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Updated the EFI codesets to include SNOMED (#193)
* Added SNOMED codes to EFI code sets * Reduced file size of terminolgy mapping file
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| // This is a one-off script to generate SNOMED lists for all the EFI code sets | ||
| // | ||
| // EFI currently only has Readv2 and CTV3 code sets. This is what is implemented | ||
| // in any system that calculates EFI. In order to be consistent with what exists | ||
| // in GP practices, we keep the Readv2 and CTV3 codes and do not attempt to | ||
| // validate them. However, now that all codes in the database are SNOMED, we need | ||
| // a way to generate the equivalent SNOMED code sets. Therefore we use the NHS | ||
| // mapping from Read and CTV to SNOMED. This script is therefore a one off process | ||
| // to create those files, but is retained here for transparency, and also in case | ||
| // a similar script is needed in future. | ||
|
|
||
| // Get all efi scripts | ||
| const fs = require('fs'); | ||
| const { join } = require('path'); | ||
|
|
||
| console.log('Loading lookup files...'); | ||
| const ctv3ToSNOMED = {}; | ||
| fs.readFileSync( | ||
| join(__dirname, '..', 'shared', 'terminology-mapping', 'ctv3sctmap2_uk_20200401000001.txt'), | ||
| 'utf8' | ||
| ) | ||
| .split('\n') | ||
| .slice(1) | ||
| .map((x) => { | ||
| const [mapId, code, termId, termType, conceptId] = x.split('\t'); | ||
| if (conceptId === '_DRUG') return; | ||
| if (!ctv3ToSNOMED[code]) ctv3ToSNOMED[code] = [conceptId]; | ||
| else ctv3ToSNOMED[code].push(conceptId); | ||
| }); | ||
| const readv2ToSNOMED = {}; | ||
| fs.readFileSync( | ||
| join(__dirname, '..', 'shared', 'terminology-mapping', 'rcsctmap2_uk_20200401000001.txt'), | ||
| 'utf8' | ||
| ) | ||
| .split('\n') | ||
| .slice(1) | ||
| .map((x) => { | ||
| const [mapId, code, termId, conceptId] = x.split('\t'); | ||
| if (!readv2ToSNOMED[code]) readv2ToSNOMED[code] = [conceptId]; | ||
| else readv2ToSNOMED[code].push(conceptId); | ||
| }); | ||
| const SNOMED_DEFINITIONS = JSON.parse( | ||
| fs.readFileSync( | ||
| join(__dirname, '..', '..', 'nhs-snomed', 'files', 'processed', 'latest', 'defs-single.json'), | ||
| 'utf8' | ||
| ) | ||
| ); | ||
|
|
||
| console.log('Processing EFI files...'); | ||
| const CODE_SET_DIR = join(__dirname, '..', 'shared', 'clinical-code-sets'); | ||
| fs.readdirSync(CODE_SET_DIR).forEach((dir) => { | ||
| fs.readdirSync(join(CODE_SET_DIR, dir)).forEach((condition) => { | ||
| if (condition.indexOf('efi') === 0) { | ||
| const snomedCodes = {}; | ||
| fs.readFileSync(join(CODE_SET_DIR, dir, condition, '1', `${condition}.ctv3.txt`), 'utf8') | ||
| .split('\n') | ||
| .map((x) => { | ||
| if (x.trim().length < 3) return; | ||
| const [code] = x.trim().split('\t'); | ||
| if (!ctv3ToSNOMED[code]) { | ||
| console.log(`No mapping for ctv3 code ${code} in ${condition}`); | ||
| } else { | ||
| ctv3ToSNOMED[code].forEach((conceptId) => { | ||
| snomedCodes[conceptId] = true; | ||
| }); | ||
| } | ||
| }); | ||
| fs.readFileSync(join(CODE_SET_DIR, dir, condition, '1', `${condition}.readv2.txt`), 'utf8') | ||
| .split('\n') | ||
| .map((x) => { | ||
| if (x.trim().length < 3) return; | ||
| const [code] = x.trim().split('\t'); | ||
| if (!readv2ToSNOMED[code]) { | ||
| console.log(`No mapping for readv2 code ${code} in ${condition}`); | ||
| } else { | ||
| readv2ToSNOMED[code].forEach((conceptId) => { | ||
| snomedCodes[conceptId] = true; | ||
| }); | ||
| } | ||
| }); | ||
| fs.writeFileSync( | ||
| join(CODE_SET_DIR, dir, condition, '1', `${condition}.snomed.txt`), | ||
| Object.keys(snomedCodes) | ||
