Andrew Charlwood
a31907aa1f
- Remove app_v2.py (consolidated into pathways_app.py), fix __init__ import - Add DimSearchTerm.csv, drug_indication_clusters.csv, drug_snomed_mapping_enriched.csv as reference data for SNOMED-based indication matching - Add snomed_indication_mapping_query.sql (source for embedded cluster mapping) - Update DESIGN_SYSTEM.md, RALPH_PROMPT.md, ralph.ps1, uv.lock
187 lines
8.6 KiB
SQL
187 lines
8.6 KiB
SQL
-- NICE TA Indication SNOMED Mapping Query (v2 - optimized clusters)
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-- Excludes overly broad clusters (GDPPR_COD, GDPPR2YR_COD)
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WITH SearchTermClusters AS (
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SELECT Search_Term, Cluster_ID FROM (VALUES
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('acute lymphoblastic leukaemia', 'HAEMCANMORPH_COD'),
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('acute myeloid leukaemia', 'C19HAEMCAN_COD'),
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('acute promyelocytic leukaemia', 'HAEMCANMORPH_COD'),
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('allergic asthma', 'AST_COD'),
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('allergic rhinitis', 'MILDINTAST_COD'),
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('alzheimer''s disease', 'DEMALZ_COD'),
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('amyloidosis', 'AMYLOID_COD'),
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('anaemia', 'eFI2_AnaemiaTimeSensitive'),
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('anaplastic large cell lymphoma', 'C19HAEMCAN_COD'),
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('apixaban', 'DOACCON_COD'),
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('aplastic anaemia', 'eFI2_AnaemiaEver'),
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('arthritis', 'eFI2_InflammatoryArthritis'),
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('asthma', 'eFI2_Asthma'),
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('atopic dermatitis', 'ATOPDERM_COD'),
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('atrial fibrillation', 'eFI2_AtrialFibrillation'),
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('attention deficit hyperactivity disorder', 'ADHD_COD'),
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('bipolar disorder', 'MH_COD'),
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('bladder', 'eFI2_UrinaryIncontinence'),
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('breast cancer', 'BRCANSCR_COD'),
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('cardiomyopathy', 'eFI2_HarmfulDrinking'),
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('cardiovascular disease', 'CVDRISKASS_COD'),
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('cervical cancer', 'CSDEC_COD'),
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('cholangiocarcinoma', 'eFI2_Cancer'),
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('chronic kidney disease', 'CKD_COD'),
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('chronic liver disease', 'eFI2_LiverProblems'),
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('chronic lymphocytic leukaemia', 'EPPHAEMCAN_COD'),
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('chronic myeloid leukaemia', 'EPPHAEMCAN_COD'),
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('chronic obstructive pulmonary disease', 'eFI2_COPD'),
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('colon cancer', 'eFI2_Cancer'),
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('colorectal cancer', 'GICANREF_COD'),
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('constipation', 'CHRONCONSTIP_COD'),
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('covid-19', 'POSSPOSTCOVID_COD'),
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('crohn''s disease', 'eFI2_InflammatoryBowelDisease'),
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('cutaneous t-cell lymphoma', 'C19HAEMCAN_COD'),
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('cystic fibrosis', 'CUST_ICB_CYSTIC_FIBROSIS'),
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('deep vein thrombosis', 'VTE_COD'),
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('depression', 'eFI2_Depression'),
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('diabetes', 'eFI2_DiabetesEver'),
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('diabetic retinopathy', 'DRSELIGIBILITY_COD'),
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('diffuse large b-cell lymphoma', 'C19HAEMCAN_COD'),
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('dravet syndrome', 'EPIL_COD'),
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('drug misuse', 'ILLSUBINT_COD'),
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('dyspepsia', 'eFI2_AbdominalPain'),
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('epilepsy', 'eFI2_Seizures'),
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('fallopian tube', 'STERIL_COD'),
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('follicular lymphoma', 'C19HAEMCAN_COD'),
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('gastric cancer', 'eFI2_Cancer'),
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('giant cell arteritis', 'GCA_COD'),
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('glioma', 'NHAEMCANMORPH_COD'),
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('gout', 'eFI2_InflammatoryArthritis'),
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('graft versus host disease', 'GVHD_COD'),
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('granulomatosis with polyangiitis', 'WEGENERVASC_COD'),
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('growth hormone deficiency', 'HYPOPITUITARY_COD'),
