Andrew Charlwood
bb93c1673e
archive/ — unused reference files (no active code references): - LookupSearchTermCleanedDrugName.csv, condition_directorate_mapping.csv - na_directory_rows.csv (diagnostic output), ta-recommendations.xlsx - snomed_indication_mapping_query.sql (source for embedded SQL) - IMPROVEMENT_RECOMMENDATIONS.md, power query.pq archive/can_delete/ — legacy code and logs safe to remove: - dashboard_gui.py (replaced by Reflex app) - pathways_app_old.py.bak (old backup) - Ralph loop iteration logs (iterations 2-8)
187 lines
8.6 KiB
SQL
187 lines
8.6 KiB
SQL
-- NICE TA Indication SNOMED Mapping Query (v2 - optimized clusters)
|
|
-- Excludes overly broad clusters (GDPPR_COD, GDPPR2YR_COD)
|
|
|
|
WITH SearchTermClusters AS (
|
|
SELECT Search_Term, Cluster_ID FROM (VALUES
|
|
('acute lymphoblastic leukaemia', 'HAEMCANMORPH_COD'),
|
|
('acute myeloid leukaemia', 'C19HAEMCAN_COD'),
|
|
('acute promyelocytic leukaemia', 'HAEMCANMORPH_COD'),
|
|
('allergic asthma', 'AST_COD'),
|
|
('allergic rhinitis', 'MILDINTAST_COD'),
|
|
('alzheimer''s disease', 'DEMALZ_COD'),
|
|
('amyloidosis', 'AMYLOID_COD'),
|
|
('anaemia', 'eFI2_AnaemiaTimeSensitive'),
|
|
('anaplastic large cell lymphoma', 'C19HAEMCAN_COD'),
|
|
('apixaban', 'DOACCON_COD'),
|
|
('aplastic anaemia', 'eFI2_AnaemiaEver'),
|
|
('arthritis', 'eFI2_InflammatoryArthritis'),
|
|
('asthma', 'eFI2_Asthma'),
|
|
('atopic dermatitis', 'ATOPDERM_COD'),
|
|
('atrial fibrillation', 'eFI2_AtrialFibrillation'),
|
|
('attention deficit hyperactivity disorder', 'ADHD_COD'),
|
|
('bipolar disorder', 'MH_COD'),
|
|
('bladder', 'eFI2_UrinaryIncontinence'),
|
|
('breast cancer', 'BRCANSCR_COD'),
|
|
('cardiomyopathy', 'eFI2_HarmfulDrinking'),
|
|
('cardiovascular disease', 'CVDRISKASS_COD'),
|
|
('cervical cancer', 'CSDEC_COD'),
|
|
('cholangiocarcinoma', 'eFI2_Cancer'),
|
|
('chronic kidney disease', 'CKD_COD'),
|
|
('chronic liver disease', 'eFI2_LiverProblems'),
|
|
('chronic lymphocytic leukaemia', 'EPPHAEMCAN_COD'),
|
|
('chronic myeloid leukaemia', 'EPPHAEMCAN_COD'),
|
|
('chronic obstructive pulmonary disease', 'eFI2_COPD'),
|
|
('colon cancer', 'eFI2_Cancer'),
|
|
('colorectal cancer', 'GICANREF_COD'),
|
|
('constipation', 'CHRONCONSTIP_COD'),
|
|
('covid-19', 'POSSPOSTCOVID_COD'),
|
|
('crohn''s disease', 'eFI2_InflammatoryBowelDisease'),
|
|
('cutaneous t-cell lymphoma', 'C19HAEMCAN_COD'),
|
|
('cystic fibrosis', 'CUST_ICB_CYSTIC_FIBROSIS'),
|
|
('deep vein thrombosis', 'VTE_COD'),
|
|
('depression', 'eFI2_Depression'),
|
|
('diabetes', 'eFI2_DiabetesEver'),
|
|
('diabetic retinopathy', 'DRSELIGIBILITY_COD'),
|
|
('diffuse large b-cell lymphoma', 'C19HAEMCAN_COD'),
|
|
('dravet syndrome', 'EPIL_COD'),
|
|
('drug misuse', 'ILLSUBINT_COD'),
|
|
('dyspepsia', 'eFI2_AbdominalPain'),
|
|
('epilepsy', 'eFI2_Seizures'),
|
|
('fallopian tube', 'STERIL_COD'),
|
|
('follicular lymphoma', 'C19HAEMCAN_COD'),
|
|
('gastric cancer', 'eFI2_Cancer'),
