS SATELLITE -RR1+,RXL06,CLIFTON HOSPITAL -RR1+,RXM56,ILKESTON COMMUNITY HOSPITAL -RR1+,RXQ02,AYLESBURY -RR1+,RXQ50,WYCOMBE GENERAL HOSPITAL -RR1+,RXR01,ROYAL BLACKBURN HOSPITAL -RR1+,RXWAT,PRINCESS ROYAL HOSPITAL -RR1+,SAC02,NORTH AYRSHIRE & ARRAN NHS TRUST -RR1+,Sat2,Dummy Sat2 -RR1+,Sat3,Dummy Sat3 -RR1+,SFC01,QUEEN MARGARET HOSPITAL NHS TRUST -RR1+,SGC02,YORKHILL NHS TRUST -RR1+,SGC04,WEST GLASGOW HOSPITALS UNIVERSITY NHS TRUST -RR1+,SHC01,RAIGMORE HOSPITAL NHS TRUST -RR1+,SLC01,MONKLANDS & BELLSHILL HOSPITALS NHS TRUST -RR1+,SNC01,THE ABERDEEN ROYAL HOSPITALS NHS TRUST -RR1+,SSC02,ROYAL INFIRMARY OF EDINBURGH NHS TRUST -RR1+,SSC04,WESTERN GENERAL HOSPITALS NHS TRUST -RR1+,STC01,DUNDEE TEACHING HOSPITALS NHS TRUST -RR1+,SYC02,DUMFRIES & GALLOWAY COMMUNITY HEALTH NHS TRUST -RR1+,TAF21,CAMDEN -RR1+,XXX01,CARDIFF SOUTH -RR1+,XXX03,NEWPORT RENAL UNIT (BBRAUN) -RR1+,DEMO,DEMO UNIT -RR1+,PV,PATIENTVIEW SYSTEM -RR1+,RADAR,RADAR SYSTEM -RR1+,RVWAA,UNIVERSITY HOSPITAL OF HARTLEPOOL -RR1+,3C,3C TRIAL -RR1+,RG224,THAMESMEAD SATELLITE UNIT -RR1+,NHSWLS,NHS WALES -RR1+,PKB,PATIENTS KNOW BEST -RR1+,TRACING,UKRDC TRACING RECORD -RR1+,UKRR,UK RENAL REGISTRY -RR1+,RY5K7,CHANDRA MISTRY DIALYSIS UNIT -RR1+,RAJ,MID & SOUTH ESSEX TRUST -RR1+,BAPN,Migrated BAPN Data -RR1+,RTR45,Friarage Dialysis Centre -RR1+,RTG54,Samuel Johnson Community Hospital (Litchfield) -RR1+,996,BHLY - 996 -RR1+,997,BHLY - 997 -RR1+,RA702,BRISTOL GENERAL HOSPITAL -RR1+,RD304,POOLE GENERAL HOSPITAL -RR1+,RVR50,EPSOM HOSPITAL -RR1+,RNZ36,ST MARYS HOSPITAL (PORTSMOUTH) -RR1+,RLT14,COVENTRY & WARWICKS HOSPITAL FACILITIES -RR1+,E102H,London Hospital -RR1+,RK5BC,KING'S MILL HOSPITAL -RR1+,RG303,FARNBOROUGH HOSPITAL -RR1+,RVN3N,SOUTHMEAD HOSPITAL AWP -RR1+,RGP72,LOWESTOFT HOSPITAL -RR1+,RT302,ROYAL BROMPTON HOSPITAL -RR1+,RED03,PLYMPTON HOSPITAL -RR1+,RD300,POOLE GENERAL HOSPITAL -RR1+,RUE01,STAFFORD DISTRICT GENERAL HOSPITAL -RR1+,RCPAA,BASSETLAW HOSPITAL -RR1+,RA503,GLOUCESTERSHIRE ROYAL HOSPITAL -RR1+,RT301,HAREFIELD HOSPITAL -RR1+,RJD01,STAFFORD HOSPITAL -RR1+,RLY02,STOKE CITY GENERAL HOSPITAL -RR1+,RFJBL,MANSFIELD COMMUNITY HOSPITAL -RR1+,RP1L2,JOHN RADCLIFFE HOSPITAL -RR1+,RKB13,WARWICK NUFFIELD -RR1+,RKB28,Oxford University Hospitals NHS Foundation Trust -RR1+,M5O5A,Somers Place Kidney Unit -RR1+,RJE55,Burton Hospital -RR1+,RTG08,Long Eaton Health Centre -RR1+,RTG05,St Oswalds Hospital -RR1+,R7Y4J,Somers Place Kidney Unit -RR1+,RF202,PRINCESS ROYAL HOSPITAL -RR1+,RF316,CASTLE HILL HOSPITAL -RR1+,RNS,Northampton General Hospital NHS Trust -RR1+,RQ309,Birmingham Children's 'Dialysis Provider' -RR1+,P7U2H,LEICESTER SOUTH DIALYSIS UNIT - Wigston South diff --git a/codes/code_lists/snomed_access_device.csv b/codes/code_lists/snomed_access_device.csv deleted file mode 100644 index 6d5b97a..0000000 --- a/codes/code_lists/snomed_access_device.csv +++ /dev/null @@ -1,3 +0,0 @@ -SNOMED,449859004,Non-Tunneled central venous catheter -SNOMED,445085009,Tunnelled central venous catheter -SNOMED,258622003,Arteriovenous shunt diff --git a/codes/code_lists/snomed_access_finding.csv b/codes/code_lists/snomed_access_finding.csv deleted file mode 100644 index dbf9e57..0000000 --- a/codes/code_lists/snomed_access_finding.csv +++ /dev/null @@ -1,6 +0,0 @@ -SNOMED,440535009,Nontunneled central venous catheter in situ -SNOMED,439012009,Tunneled central venous catheter in situ -SNOMED,439784005,Surgically constructed arteriovenous fistula -SNOMED,699007002,Arteriovenous shunt in situ -SNOMED,366161000000100,Surgically created vein loop -SNOMED,440926006,Temporary peritoneal dialysis catheter in situ diff --git a/codes/code_lists/snomed_access_procedure.csv b/codes/code_lists/snomed_access_procedure.csv deleted file mode 100644 index eebc874..0000000 --- a/codes/code_lists/snomed_access_procedure.csv +++ /dev/null @@ -1,5 +0,0 @@ -SNOMED,449860009,Insertion of nontunneled central venous catheter -SNOMED,442309004,Insertion of tunneled venous catheter -SNOMED,27929005,Construction of arteriovenous fistula -SNOMED,46196009,Surgical construction of arteriovenous shunt -SNOMED,180277007,Insertion of temporary peritoneal dialysis catheter diff --git a/codes/code_lists/snomed_diabetes.csv b/codes/code_lists/snomed_diabetes.csv deleted file mode 100644 index c9d9f3f..0000000 --- a/codes/code_lists/snomed_diabetes.csv +++ /dev/null @@ -1,3 +0,0 @@ -SNOMED,73211009,Diabetes - Unspecified -SNOMED,46635009,Diabetes - Type I -SNOMED,44054006,Diabetes - Type II diff --git a/codes/code_lists/snomed_diagnosis.csv b/codes/code_lists/snomed_diagnosis.csv deleted file mode 100644 index 15abe54..0000000 --- a/codes/code_lists/snomed_diagnosis.csv +++ /dev/null @@ -1,28 +0,0 @@ -SNOMED,73211009,Diabetes - Unspecified -SNOMED,46635009,Diabetes - Type I -SNOMED,44054006,Diabetes - Type II -SNOMED,414545008,Ischaemic Heart Disease -SNOMED,401303003,STEMI First Date -SNOMED,401314000,NSTEMI First Date -SNOMED,194828000,Angina Date First Diagnosed -SNOMED,232717009,CABG or Coronary Angioplasty -SNOMED,84114007,Episode of Heart Failure -SNOMED,49436004,Arterial Fibrillation Date First Diagnosed -SNOMED,86049000,Malignancy Date First Diagnosed -SNOMED,62914000,Cerebrovascular Disease -SNOMED,266257000,TIA First Date -SNOMED,230690007,CVE / Stroke First Date -SNOMED,77176002,Smoking - Current -SNOMED,8517006,Smoking - Ex -SNOMED,8392000,Smoking - Non -SNOMED,13645005,COPD Date Diagnosed -SNOMED,235856003,Liver Disease Date Diagnosed -SNOMED,400047006,PVD Date Diagnosed -SNOMED,81723002,Date of Amputation for PVD -SNOMED,275520000,Claudication Date Diagnosed -SNOMED,13954005,Ischaemic or Neuropathic Ulcers -SNOMED,418285008,Non-Coronary Vascular Intervention - Angioplasty -SNOMED,312288001,Non-Coronary Vascular Intervention - Vascular graft -SNOMED,432119003,Non-Coronary Vascular Intervention - Aneurysm -SNOMED,360042007,Non-Coronary Vascular Intervention - Stent -SNOMED,52448006,Dementia Date Diagnosed diff --git a/codes/code_lists/snomed_dialysis.csv b/codes/code_lists/snomed_dialysis.csv deleted file mode 100644 index 3ddcd94..0000000 --- a/codes/code_lists/snomed_dialysis.csv +++ /dev/null @@ -1,2 +0,0 @@ -SNOMED,302497006,Haemodialyis -SNOMED,19647005,Plasma Exchange diff --git a/codes/code_lists/snomed_graft_type.csv b/codes/code_lists/snomed_graft_type.csv deleted file mode 100644 index d3e7e34..0000000 --- a/codes/code_lists/snomed_graft_type.csv +++ /dev/null @@ -1,3 +0,0 @@ -SNOMED,62438007,Pancreas Transplant -SNOMED,70536003,Kidney Transplant -SNOMED,6471000179103,Kidney & Pancreas Transplant diff --git a/codes/code_lists/snomed_malignancy.csv b/codes/code_lists/snomed_malignancy.csv deleted file mode 100644 index 863106a..0000000 --- a/codes/code_lists/snomed_malignancy.csv +++ /dev/null @@ -1,30 +0,0 @@ -SNOMED,254701007,Malignant basal cell neoplasm of skin (disorder) -SNOMED,254651007,Squamous cell carcinoma of skin (disorder) -SNOMED,93655004,Malignant melanoma of skin (disorder) -SNOMED,254837009,Malignant neoplasm of breast (disorder) -SNOMED,363402007,Malignant tumor of esophagus (disorder) -SNOMED,363349007,Malignant tumor of stomach (disorder) -SNOMED,363509000,Malignant tumor of small intestine (disorder) -SNOMED,363418001,Malignant tumor of pancreas (disorder) -SNOMED,363353009,Malignant tumor of gallbladder (disorder) -SNOMED,93870000,Malignant neoplasm of liver (disorder) -SNOMED,363510005,Malignant tumor of large intestine (disorder) -SNOMED,363351006,Malignant tumor of rectum (disorder) -SNOMED,363358000,Malignant tumor of lung (disorder) -SNOMED,363518003,Malignant tumor of kidney (disorder) -SNOMED,399326009,Malignant tumor of urinary bladder (disorder) -SNOMED,399068003,Malignant tumor of prostate (disorder) -SNOMED,363449006,Malignant tumor of testis (disorder) -SNOMED,371973000,Malignant neoplasm of uterus (disorder) -SNOMED,93143009,Leukemia, disease (disorder) -SNOMED,118600007,Malignant lymphoma (disorder) -SNOMED,109989006,Multiple myeloma (disorder) -SNOMED,372062007,Malignant neoplasm of central nervous system (disorder) -SNOMED,363475005,Malignant tumor of spinal cord (disorder) -SNOMED,372063002,Malignant neoplasm of nervous system (disorder) -SNOMED,428061005,Malignant neoplasm of brain (disorder) -SNOMED,363229000,Neoplasm of musculoskeletal system (disorder) -SNOMED,428281000,Malignant neoplasm of bone (disorder) -SNOMED,363495004,Malignant tumor of muscle (disorder) -SNOMED,255056009,Malignant tumor of head and/or neck (disorder) -SNOMED,363346000,Malignant neoplastic disease (disorder) diff --git a/codes/code_lists/snomed_observation.csv b/codes/code_lists/snomed_observation.csv deleted file mode 100644 index 2bd446a..0000000 --- a/codes/code_lists/snomed_observation.csv +++ /dev/null @@ -1,11 +0,0 @@ -SNOMED,27113001,Weight,obs,kg -SNOMED,162755006,Height,obs,cm -SNOMED,301331008,BMI,obs,kg/m^2 -SNOMED,162986007,Pulse,obs,bpm -SNOMED,163030003,Systolic Blood Pressure,obs,mmHg (systolic) -SNOMED,163031004,Diastolic Blood Pressure,obs,mmHg (diastolic) -SNOMED,75367002,Blood Pressure,obs -SNOMED,763264000,Canadian Study of Health and Aging Clinical Frailty Scale score (observable entity),obs -SNOMED,1366111000000102,Kidney Failure Risk Equation (4 Variable ) 2 year risk score (observable entity),obs -SNOMED,1365921000000102,Kidney Failure Risk Equation (4 Variable) 5 year risk score (observable entity),obs -SNOMED,386725007,Body temperature (observable entity),obs diff --git a/codes/code_lists/snomed_relationship.csv b/codes/code_lists/snomed_relationship.csv deleted file mode 100644 index a0aaaa7..0000000 --- a/codes/code_lists/snomed_relationship.csv +++ /dev/null @@ -1,9 +0,0 @@ -SNOMED,1076781000000103,Cadaver donor with donation after brain stem death -SNOMED,1128041000000103,Live related sibling donor -SNOMED,1128051000000100,Live related father donor -SNOMED,1128071000000109,Live related mother donor -SNOMED,1128061000000102,Live related child donor -SNOMED,220751000000102,Live Related Donor -SNOMED,220741000000100,Live Unrelated Donor -SNOMED,1076791000000101,Cadaver donor with donation after cardiac death -SNOMED,105455006,Donor for medical or surgical procedure diff --git a/codes/code_lists/snomed_renal_diagnosis.csv b/codes/code_lists/snomed_renal_diagnosis.csv deleted file mode 100644 index 4c28bde..0000000 --- a/codes/code_lists/snomed_renal_diagnosis.csv +++ /dev/null @@ -1,232 +0,0 @@ -SNOMED,52254009,Nephrotic syndrome -SNOMED,445119005,Steroid sensitive nephrotic syndrome of childhood -SNOMED,48796009,Congenital nephrotic syndrome -SNOMED,197601003,Finnish congenital nephrotic syndrome -SNOMED,722369003,Congenital nephrotic syndrome due to diffuse mesangial sclerosis -SNOMED,236384008,Congenital nephrotic syndrome with focal glomerulosclerosis -SNOMED,236385009,Drash syndrome -SNOMED,722118005,Congenital nephrotic syndrome due to congenital infection -SNOMED,44785005,Minimal change disease -SNOMED,236407003,IgA nephropathy -SNOMED,445404003,Familial immunoglobulin A nephropathy -SNOMED,282364005,IgA nephropathy associated with liver disease -SNOMED,236411009,IgM nephropathy -SNOMED,722119002,Idiopathic membranous glomerulonephritis -SNOMED,722086002,Membranous glomerulonephritis due to malignant neoplastic disease -SNOMED,722120008,Drug-induced membranous glomerulonephritis -SNOMED,722168002,Membranous glomerulonephritis with infectious disease -SNOMED,75888001,"Mesangiocapillary glomerulonephritis, type I " -SNOMED,722760002,"Mesangiocapillary glomerulonephritis, type II " -SNOMED,236409000,Mesangiocapillary glomerulonephritis type III -SNOMED,197697005,Rapidly progressive nephritic syndrome - diffuse crescentic glomerulonephritis -SNOMED,236404005,Classical focal segmental glomerulosclerosis -SNOMED,445388002,Autosomal recessive focal segmental glomerulosclerosis -SNOMED,444977005,Autosomal dominant focal segmental glomerulosclerosis -SNOMED,1269761000000101,Focal segmental glomerulosclerosis (FSGS) secondary to obesity -SNOMED,3704008,Diffuse endocapillary proliferative glomerulonephritis -SNOMED,35546006,Mesangial proliferative glomerulonephritis -SNOMED,83866005,Focal AND segmental proliferative glomerulonephritis -SNOMED, 724599009,Systemic vasculitis - histologically proven -SNOMED,722191003,Antineutrophil cytoplasmic antibody positive vasculitis -SNOMED,195353004,Granulomatosis with polyangiitis -SNOMED,1144805008,Microscopic polyarteritis nodosa -SNOMED,82275008,EGPA - eosinophilic granulomatosis with polyangiitis -SNOMED,155441006,Polyarteritis nodosa -SNOMED,50581000,Goodpasture syndrome -SNOMED,68815009,Lupus nephritis -SNOMED,191306005,Henoch-Schönlein purpura -SNOMED,236502006,Renal involvement in scleroderma -SNOMED,239947001,Essential mixed cryoglobulinemia -SNOMED,128971000119101,Cryoglobulinemia due to chronic hepatitis C -SNOMED,30911005,Cryoglobulinemia -SNOMED,197764002,Non-obstructive reflux-associated chronic pyelonephritis -SNOMED,707208009,Familial non-obstructive reflux-associated chronic pyelonephritis -SNOMED,204949001,Renal dysplasia -SNOMED,737562008,Multicystic dysplastic kidney -SNOMED,710571007,Renal dysplasia due to fetal exposure to angiotensin converting enzyme inhibitor -SNOMED,253864004,"Familial hypoplastic, glomerulocystic kidney" -SNOMED,373584008,Congenital pelviureteric junction obstruction -SNOMED,373585009,Congenital ureterovesical obstruction -SNOMED,253900005,Congenital posterior urethral valves -SNOMED,5187006,Prune belly syndrome -SNOMED,445387007,Congenital neurogenic urinary bladder -SNOMED,61758007,Exstrophy of bladder sequence -SNOMED,253904001,Megacystis-megaureter syndrome -SNOMED,18417009,Oligomeganephronic hypoplasia of kidney -SNOMED,90241004,Papillary necrosis -SNOMED,86249007,Obstructive nephropathy -SNOMED,722078002,Obstructive nephropathy due to neurogenic bladder -SNOMED,722082000,Obstructive nephropathy due to benign prostatic hyperplasia -SNOMED,722081007,Obstructive nephropathy due to carcinoma of prostate -SNOMED,722089009,Obstructive nephropathy due to bladder cancer -SNOMED,722088001,Obstructive nephropathy due to malignancy -SNOMED,197808006,Idiopathic