| .map((x) => { | ||
| if (!SNOMED_DEFINITIONS[x]) { | ||
| console.log(`No defintion for ${x}`); | ||
| process.exit(); | ||
| } | ||
| return `${x}\t${SNOMED_DEFINITIONS[x]}`; | ||
| }) | ||
| .join('\n') | ||
| ); | ||
| } | ||
| }); | ||
| }); |
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shared/clinical-code-sets/conditions/efi-arthritis/1/efi-arthritis.snomed.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| 3723001 Arthritis (disorder) | ||
| 8847002 Spondylosis (disorder) | ||
| 9631008 Ankylosing spondylitis (disorder) | ||
| 19063003 Arthroplasty of knee (procedure) | ||
| 22193007 Degenerative joint disease of hand (disorder) | ||
| 27813003 Intra-articular injection (procedure) | ||
| 33952002 Localized osteoarthrosis (disorder) | ||
| 35885006 Hyperuricemia (disorder) | ||
| 37895003 Osteoarthrosis of the carpometacarpal joint of the thumb (disorder) | ||
| 48440001 Arthritis due to gout (disorder) | ||
| 67315001 Degenerative joint disease of shoulder region (disorder) | ||
| 68449006 Coxitis (disorder) | ||
| 69896004 Rheumatoid arthritis (disorder) | ||
| 90560007 Inflammatory disorder due to increased blood urate level (disorder) | ||
| 161567008 History of rheumatoid arthritis (situation) | ||
| 161568003 History of osteoarthritis (situation) | ||
| 168662003 Plain X-ray hip joint abnormal (finding) | ||
| 168668004 Plain X-ray knee abnormal (finding) | ||
| 179342005 Knee joint operation (procedure) | ||
| 179343000 Cemented knee arthroplasty (& total (& named variants)) (procedure) | ||
| 190828008 Gouty arthropathy (disorder) | ||
| 201727001 Arthropathy in ulcerative colitis (disorder) | ||
| 201764007 Rheumatoid arthritis of cervical spine (disorder) | ||
| 201766009 Rheumatoid arthritis of shoulder (disorder) | ||
| 201768005 Rheumatoid arthritis of acromioclavicular joint (disorder) | ||
| 201769002 Rheumatoid arthritis of elbow (disorder) | ||
| 201771002 Rheumatoid arthritis of wrist (disorder) | ||
| 201772009 Rheumatoid arthritis of metacarpophalangeal joint (disorder) | ||
| 201773004 Rheumatoid arthritis of proximal interphalangeal joint of finger (disorder) | ||
| 201774005 Rheumatoid arthritis of distal interphalangeal joint of finger (disorder) | ||
| 201775006 Rheumatoid arthritis of hip (disorder) | ||
| 201776007 Rheumatoid arthritis of sacroiliac joint (disorder) | ||
| 201777003 Rheumatoid arthritis of knee (disorder) | ||
| 201779000 Rheumatoid arthritis of ankle (disorder) | ||
| 201780002 Rheumatoid arthritis of subtalar joint (disorder) | ||
| 201781003 Rheumatoid arthritis of talonavicular joint (disorder) | ||
| 201783000 Rheumatoid arthritis of first metatarsophalangeal joint (disorder) | ||
| 201784006 Rheumatoid arthritis of lesser metatarsophalangeal joint (disorder) | ||
| 201785007 Rheumatoid arthritis of interphalangeal joint of toe (disorder) | ||
| 201791009 Flare of rheumatoid arthritis (disorder) | ||
| 201818008 Osteoarthritis (& [allied disorders]) | ||
| 201819000 Generalized osteoarthritis (disorder) | ||
| 201826000 Erosive osteoarthrosis (disorder) | ||
| 201893003 Osteoarthritis NOS: [lower leg] or [knee] (disorder) | ||
| 202655008 (Spondylosis and allied disorders) or (arthritis of spine) or (osteoarthritis of spine) | ||
| 239791005 Seropositive rheumatoid arthritis (disorder) | ||
| 239792003 Seronegative rheumatoid arthritis (disorder) | ||
| 239793008 Rheumatoid arthritis with organ / system involvement (disorder) | ||
| 239795001 Rheumatoid arthritis with multisystem involvement (disorder) | ||
| 239862000 Idiopathic osteoarthritis (disorder) | ||
| 239868001 Osteoarthritis of finger joint (disorder) | ||
| 239872002 Osteoarthritis of hip (disorder) | ||