|
|
('giant cell arteritis', 'GCA_COD'),
|
|
('glioma', 'NHAEMCANMORPH_COD'),
|
|
('gout', 'eFI2_InflammatoryArthritis'),
|
|
('graft versus host disease', 'GVHD_COD'),
|
|
('granulomatosis with polyangiitis', 'WEGENERVASC_COD'),
|
|
('growth hormone deficiency', 'HYPOPITUITARY_COD'),
|
|
('hand eczema', 'ECZEMA_COD'),
|
|
('heart failure', 'eFI2_HeartFailure'),
|
|
('hepatitis b', 'HEPBCVAC_COD'),
|
|
('hepatocellular carcinoma', 'eFI2_Cancer'),
|
|
('hiv', 'PREFLANG_COD'),
|
|
('hodgkin lymphoma', 'HAEMCANMORPH_COD'),
|
|
('hormone receptor', 'eFI2_ThyroidProblems'),
|
|
('hypercholesterolaemia', 'CLASSFH_COD'),
|
|
('immune thrombocytopenia', 'ITP_COD'),
|
|
('influenza', 'FLUINVITE_COD'),
|
|
('insomnia', 'eFI2_SleepProblems'),
|
|
('irritable bowel syndrome', 'IBS_COD'),
|
|
('ischaemic stroke', 'OSTR_COD'),
|
|
('juvenile idiopathic arthritis', 'RARTHAD_COD'),
|
|
('kidney transplant', 'RENALTRANSP_COD'),
|
|
('leukaemia', 'eFI2_Cancer'),
|
|
('lung cancer', 'FTCANREF_COD'),
|
|
('lymphoma', 'C19HAEMCAN_COD'),
|
|
('macular degeneration', 'CUST_ICB_VISUAL_IMPAIRMENT'),
|
|
('macular oedema', 'CUST_ICB_VISUAL_IMPAIRMENT'),
|
|
('major depressive episodes', 'eFI2_Depression'),
|
|
('malignant melanoma', 'eFI2_Cancer'),
|
|
('malignant pleural mesothelioma', 'LUNGCAN_COD'),
|
|
('manic episode', 'MH_COD'),
|
|
('mantle cell lymphoma', 'HAEMCANMORPH_COD'),
|
|
('melanoma', 'eFI2_Cancer'),
|
|
('merkel cell carcinoma', 'C19CAN_COD'),
|
|
('migraine', 'eFI2_Headache'),
|
|
('motor neurone disease', 'MND_COD'),
|
|
('multiple myeloma', 'C19HAEMCAN_COD'),
|
|
('multiple sclerosis', 'MS_COD'),
|
|
('myelodysplastic', 'eFI2_AnaemiaEver'),
|
|
('myelofibrosis', 'MDS_COD'),
|
|
('myocardial infarction', 'eFI2_IschaemicHeartDisease'),
|
|
('myotonia', 'CNDATRISK2_COD'),
|
|
('narcolepsy', 'LD_COD'),
|
|
('neuroendocrine tumour', 'LUNGCAN_COD'),
|
|
('non-small cell lung cancer', 'LUNGCAN_COD'),
|
|
('non-small-cell lung cancer', 'FTCANREF_COD'),
|
|
('obesity', 'BMI30_COD'),
|
|
('osteoarthritis', 'CUST_ICB_OSTEOARTHRITIS'),
|
|
('osteoporosis', 'eFI2_Osteoporosis'),
|
|
('osteosarcoma', 'NHAEMCANMORPH_COD'),
|
|
('ovarian cancer', 'C19CAN_COD'),
|
|
('peripheral arterial disease', 'PADEXC_COD'),
|
|
('plaque psoriasis', 'PSORIASIS_COD'),
|
|
('polycystic kidney disease', 'EPPCONGMALF_COD'),
|
|
('polycythaemia vera', 'C19HAEMCAN_COD'),
|
|
('pregnancy', 'C19PREG_COD'),
|
|
('primary biliary cholangitis', 'eFI2_LiverProblems'),
|
|
('primary hypercholesterolaemia', 'FNFHYP_COD'),
|
|
('prostate cancer', 'EPPSOLIDCAN_COD'),
|
|
('psoriasis', 'PSORIASIS_COD'),
|
|
('psoriatic arthritis', 'RARTHAD_COD'),
|
|
('pulmonary embolism', 'eFI2_RespiratoryDiseaseTimeSensitive'),
|
|
('pulmonary fibrosis', 'ILD_COD'),
|
|
('relapsing multiple sclerosis', 'MS_COD'),
|
|
('renal cell carcinoma', 'C19CAN_COD'),
|
|
('renal transplantation', 'RENALTRANSP_COD'),
|
|
('retinal vein occlusion', 'CUST_ICB_VISUAL_IMPAIRMENT'),