retroperitoneal fibrosis -SNOMED,236017004,Malignant retroperitoneal fibrosis -SNOMED,95566004,Urolithiasis -SNOMED,444717006,Calcium oxalate urolithiasis -SNOMED,37497004,Enteric hyperoxaluria -SNOMED,444690001,Magnesium ammonium phosphate urolithiasis -SNOMED,267441009,Uric acid urolithiasis -SNOMED,428255004,Tubulointerstitial nephritis -SNOMED,83923004,Familial interstitial nephritis -SNOMED,45927004,Immunologic mediated tubulointerstitial nephritis -SNOMED,418839003,Tubulointerstitial nephritis with uveitis syndrome -SNOMED,37061001,Granulomatous sarcoid nephropathy -SNOMED,717770008,Aristolochic acid nephropathy -SNOMED,439990003,Drug-induced tubulointerstitial nephritis -SNOMED,59400006,Analgesic nephropathy -SNOMED,704203009,Nephropathy induced by ciclosporin -SNOMED,704205002,Nephropathy induced by tacrolimus -SNOMED,704206001,Nephropathy induced by aminoglycosides -SNOMED,704055002,Nephropathy induced by amphotericin -SNOMED,53556002,Cis-platinum nephropathy -SNOMED,4390004,Lithium nephropathy -SNOMED,704204003,Nephropathy induced by lead -SNOMED,236496000,Acute urate nephropathy -SNOMED,7725007,Radiation nephritis -SNOMED,197772000,Renal abscess OR Perirenal abscess -SNOMED,44323002,Tuberculosis of kidney -SNOMED,77377001,Leptospirosis -SNOMED,716864001,Haemorrhagic fever with renal syndrome -SNOMED,38898003,Xanthogranulomatous pyelonephritis -SNOMED,713504001,HIV-associated nephropathy -SNOMED,236706006,Urinary schistosomiasis -SNOMED,40733004,Infectious disease -SNOMED,96441000119101,Chronic kidney disease due to type 1 diabetes mellitus -SNOMED,771000119108,Chronic kidney disease due to type 2 diabetes mellitus -SNOMED,38481006,Hypertensive renal disease -SNOMED,65443008,Malignant hypertensive renal disease -SNOMED,445108007,Age related reduction of renal function -SNOMED,710565001,Ischaemic nephropathy -SNOMED,302233006,Renal artery stenosis -SNOMED,51677000,Atheroembolism of renal arteries -SNOMED,783730009,Fibromuscular dysplasia of renal artery -SNOMED,236488005,Renal artery occlusion -SNOMED,15842009,Thrombosis of renal vein -SNOMED,445236007,Cardiorenal syndrome -SNOMED,51292008,Hepatorenal syndrome -SNOMED,48713002,Renal amyloidosis -SNOMED,274945004,AA amyloidosis -SNOMED,23132008,AL amyloidosis -SNOMED,66451004,Familial renal amyloidosis -SNOMED,367528006,Amyloid of familial Mediterranean fever -SNOMED,32278006,Myeloma kidney -SNOMED,373604002,Light chain deposition disease -SNOMED,73305009,Fibrillary glomerulonephritis -SNOMED,373421000,Diarrhea-associated hemolytic uremic syndrome -SNOMED,373422007,Atypical haemolytic uraemic syndrome -SNOMED,78129009,Thrombotic thrombocytopenic purpura -SNOMED, 111407006,Hemolytic uremic syndrome -SNOMED,444976001,Congenital hemolytic uremic syndrome -SNOMED,722721004,Familial haemolytic-uraemic syndrome -SNOMED,373420004,Upshaw-Schulman syndrome -SNOMED,736993008,Nephropathy following eclampsia -SNOMED,13886001,Sickle cell nephropathy -SNOMED,765330003,Autosomal dominant polycystic kidney disease -SNOMED,253878003,Autosomal dominant polycystic kidney disease type 1 -SNOMED,253879006,Autosomal dominant polycystic kidney disease type 2 -SNOMED,28770003,Autosomal recessive polycystic kidney disease -SNOMED,770414008,Alport syndrome -SNOMED,236418003,Thin basement membrane disease -SNOMED, 722223000,Cystic kidney disease -SNOMED,726017001,Medullary cystic kidney disease type 1 -SNOMED,723373006,Medullary cystic kidney disease type 2 -SNOMED,46785007,Familial juvenile hyperuricaemia nephropathy -SNOMED,204958008,Nephronophthisis -SNOMED,444830001,Familial juvenile nephronophthisis -SNOMED,444558002,Infantile nephronophthisis -SNOMED,444749006,Adolescent nephronophthisis -SNOMED,446989009,Juvenile nephronophthisis -SNOMED,446991001,Nephronophthisis type 5 -SNOMED,447335007,Nephronophthisis type 6 -SNOMED,236466005,Congenital Fanconi syndrome -SNOMED,197744007,Renal tubulo-interstitial disorders in metabolic diseases -SNOMED,444645005,Dent's disease -SNOMED,79385002,Lowe syndrome -SNOMED,698953004,Inherited aminoaciduria -SNOMED,85020001,Cystinuria -SNOMED,190681003,Cystinosis -SNOMED,226309007,Familial renal glucosuria -SNOMED,82236004,Familial x-linked hypophosphatemic vitamin D refractory rickets -SNOMED,726080006,Autosomal recessive hypophosphatemic vitamin D refractory rickets -SNOMED,1776003,Renal tubular acidosis -SNOMED,24790002,Proximal renal tubular acidosis -SNOMED,236461000,Distal renal tubular acidosis -SNOMED,722468005,Distal renal tubular acidosis with sensorineural hearing loss (SNHL) -SNOMED,111395007,Nephrogenic diabetes insipidus -SNOMED,10406007,Lesch-Nyhan syndrome -SNOMED,35759001,Phosphoribosyl pyrophosphate synthase