| 239873007 Osteoarthritis of knee (disorder) | ||
| 239881008 Otto's pelvis (disorder) | ||
| 265170009 Total prosthetic replacement of knee joint using cement (procedure) | ||
| 267004000 History of musculoskeletal disease (situation) | ||
| 267891004 Localized osteoarthritis, unspecified, of the pelvic region and thigh (disorder) | ||
| 267969005 Spondylosis and allied disorders (disorder) | ||
| 268524007 Rheumatology disorder monitoring (regime/therapy) | ||
| 274135002 Arthritis/arthrosis (disorder) | ||
| 275554004 History of arthritis (situation) | ||
| 275902004 Rheumatoid arthritis monitoring (regime/therapy) | ||
| 275920008 Arthritis monitoring (regime/therapy) | ||
| 287006005 Rheumatoid arthritis of multiple joints (disorder) | ||
| 287007001 Rheumatoid arthritis of hand joint (disorder) | ||
| 287008006 Rheumatoid arthritis of ankle and/or foot (disorder) | ||
| 301877006 Injection of steroid into knee joint (procedure) | ||
| 307817008 Arthroplasty of knee using cement (procedure) | ||
| 308143008 Seropositive erosive rheumatoid arthritis (disorder) | ||
| 371081002 Arthritis of knee (disorder) | ||
| 396275006 Osteoarthritis (disorder) | ||
| 399269003 Arthropathy (disorder) | ||
| 416956002 Undifferentiated inflammatory polyarthritis (disorder) | ||
| 417373000 Inflammatory polyarthropathy (disorder) | ||
| 429192004 Rheumatoid arthritis of foot (disorder) | ||
| 430698003 Replacement of total knee joint (procedure) | ||
| 443349002 Disease activity score in rheumatoid arthritis (assessment scale) | ||
| 445478004 Degenerative joint disease of pelvis (disorder) | ||
| 450521003 Osteoarthritis of patellofemoral joint (disorder) | ||
| 414821000000101 [X]Seropositive rheumatoid arthritis, unspecified (disorder) | ||
| 408751000000108 [X]Other seropositive rheumatoid arthritis (disorder) | ||
| 425481000000106 [X]Other specified rheumatoid arthritis (disorder) | ||
| 425091000000101 [X]Rheumatoid arthritis with involvement of other organs or systems (disorder) |
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...linical-code-sets/conditions/efi-atrial-fibrillation/1/efi-atrial-fibrillation.snomed.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| 5370000 Atrial flutter (disorder) | ||
| 49436004 Atrial fibrillation (disorder) | ||
| 134377004 Atrial fibrillation monitoring (regime/therapy) | ||
| 163000006 On examination - pulse irregularly irregular (finding) | ||
| 164889003 Electrocardiographic atrial fibrillation (finding) | ||
| 164890007 Electrocardiographic atrial flutter (finding) | ||
| 175146007 Implantation of intravenous pacemaker for atrial fibrillation (procedure) | ||
| 195080001 Atrial fibrillation and flutter (disorder) | ||
| 233910005 Lone atrial fibrillation (disorder) | ||
| 233911009 Non-rheumatic atrial fibrillation (disorder) | ||
| 266306001 (Atrial fibrillation) or (atrial flutter) (disorder) | ||
| 282825002 Paroxysmal atrial fibrillation (disorder) | ||
| 300996004 Controlled atrial fibrillation (disorder) | ||
| 312442005 History of atrial fibrillation (situation) | ||
| 314208002 Rapid atrial fibrillation (disorder) | ||
| 440028005 Permanent atrial fibrillation (disorder) | ||
| 440059007 Persistent atrial fibrillation (disorder) | ||
| 248411000000105 Atrial fibrillation annual review (regime/therapy) | ||
| 716981000000106 Atrial fibrillation monitoring second letter (procedure) | ||
| 715941000000109 Excepted from atrial fibrillation quality indicators - patient unsuitable (finding) | ||
| 717381000000109 Excepted from atrial fibrillation quality indicators - informed dissent (finding) |