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('hand eczema', 'ECZEMA_COD'),
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('heart failure', 'eFI2_HeartFailure'),
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('hepatitis b', 'HEPBCVAC_COD'),
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('hepatocellular carcinoma', 'eFI2_Cancer'),
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('hiv', 'PREFLANG_COD'),
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('hodgkin lymphoma', 'HAEMCANMORPH_COD'),
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('hormone receptor', 'eFI2_ThyroidProblems'),
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('hypercholesterolaemia', 'CLASSFH_COD'),
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('immune thrombocytopenia', 'ITP_COD'),
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('influenza', 'FLUINVITE_COD'),
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('insomnia', 'eFI2_SleepProblems'),
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('irritable bowel syndrome', 'IBS_COD'),
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('ischaemic stroke', 'OSTR_COD'),
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('juvenile idiopathic arthritis', 'RARTHAD_COD'),
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('kidney transplant', 'RENALTRANSP_COD'),
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('leukaemia', 'eFI2_Cancer'),
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('lung cancer', 'FTCANREF_COD'),
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('lymphoma', 'C19HAEMCAN_COD'),
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('macular degeneration', 'CUST_ICB_VISUAL_IMPAIRMENT'),
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('macular oedema', 'CUST_ICB_VISUAL_IMPAIRMENT'),
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('major depressive episodes', 'eFI2_Depression'),
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('malignant melanoma', 'eFI2_Cancer'),
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('malignant pleural mesothelioma', 'LUNGCAN_COD'),
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('manic episode', 'MH_COD'),
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('mantle cell lymphoma', 'HAEMCANMORPH_COD'),
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('melanoma', 'eFI2_Cancer'),
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('merkel cell carcinoma', 'C19CAN_COD'),
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('migraine', 'eFI2_Headache'),
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('motor neurone disease', 'MND_COD'),
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('multiple myeloma', 'C19HAEMCAN_COD'),
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('multiple sclerosis', 'MS_COD'),
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('myelodysplastic', 'eFI2_AnaemiaEver'),
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('myelofibrosis', 'MDS_COD'),
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('myocardial infarction', 'eFI2_IschaemicHeartDisease'),
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('myotonia', 'CNDATRISK2_COD'),
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('narcolepsy', 'LD_COD'),
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('neuroendocrine tumour', 'LUNGCAN_COD'),
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('non-small cell lung cancer', 'LUNGCAN_COD'),
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('non-small-cell lung cancer', 'FTCANREF_COD'),
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('obesity', 'BMI30_COD'),
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('osteoarthritis', 'CUST_ICB_OSTEOARTHRITIS'),
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('osteoporosis', 'eFI2_Osteoporosis'),
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('osteosarcoma', 'NHAEMCANMORPH_COD'),
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('ovarian cancer', 'C19CAN_COD'),
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('peripheral arterial disease', 'PADEXC_COD'),
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('plaque psoriasis', 'PSORIASIS_COD'),
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('polycystic kidney disease', 'EPPCONGMALF_COD'),
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('polycythaemia vera', 'C19HAEMCAN_COD'),
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('pregnancy', 'C19PREG_COD'),
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('primary biliary cholangitis', 'eFI2_LiverProblems'),
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('primary hypercholesterolaemia', 'FNFHYP_COD'),
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('prostate cancer', 'EPPSOLIDCAN_COD'),
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('psoriasis', 'PSORIASIS_COD'),
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('psoriatic arthritis', 'RARTHAD_COD'),
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('pulmonary embolism', 'eFI2_RespiratoryDiseaseTimeSensitive'),
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('pulmonary fibrosis', 'ILD_COD'),
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('relapsing multiple sclerosis', 'MS_COD'),
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('renal cell carcinoma', 'C19CAN_COD'),
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('renal transplantation', 'RENALTRANSP_COD'),
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('retinal vein occlusion', 'CUST_ICB_VISUAL_IMPAIRMENT'),
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('rheumatoid arthritis', 'eFI2_InflammatoryArthritis'),
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('rivaroxaban', 'DOACCON_COD'),
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('schizophrenia', 'MH_COD'),