superactivity -SNOMED,31742004,Alagille syndrome -SNOMED,707742001,Bartter syndrome -SNOMED,707756004,Gitelman syndrome -SNOMED,707747007,Liddle syndrome -SNOMED,237770005,Syndrome of apparent mineralocorticoid excess -SNOMED,237743003,Glucocorticoid-suppressible hyperaldosteronism -SNOMED,237604008,Diabetes mellitus autosomal dominant type II -SNOMED,43941006,"Pseudohypoaldosteronism, type 1 " -SNOMED,15689008,"Pseudohypoaldosteronism, type 2 " -SNOMED,237885008,Familial hypocalciuric hypercalcemia -SNOMED,711152006,Familial hypercalciuric hypocalcaemia -SNOMED,48655003,Isolated familial renal hypomagnesaemia -SNOMED,17901006,Primary hyperoxaluria -SNOMED,65520001,Primary hyperoxaluria type I -SNOMED,40951006,"Primary hyperoxaluria, type II " -SNOMED,16652001,Fabry's disease -SNOMED,190919008,Xanthinuria -SNOMED,22199006,Nail patella-like renal disease -SNOMED,45582004,Rubinstein-Taybi syndrome -SNOMED,7199000,Tuberous sclerosis syndrome -SNOMED,46659004,Von Hippel-Lindau syndrome -SNOMED,236443009,Medullary sponge kidney -SNOMED,41729002,Horseshoe kidney -SNOMED,445431000,Frasier syndrome -SNOMED,290006,Branchio-oto-renal syndrome -SNOMED,63247009,Williams syndrome -SNOMED,24750000,Townes-Brocks syndrome -SNOMED,5619004,Laurence-Moon syndrome -SNOMED,240096000,Mitochondrial cytopathy -SNOMED,236419006,Familial nephropathy -SNOMED,14669001,Acute kidney injury -SNOMED,1048451000000103,Acute kidney injury due to acute tubular necrosis due to hypovolaemia -SNOMED,1048481000000109,Acute kidney injury due to acute tubular necrosis due to circulatory failure -SNOMED,1048491000000106,Acute kidney injury due to acute tubular necrosis due to sepsis -SNOMED,23697004,Acute kidney injury due to rhabdomyolysis -SNOMED,236428007,Acute kidney injury due to nephrotoxicity -SNOMED,444794000,Acute cortical necrosis -SNOMED,36689008,Acute pyelonephritis -SNOMED,126880001,Neoplasm of kidney -SNOMED,702391001,Renal cell carcinoma -SNOMED,408642003,Transitional cell carcinoma of kidney -SNOMED,302849000,Nephroblastoma -SNOMED,307604008,Mesoblastic nephroma -SNOMED,824131000000108,Solitary kidney -SNOMED,722149000,Chronic kidney disease (CKD) caused by tumour nephrectomy -SNOMED,722467000,Chronic kidney disease due to traumatic loss of kidney -SNOMED,722098007,Chronic kidney disease after donor nephrectomy -SNOMED,709044004,Chronic kidney disease - aetiology uncertain / unknown -SNOMED,449820008,Steroid resistant nephrotic syndrome of childhood -SNOMED,705065000,Childhood nephrotic syndrome -SNOMED,609572000,Renal cysts and diabetes syndrome -SNOMED,190829000,Chronic urate nephropathy -SNOMED,722150000,Chronic kidney disease due to systemic infection -SNOMED,446449009,Renal coloboma syndrome -SNOMED,33763006,Hypercalcemic nephropathy -SNOMED,49120005,Retroperitoneal fibrosis -SNOMED,236015007,Drug-induced retroperitoneal fibrosis -SNOMED,42399005,Renal failure syndrome -SNOMED,90688005,Chronic renal failure syndrome -SNOMED,53298003,Hematuria -SNOMED,53298000,Hematuria syndrome -SNOMED,12491000132101,Proteinuria -SNOMED,734990008,"Primary hyperoxaluria, type III " -SNOMED,36171008,Glomerulonephritis -SNOMED, 713887002,Focal segmental glomerulosclerosis co-occurrent with human immunodeficiency virus infection -SNOMED, 722139003,Focal segmental glomerulosclerosis caused by lithium -SNOMED,722147003,Focal segmental glomerulosclerosis due to sickle cell disease -SNOMED,723074006,Renal papillary necrosis due to diabetes mellitus -SNOMED,722077007,Renal papillary necrosis caused by analgesic drug -SNOMED, 722085003,Renal papillary necrosis due to sickle cell disease -SNOMED, 95570007,Kidney stone -SNOMED,118600007,Malignant lymphoma  -SNOMED,736992003,Nephropathy following pre-eclampsia -SNOMED,6956008,Systemic Vasculitis diff --git a/codes/code_lists/snomed_result.csv b/codes/code_lists/snomed_result.csv deleted file mode 100644 index 482acf0..0000000 --- a/codes/code_lists/snomed_result.csv +++ /dev/null @@ -1,47 +0,0 @@ -SNOMED,1107001000000108,Substance concentration of creatinine in serum -SNOMED,1110281000000107,Substance concentration of urea in serum -SNOMED,1106011000000107,Substance concentration of bicarbonate in serum -SNOMED,1107871000000107,Substance concentration of sodium in serum -SNOMED,1107761000000109,Substance concentration of potassium in serum -SNOMED,1107411000000104,Estimated glomerular filtration rate by laboratory calculation -SNOMED,1109851000000106,Substance concentration of urate in serum -SNOMED,857971000000104,Estimated glomerular filtration rate using Chronic Kidney Disease Epidemiology Collaboration formula -SNOMED,1020291000000106,Glomerular filtration rate calculated by abbreviated Modification