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shared/clinical-code-sets/conditions/efi-chd/1/efi-chd.snomed.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| 1755008 Old myocardial infarction (disorder) | ||
| 3546002 Aortocoronary artery bypass graft with saphenous vein graft (procedure) | ||
| 4557003 Preinfarction syndrome (disorder) | ||
| 11101003 Percutaneous transluminal coronary angioplasty (procedure) | ||
| 22298006 Myocardial infarction (disorder) | ||
| 23687008 Coronary artery spasm (disorder) | ||
| 25106000 Impending infarction (disorder) | ||
| 31413008 Operative procedure on coronary artery (procedure) | ||
| 36969009 Placement of stent in coronary artery (procedure) | ||
| 46109009 Subendocardial ischemia (disorder) | ||
| 53741008 Coronary arteriosclerosis (disorder) | ||
| 57054005 Acute myocardial infarction (disorder) | ||
| 59021001 Angina decubitus (disorder) | ||
| 59139008 Crushing chest pain (finding) | ||
| 67682002 Coronary artery atheroma (disorder) | ||
| 73795002 Acute myocardial infarction of inferior wall (disorder) | ||
| 102594003 Electrocardiogram abnormal (finding) | ||
| 161499004 H/O: cardiovascular disease (& [heart disorder] or [myocardial problem]) (situation) | ||
| 161503005 History of myocardial infarct at age greater than sixty (situation) | ||
| 161504004 History of angina pectoris (situation) | ||
| 164861001 Electrocardiographic myocardial ischemia (finding) | ||
| 170594001 Angina control - good (finding) | ||
| 170595000 Angina control - poor (finding) | ||
| 170597008 Angina control - worsening (finding) | ||
| 175006004 Coronary artery operations (& bypass) (procedure) | ||
| 194795001 Ischaemic heart disease (& [arteriosclerotic]) (disorder) | ||
| 194796000 (Myocardial infarction (& [acute] or [silent] or [cardiac rupture following])) or (coronary thrombosis) (disorder) | ||
| 194828000 Angina (disorder) | ||
| 194841001 Coronary (atherosclerosis or artery disease) or triple vessel disease of the heart (disorder) | ||
| 194861007 Certain current complications following acute myocardial infarction (disorder) | ||
| 194863005 Atrial septal defect due to and following acute myocardial infarction (disorder) | ||
| 225566008 Ischemic chest pain (finding) | ||
| 232717009 Coronary artery bypass grafting (procedure) | ||
| 233817007 Triple vessel disease of the heart (disorder) | ||
| 233819005 Stable angina (disorder) | ||
| 233823002 Silent myocardial ischemia (disorder) | ||
| 233843008 Silent myocardial infarction (disorder) | ||
| 233845001 Cardiac syndrome X (finding) | ||
| 233846000 Post-infarction ventricular septal defect (disorder) | ||
| 233847009 Cardiac rupture due to and following acute myocardial infarction (disorder) | ||
| 266288001 Myocardial infarction (& [acute]) or coronary thrombosis (disorder) | ||
| 266995000 History of cardiovascular disease (situation) | ||
| 275544003 History of heart disorder (situation) | ||
| 275905002 History of myocardial problem (situation) | ||
| 279019008 Central crushing chest pain (finding) | ||
| 300995000 Exercise-induced angina (disorder) | ||
| 315026000 Transient myocardial ischemia (disorder) | ||
| 315287002 Diabetes mellitus insulin-glucose infusion in acute myocardial infarction (procedure) | ||
| 315614006 Coronary heart disease annual review (procedure) | ||
| 371068009 Myocardial infarction with complication (disorder) | ||
| 390799004 Coronary heart disease review (procedure) | ||
| 398274000 Coronary artery thrombosis (disorder) | ||
| 399211009 History of myocardial infarction (situation) | ||
| 401314000 Acute non-ST segment elevation myocardial infarction (disorder) | ||
| 413838009 Chronic ischemic heart disease (disorder) | ||