|
|
('rheumatoid arthritis', 'eFI2_InflammatoryArthritis'),
|
|
('rivaroxaban', 'DOACCON_COD'),
|
|
('schizophrenia', 'MH_COD'),
|
|
('seizures', 'LSZFREQ_COD'),
|
|
('sepsis', 'C19ACTIVITY_COD'),
|
|
('severe persistent allergic asthma', 'SEVAST_COD'),
|
|
('sickle cell disease', 'SICKLE_COD'),
|
|
('sleep apnoea', 'CUST_ICB_NON_SEVERE_LDA'),
|
|
('smoking cessation', 'SMOKINGINT_COD'),
|
|
('soft tissue sarcoma', 'NHAEMCANMORPH_COD'),
|
|
('spinal muscular atrophy', 'MND_COD'),
|
|
('squamous cell', 'C19CAN_COD'),
|
|
('squamous cell carcinoma', 'C19CAN_COD'),
|
|
('stem cell transplant', 'ALLOTRANSP_COD'),
|
|
('stroke', 'eFI2_Stroke'),
|
|
('systemic lupus erythematosus', 'SLUPUS_COD'),
|
|
('systemic mastocytosis', 'HAEMCANMORPH_COD'),
|
|
('thrombocytopenic purpura', 'TTP_COD'),
|
|
('thrombotic thrombocytopenic purpura', 'TTP_COD'),
|
|
('thyroid cancer', 'C19CAN_COD'),
|
|
('tophaceous gout', 'CUST_ICB_OSTEOARTHRITIS'),
|
|
('transitional cell carcinoma', 'C19CAN_COD'),
|
|
('type 1 diabetes', 'DMTYPE1_COD'),
|
|
('type 2 diabetes', 'DMTYPE2_COD'),
|
|
('ulcerative colitis', 'eFI2_InflammatoryBowelDisease'),
|
|
('urothelial carcinoma', 'NHAEMCANMORPH_COD'),
|
|
('urticaria', 'XSAL_COD'),
|
|
('uveitis', 'CUST_ICB_VISUAL_IMPAIRMENT'),
|
|
('vascular disease', 'CVDINVITE_COD'),
|
|
('vasculitis', 'CRYOGLOBVASC_COD')
|
|
) AS t(Search_Term, Cluster_ID)
|
|
),
|
|
|
|
ClusterCodes AS (
|
|
SELECT
|
|
stc.Search_Term,
|
|
c."SNOMEDCode",
|
|
c."SNOMEDDescription"
|
|
FROM SearchTermClusters stc
|
|
JOIN DATA_HUB.PHM."ClinicalCodingClusterSnomedCodes" c
|
|
ON stc.Cluster_ID = c."Cluster_ID"
|
|
WHERE c."SNOMEDCode" IS NOT NULL
|
|
),
|
|
|
|
ExplicitCodes AS (
|
|
SELECT Search_Term, SNOMEDCode, SNOMEDDescription FROM (VALUES
|
|
('acute coronary syndrome', '837091000000100', 'Manual mapping'),
|
|
('ankylosing spondylitis', '162930007', 'Manual mapping'),
|
|
('ankylosing spondylitis', '239805001', 'Manual mapping'),
|
|
('ankylosing spondylitis', '239810002', 'Manual mapping'),
|
|
('ankylosing spondylitis', '239811003', 'Manual mapping'),
|
|
('ankylosing spondylitis', '394990003', 'Manual mapping'),
|
|
('ankylosing spondylitis', '429712009', 'Manual mapping'),
|
|
('ankylosing spondylitis', '441562009', 'Manual mapping'),
|
|
('ankylosing spondylitis', '441680005', 'Manual mapping'),
|
|
('ankylosing spondylitis', '441930001', 'Manual mapping'),
|
|
('axial spondyloarthritis', '723116002', 'Manual mapping'),
|
|
('choroidal neovascularisation', '380621000000102', 'Manual mapping'),
|
|
('choroidal neovascularisation', '733124000', 'Manual mapping')
|
|
) AS t(Search_Term, SNOMEDCode, SNOMEDDescription)
|
|
)
|
|
|
|
SELECT Search_Term, "SNOMEDCode" AS SNOMEDCode, "SNOMEDDescription" AS SNOMEDDescription
|
|
FROM ClusterCodes
|
|
UNION ALL
|
|
SELECT Search_Term, SNOMEDCode, SNOMEDDescription
|
|
FROM ExplicitCodes
|
|
ORDER BY Search_Term, SNOMEDCode;
|