of Diet in Renal Disease Study Group calculation -SNOMED,1107711000000107,Substance concentration of phosphate in serum -SNOMED,1106621000000109,Substance concentration of calcium in serum -SNOMED,1107251000000104,Substance concentration of calcium in serum adjusted for albumin -SNOMED,1106051000000106,Enzyme activity of alkaline phosphatase in serum -SNOMED,1105861000000106,Albumin mass concentration in serum -SNOMED,1109581000000102,Mass concentration of parathyroid hormone in serum -SNOMED,1023491000000104,Urine albumin:creatinine ratio -SNOMED,1106541000000101,Substance concentration of cholesterol in serum -SNOMED,1107681000000108,Substance concentration of high density lipoprotein cholesterol in serum -SNOMED,1108551000000102,Substance concentration of low density lipoprotein cholesterol in serum -SNOMED,1109831000000104,Substance concentration of triglyceride in serum -SNOMED,1106741000000105,Mass concentration of C reactive protein in serum -SNOMED,999791000000106,Haemoglobin A1c level - IFCC standardised -SNOMED,1022471000000107,Mean corpuscular haemoglobin -SNOMED,1108041000000107,Platelet count in blood -SNOMED,1110441000000100,White blood cell count in blood -SNOMED,1108611000000102,Mass concentration of ferritin in serum -SNOMED,1111581000000104,Hypochromic red blood cells percent count in blood -SNOMED,1108651000000103,Mass concentration of folate in serum -SNOMED,1108641000000101,Mass concentration of folate in red blood cells -SNOMED,12711000237100,Substance concentration of aluminium in serum -SNOMED,1111311000000103,Mass concentration of tacrolimus in whole blood -SNOMED,1107851000000103,Mass concentration of sirolimus in whole blood -SNOMED,1107021000000104,Mass concentration of cyclosporin in whole blood -SNOMED,1110411000000101,Urea reduction ratio in serum -SNOMED,1107011000000105,Substance concentration of creatinine in urine -SNOMED,1106081000000100,Enzyme activity of alanine aminotransferase in serum -SNOMED,1108071000000101,Neutrophil count in blood -SNOMED,1107961000000106,Lymphocyte count in blood -SNOMED,1111161000000103,Presence of hepatitis B virus core antibody in serum -SNOMED,1111171000000105,Presence of hepatitis B virus surface antigen in serum -SNOMED,1111131000000108,Presence of hepatitis C virus antibody in serum -SNOMED,1111211000000108,Presence of cytomegalovirus antibody in serum -SNOMED,1111341000000102,Presence of human immunodeficiency virus 1 antibody in serum -SNOMED,1111351000000104,Presence of varicella zoster virus antibody in serum -SNOMED,1111041000000100,Presence of Epstein-Barr virus antibody in serum -SNOMED,996101000000106,Epstein-Barr virus viral load -SNOMED,165581004,International normalized ratio diff --git a/codes/code_lists/snomed_units_of_measure.csv b/codes/code_lists/snomed_units_of_measure.csv deleted file mode 100644 index 9b2fcbb..0000000 --- a/codes/code_lists/snomed_units_of_measure.csv +++ /dev/null @@ -1,11 +0,0 @@ -SNOMED,258771000,Deciliters -SNOMED,258682000,Grams -SNOMED,258770004,Litres -SNOMED,258684004,Milligrams -SNOMED,258773002,Milliliters -SNOMED,258718000,Millimols -SNOMED,258686002,Nanograms -SNOMED,767524001,Other - please specify in comments -SNOMED,428673006,Tablets -SNOMED,258997004,International Units (i.e. for Epoetins) -SNOMED,258685003,Micro-grams diff --git a/codes/code_lists/survey_questions.csv b/codes/code_lists/survey_questions.csv deleted file mode 100644 index 5805a46..0000000 --- a/codes/code_lists/survey_questions.csv +++ /dev/null @@ -1,28 +0,0 @@ -YOUR_HEALTH,YOHQ1 -YOUR_HEALTH,YOHQ2 -YOUR_HEALTH,YOHQ3 -YOUR_HEALTH,YOHQ4 -YOUR_HEALTH,YOHQ5 -YOUR_HEALTH,YOHQ6 -YOUR_HEALTH,YSQ1 -YOUR_HEALTH,YSQ10 -YOUR_HEALTH,YSQ11 -YOUR_HEALTH,YSQ12 -YOUR_HEALTH,YSQ13 -YOUR_HEALTH,YSQ14 -YOUR_HEALTH,YSQ15 -YOUR_HEALTH,YSQ16 -YOUR_HEALTH,YSQ17 -YOUR_HEALTH,YSQ18 -YOUR_HEALTH,YSQ19 -YOUR_HEALTH,YSQ2 -YOUR_HEALTH,YSQ20 -YOUR_HEALTH,YSQ21 -YOUR_HEALTH,YSQ22 -YOUR_HEALTH,YSQ3 -YOUR_HEALTH,YSQ4 -YOUR_HEALTH,YSQ5 -YOUR_HEALTH,YSQ6 -YOUR_HEALTH,YSQ7 -YOUR_HEALTH,YSQ8 -YOUR_HEALTH,YSQ9 diff --git a/codes/code_lists/survey_types.csv b/codes/code_lists/survey_types.csv deleted file mode 100644 index 118ac2d..0000000 --- a/codes/code_lists/survey_types.csv +++ /dev/null @@ -1,4 +0,0 @@ -SURVEY,EQ5D -SURVEY,PROM -SURVEY,PAM -SURVEY,PREM diff --git a/codes/code_lists/ukrr_observations.csv b/codes/code_lists/ukrr_observations.csv deleted file mode 100644 index f4ea78e..0000000 --- a/codes/code_lists/ukrr_observations.csv +++ /dev/null @@ -1,61 +0,0 @@ -UKRR,QBLA1,Serum Creatinine,result,umol/L -UKRR,QBLA3,Serum Urea,result,mmol/L -UKRR,QBLA4,Serum Bicarbonate,result,mmol/L -UKRR,QBLA6,Serum Sodium,result,mmol/L -UKRR,QBLA9,Serum