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('seizures', 'LSZFREQ_COD'),
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('sepsis', 'C19ACTIVITY_COD'),
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('severe persistent allergic asthma', 'SEVAST_COD'),
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('sickle cell disease', 'SICKLE_COD'),
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('sleep apnoea', 'CUST_ICB_NON_SEVERE_LDA'),
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('smoking cessation', 'SMOKINGINT_COD'),
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('soft tissue sarcoma', 'NHAEMCANMORPH_COD'),
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('spinal muscular atrophy', 'MND_COD'),
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('squamous cell', 'C19CAN_COD'),
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('squamous cell carcinoma', 'C19CAN_COD'),
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('stem cell transplant', 'ALLOTRANSP_COD'),
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('stroke', 'eFI2_Stroke'),
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('systemic lupus erythematosus', 'SLUPUS_COD'),
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('systemic mastocytosis', 'HAEMCANMORPH_COD'),
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('thrombocytopenic purpura', 'TTP_COD'),
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('thrombotic thrombocytopenic purpura', 'TTP_COD'),
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('thyroid cancer', 'C19CAN_COD'),
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('tophaceous gout', 'CUST_ICB_OSTEOARTHRITIS'),
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('transitional cell carcinoma', 'C19CAN_COD'),
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('type 1 diabetes', 'DMTYPE1_COD'),
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('type 2 diabetes', 'DMTYPE2_COD'),
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('ulcerative colitis', 'eFI2_InflammatoryBowelDisease'),
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('urothelial carcinoma', 'NHAEMCANMORPH_COD'),
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('urticaria', 'XSAL_COD'),
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('uveitis', 'CUST_ICB_VISUAL_IMPAIRMENT'),
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('vascular disease', 'CVDINVITE_COD'),
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('vasculitis', 'CRYOGLOBVASC_COD')
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) AS t(Search_Term, Cluster_ID)
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),
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ClusterCodes AS (
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SELECT
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stc.Search_Term,
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c."SNOMEDCode",
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c."SNOMEDDescription"
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FROM SearchTermClusters stc
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JOIN DATA_HUB.PHM."ClinicalCodingClusterSnomedCodes" c
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ON stc.Cluster_ID = c."Cluster_ID"
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WHERE c."SNOMEDCode" IS NOT NULL
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),
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ExplicitCodes AS (
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SELECT Search_Term, SNOMEDCode, SNOMEDDescription FROM (VALUES
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('acute coronary syndrome', '837091000000100', 'Manual mapping'),
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('ankylosing spondylitis', '162930007', 'Manual mapping'),
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('ankylosing spondylitis', '239805001', 'Manual mapping'),
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('ankylosing spondylitis', '239810002', 'Manual mapping'),
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('ankylosing spondylitis', '239811003', 'Manual mapping'),
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('ankylosing spondylitis', '394990003', 'Manual mapping'),
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('ankylosing spondylitis', '429712009', 'Manual mapping'),
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('ankylosing spondylitis', '441562009', 'Manual mapping'),
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('ankylosing spondylitis', '441680005', 'Manual mapping'),
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('ankylosing spondylitis', '441930001', 'Manual mapping'),
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('axial spondyloarthritis', '723116002', 'Manual mapping'),
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('choroidal neovascularisation', '380621000000102', 'Manual mapping'),
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('choroidal neovascularisation', '733124000', 'Manual mapping')
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) AS t(Search_Term, SNOMEDCode, SNOMEDDescription)
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)
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SELECT Search_Term, "SNOMEDCode" AS SNOMEDCode, "SNOMEDDescription" AS SNOMEDDescription
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FROM ClusterCodes
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UNION ALL
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SELECT Search_Term, SNOMEDCode, SNOMEDDescription
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FROM ExplicitCodes
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ORDER BY Search_Term, SNOMEDCode;
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