Potassium,result,mmol/L -UKRR,QBLAB,Lab Calculated eGFR,result,mL/min/1.72m^2 -UKRR,QBLAC,Serum Uric Acid (Urate),result,mmol/L -UKRR,QBLAL,Unit Calculated eGFR,result,mL/min/1.72m^2 -UKRR,QBLB1,Serum Phosphate,result,mmol/L -UKRR,QBLB3,Serum Calcium,result,mmol/L -UKRR,QBLB4,Corrected Serum Calcium,result,mmol/L -UKRR,QBLB5,Serum Alkaline Phosphatase,result,IU/L -UKRR,QBLB7,Serum Albumin,result,g/L -UKRR,QBLB9,Serum Parathyroid Hormone (PTH),result,pmol/L -UKRR,QBLC1,Urine Protein:Creatinine Ratio,result,mg/mmol -UKRR,QBLC3,Urine Albumin:Creatinine Ratio,result,mg/mmol -UKRR,QBLD1,Total Serium Cholesterol,result,mmol/L -UKRR,QBLD3,Serum HDL Cholesterol,result,mmol/L -UKRR,QBLD4,Serum LDL Cholesterol,result,mmol/L -UKRR,QBLD5,Serum Triglycerides,result,mmol/L -UKRR,QBLD6,CRP,result,mg/L -UKRR,QBLD8,Hba1c %,result,% -UKRR,QBLDA,Hba1c,result,mmol/mol -UKRR,QBLE1,Haemoglobin,result,g/dL -UKRR,QBLE3,MCH,result,g/dL -UKRR,QBLE4,Platelets,result,10^9/L -UKRR,QBLE5,WBC (from full blood count),result,10^9/L -UKRR,QBLEB,Haemloglobin,result,g/L -UKRR,QBLF1,Serum Ferritin,result,ug/L = ng/ml -UKRR,QBLF3,Transferrin Saturation,result,% -UKRR,QBLF5,Percentage of Hypochromic Cells,result,% -UKRR,QBLF7,Serum B12,result,ng/L -UKRR,QBLF9,Serum Folate,result,ug/L -UKRR,QBLFB,Red Cell Folate,result,ug/L -UKRR,QBLFD,Serum Aluminium,result,umol/L -UKRR,QBLFF,Tacrolimus Blood Concentration Level,result,ng/mL -UKRR,QBLFH,Sirolimus Blood Concentration Level,result,ng/mL -UKRR,QBLFK,Ciclosporin Blood Concentration Level,result,ng/mL -UKRR,QBLFM,Mycophenolate Blood Concentration Level,result,ng/mL -UKRR,QBLG1,Weight,observation,kg -UKRR,QBLG3,Systolic BP,observation,mmHg -UKRR,QBLG4,Diastolic BP,observation,mmHg -UKRR,QBLG9,Urea Reduction Ratio,result, -UKRR,QBLGG,Kt/V,result, -UKRR,QBLGB,Height,observation,cm -UKRR,QBLHA,HBV Antibody Status,result, -UKRR,QBLHC,HBV Surface Antigen Status,result, -UKRR,QBLHE,HCV Antibody Status,result, -UKRR,QBLHG,CMV Antibody Status,result, -UKRR,QBLHK,CMV PCR Copies/ML,result,IU/mL -UKRR,QBLHM,HIV Antigen Status,result, -UKRR,QBLHN,Varicella,result, -UKRR,QBLHR,EBV Status,result, -UKRR,QBLHS,EBV Log Count,result, -UKRR,QBLHV,Urine Volume in 24 Hours,observation,ml -UKRR,QBLHX,Urinary Creatinine Excretion,result,mmol/L -UKRR,QBLPA,PTH ULN,result,pmol/L -UKRR,QBLPB,PTH / PTHH ULN Ratio,result, -UKRR,QBLPC,ALT,result,IU/L -UKRR,QBLPD,ANC,result,10^9/L -UKRR,QBLPE,ALC,result,10^9/L diff --git a/codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv b/codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv deleted file mode 100644 index 4d88fcd..0000000 --- a/codes/code_lists/ukrr_testcodes_to_gl_mmoll_ratio.csv +++ /dev/null @@ -1,7 +0,0 @@ -Coding_Standard,Code,Value -RATIO,QBLA1,8.841 -RATIO,QBLA3,16.65 -RATIO,QBLA6,43.48 -RATIO,QBLA9,25.7 -RATIO,QBLB9,9.5 -RATIO,QBLF7,1.355 \ No newline at end of file diff --git a/codes/code_lists/ukt3.csv b/codes/code_lists/ukt3.csv deleted file mode 100644 index cbbe869..0000000 --- a/codes/code_lists/ukt3.csv +++ /dev/null @@ -1,2 +0,0 @@ -UKT3,K,Kidney -UKT3,KP,Kidney & Pancreas diff --git a/codes/code_lists/ukt4.csv b/codes/code_lists/ukt4.csv deleted file mode 100644 index 71504d7..0000000 --- a/codes/code_lists/ukt4.csv +++ /dev/null @@ -1,14 +0,0 @@ -UKT4,A,Active -UKT4,DA,Died while Active -UKT4,DS,Died while Suspended -UKT4,L,Live Transplant -UKT4,LA,Live Transplant while Active -UKT4,LS,Live Transplant while Suspended -UKT4,RA,Removed from Active -UKT4,RS,Removed from Suspended -UKT4,S,Suspended -UKT4,SA,Suspended from Active -UKT4,T,Transplanted -UKT4,TA,Transplanted while Active -UKT4,TR,Transplanted when Removed -UKT4,TS,Transplanted while Suspended diff --git a/codes/satellite_map/satellite_map.csv b/codes/satellite_map/satellite_map.csv deleted file mode 100644 index 070d7ac..0000000 --- a/codes/satellite_map/satellite_map.csv +++ /dev/null @@ -1,226 +0,0 @@ -RH840,RH8 -9RH05,RH8 -RH8G3,RH8 -9RH06,RH8 -RBZ19,RH8 -9RA911,RH8 -RH802,RH8 -RJ230,RJ121 -TAF21,RJ121 -99RJ121,RJ121 -98CJ06,RJ121 -9RJ121,RJ121 -RJ224,RJ121 -9RPD01,RJ121 -98A713,RJ121 -8RJ121,RJ121 -9RH641,RH641 -9RTQ,RH641 -RL109,RKHA4 -RNLBX,RLGAY -RRBBW,RRBBV -RKM,RRBBV -XXX03,RRBBV -XXX02,RRBBV -9RVEB1,RRBBV -XXX01,RRBBV -99RRBBV,RRBBV -RRS,RRBBV -RDDH1,RDDH0 -9RNA,RNA03 -9RWP31,RNA03 -RBBP3,REE01 -9RH01,REE01 -RD1,REE01 -9RVJ21,REE01 -9RA743,REE01 -RA301,REE01 -9RH02,REE01 -9REE01,REE01 -9RJH01,RL7 -99RL7,RL7 -RNG10,RL7 -RL301,RL7 -9RBD01,RBD01 -9RH03,RBD01 -RDZ00,RBD01 -RRE01,RJE01 -RBT20,RJE01 -99RJ701,RJ701 -9RJ701,RJ701 -98RQY,RJ701 -98RJ701,RJ701 -RFZ20,RQN02 -RTK02,RQN02 -RWG02,RQN02 -RAU31,RQN02 -RFW01,RQN02 -RYJ03,RQN02 -RDA03,RQN02 -RC368,RQN02 -9RCF31,RAE05 -RKZDA,RFBAK -RGN,RFBAK -RFBAT,RFBAK -9RWDLB,RFBAK -RNQ51,RFBAK -RT5DC,RFBAK -9RP7LA,RFBAK -9RFBAK,RFBAK -9RWD,RFBAK -98RFBAK,RFBAK -99RFBAK,RFBAK -RY5K7,RFBAK -P7U2H,RFBAK -9RKD,RHU02 -99RHU02,RHU02 -RDZ15,RHU02 -9RN506,RHU02 -RHS55,RHU02 -RR201,RHU02 -RPK40,RHU02 -RNZ02,RHU02 -9RFU,RAQ01 -RQW,RAQ01 -RC971,RAQ01 -RPW02,RAQ01 -REF01,REF12 -RJ866,REF12 -9RF201,RF201 -RJL,RF201 -RF832,RF201 -9RLNGH,RLNGH -RR9,RLNGH -RJC03,RKB01 -RKB03,RKB01 -RLT01,RKB01 -RJC46,RKB01 -9RQY,RAZ -99RAZ,RAZ -RJ6,RAZ -RTP02,RAZ -9RXX,RAZ -9RAZ,RAZ -99RXX,RAZ -RG303A,RAZ -RVV20,RVVKC -RVVMA,RVVKC -RPA,RVVKC -RVV11,RVVKC -RPC20,RVVKC -9RQBAU,RQBAU -RW5CA,RMF01 -RMB05,RMF01 -RXR01,RMF01 -RXL06,RMF01 -RJU01,RMF01 -RE5BW,RMF01 -RP5BA,RP5 -RP5MM,RP5 -99RJZ,RJZ -RJZW,RJZ -98RJZ,RJZ -9RJZ,RJZ -RN7,RJZ -RXJ06,RJZ -RG222,RJZ -R7Y4J,RJZ -88A713,RJZ -RKTAG,RQHC7 -RKUAJ,RQHC7 -RR6BL,RQHC7 -RGQ03,RGQ02 -RRE14,RL403 -9RL403,RL403 -9RBK,RL403 -9RNA3,RL403 -9RK7CC,RK7CC -RFSDA,RK7CC -RFRPA,RK7CC -RFRAA,RK7CC -9RWX,RHW01 -9RH108,RHW01 -RXC02,RGU01 -9RTP02,RGU01 -RDM03,RGU01 -RPL04,RGU01 -RVL07,RAL01 -98TAF,RAL01 -9RAL01,RAL01 -9TAF,RAL01 -RVL01,RAL01 -RAPNM,RAL01 -8A713,RAL01 -RCC25,RCB55 -RCB23,RCB55 -RCD35,RCB55 -9RBN01,RQ617 -RQ601,RQ617 -RKC81,RQ617 -RBN63,RQ617 -RQQ31,RGT01 -RGR50,RGT01 -RCX01,RGT01 -RBL20,RBL14 -RJR05,RBL14 -RM131,RM102 -RGP75,RM102 -REM26,RW402 -9RW402,RW402 -RVY01,RW402 -RTRNT,RCJAT -9RCJAT,RCJAT -RLBCH,RCJAT -RXWAT,RLZ01 -REFWW,RK950 -R1G55,RK950 -9RJ866,RK950 -8RA911,RK950 -9RWJ,RM574 -RW602,RM574 -RM202,RM574 -RM403,RM574 -9RXV06,RM574 -RJN71,RM574 -RMP01,RM574 -RTD03,RTD01 -RF4DG,RNJ00 -RGCNH,RNJ00 -RGCKH,RNJ00 -9RNJ00,RNJ00 -RWL25,RRK02 -98RRK02,RRK02 -9RRK02,RRK02 -RLW01,RRK02 -9RNA2,RRK02 -RWP31,RRK02 -RLQ02,RRK02 -99RRK02,RRK02 -9RLQ02,RRK02 -97RRK02,RRK02 -98RBK,RRK02 -9RNG2,RRK02 -RXQ50,RNX02 -RVNCA,RNX02 -RBF33,RNX02 -RXQ02,RNX02 -RD816,RNX02 -RMW10,RQR13 -RQR14,RQR13 -9RQR13,RQR13 -RGA02,RQR13 -RXF03,RQR13 -RGB04,RQR13 -9RQR14,RQR13 -REZ02,RM301 -7RM301,RM301 -9RM301,RM301 -RMC00,RM301 -RHANN,RCSLB -9RCSLB,RCSLB -RX1RA,RCSLB -RXM56,RCSLB -RFJBC,RCSLB -RTG54,RFPFG -RJE55,RFPFG -RTG05,RFPFG From 7de53210a94733c4b7b5b186e73c55d3a77f25e8 Mon Sep 17 00:00:00 2001 From: Marta Badji <145134861+martabadji@users.noreply.github.com> Date: Mon, 9 Feb 2026 11:10:49 +0000 Subject: [PATCH 165/166] Delete codes/code_conv_lists/snomed_unofficial_to_edta2.csv moved to https://github.com/renalreg/registry-codes --- .../code_conv_lists/snomed_unofficial_to_edta2.csv | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 codes/code_conv_lists/snomed_unofficial_to_edta2.csv diff --git a/codes/code_conv_lists/snomed_unofficial_to_edta2.csv b/codes/code_conv_lists/snomed_unofficial_to_edta2.csv deleted file mode 100644 index 712ab93..0000000 --- a/codes/code_conv_lists/snomed_unofficial_to_edta2.csv +++ /dev/null @@ -1,13 +0,0 @@ -SNOMED, 111411000119103, EDTA2, 2359 -SNOMED, 236403004, EDTA2, 1267 -SNOMED, 68779003, EDTA2, 1116 -SNOMED, 285841000119104, EDTA2, 2371 -SNOMED, 90791000119104, EDTA2, 2337 -SNOMED, 308751000119106, EDTA2, 1486 -SNOMED, 104931000119100, EDTA2, 2359 -SNOMED, 236398000, EDTA2, 1251 -SNOMED, 722278006, EDTA2, 3419 -SNOMED, 711000119100, EDTA2, 2337 -SNOMED, 717742006, EDTA2, 1625 -SNOMED, 788613004, EDTA2, 1464 -SNOMED, 86211000119102, EDTA2, 1602 From 18c6e1cd29b670eb53ea88f0d0d3a059a00c9709 Mon Sep 17 00:00:00 2001 From: OliveraReeves <158471173+OliveraReeves@users.noreply.github.com> Date: Tue, 17 Mar 2026 11:58:39 +0000 Subject: [PATCH 166/166] updated action versions (#38) * updated action versions --- .github/workflows/docs.yml | 4 ++-- .github/workflows/schema.yml | 8 ++++---- .github/workflows/scripts.yml | 4 ++-- .github/workflows/validate_samples.yml | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f16715e..1971fdf 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -8,10 +8,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 diff --git a/.github/workflows/schema.yml b/.github/workflows/schema.yml index 099fd8b..ef86799 100644 --- a/.github/workflows/schema.yml +++ b/.github/workflows/schema.yml @@ -9,10 +9,10 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 @@ -48,10 +48,10 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index 7f12f0b..3bbfd8d 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -11,10 +11,10 @@ jobs: working-directory: scripts steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.8 diff --git a/.github/workflows/validate_samples.yml b/.github/workflows/validate_samples.yml index d54b2cc..2cd1c6b 100644 --- a/.github/workflows/validate_samples.yml +++ b/.github/workflows/validate_samples.yml @@ -8,10 +8,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9