| 413844008 Chronic myocardial ischemia (disorder) | ||
| 414024009 Disorder of coronary artery (disorder) | ||
| 414545008 Ischemic heart disease (disorder) | ||
| 414795007 Myocardial ischemia (disorder) | ||
| 443502000 Atherosclerosis of coronary artery (disorder) | ||
| 699245006 Emergency hospital admission for ischemic heart disease (procedure) | ||
| 471531000000105 [X]Other forms of angina pectoris (disorder) | ||
| 302881000000102 Cardiovascular disease annual review declined (situation) | ||
| 320351000000105 Admit ischaemic heart disease emergency (procedure) |
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shared/clinical-code-sets/conditions/efi-ckd/1/efi-ckd.snomed.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| 29738008 Proteinuria (finding) | ||
| 46177005 End-stage renal disease (disorder) | ||
| 73211009 Diabetes mellitus (disorder) | ||
| 90688005 Chronic renal failure syndrome (disorder) | ||
| 127013003 Disorder of kidney due to diabetes mellitus (disorder) | ||
| 167278006 Urine protein test = ++++ (finding) | ||
| 190388001 Multiple complications due to type 2 diabetes mellitus (disorder) | ||
| 197654000 Renal failure: [chronic] or [end stage] (disorder) | ||
| 204962002 Multicystic kidney (disorder) | ||
| 236425005 Chronic renal impairment (disorder) | ||
| 236499007 Microalbuminuric nephropathy due to diabetes mellitus (disorder) | ||
| 236500003 Proteinuric nephropathy due to diabetes mellitus (disorder) | ||
| 401110002 Type 1 diabetes mellitus with persistent microalbuminuria (disorder) | ||
| 420279001 Renal disorder due to type 2 diabetes mellitus (disorder) | ||
| 420514000 Persistent proteinuria due to type 1 diabetes mellitus (disorder) | ||
| 420715001 Persistent microalbuminuria due to type 2 diabetes mellitus (disorder) | ||
| 421893009 Renal disorder due to type 1 diabetes mellitus (disorder) | ||
| 421986006 Persistent proteinuria due to type 2 diabetes mellitus (disorder) | ||
| 431857002 Chronic kidney disease stage 4 (disorder) | ||
| 433144002 Chronic kidney disease stage 3 (disorder) | ||
| 433146000 Chronic kidney disease stage 5 (disorder) | ||
| 472953006 History of chronic renal impairment (situation) | ||
| 700378005 Chronic kidney disease stage 3A (disorder) | ||
| 700379002 Chronic kidney disease stage 3B (disorder) | ||
| 709044004 Chronic kidney disease (disorder) | ||
| 737562008 Multicystic renal dysplasia (disorder) | ||
| 397201000000107 [X]Unspecified diabetes mellitus with renal complications (disorder) | ||
| 309861000000100 Chronic kidney disease stage 3A (disorder) | ||
| 309871000000107 Chronic kidney disease stage 3B (disorder) | ||
| 324251000000105 Chronic kidney disease stage 3 with proteinuria (disorder) | ||
| 324281000000104 Chronic kidney disease stage 3 without proteinuria (disorder) | ||
| 324311000000101 Chronic kidney disease stage 3A with proteinuria (disorder) | ||
| 324341000000100 Chronic kidney disease stage 3A without proteinuria (disorder) | ||
| 324371000000106 Chronic kidney disease stage 3B with proteinuria (disorder) | ||
| 324411000000105 Chronic kidney disease stage 3B without proteinuria (disorder) | ||
| 324441000000106 Chronic kidney disease stage 4 with proteinuria (disorder) | ||
| 324471000000100 Chronic kidney disease stage 4 without proteinuria (disorder) | ||
| 324501000000107 Chronic kidney disease stage 5 with proteinuria (disorder) | ||
| 324541000000105 Chronic kidney disease stage 5 without proteinuria (disorder) | ||
| 499931000000106 [D]Proteinuria (situation) | ||
| 249171000000102 Chronic kidney disease annual review (regime/therapy) | ||
| 716891000000102 Excepted from chronic kidney disease quality indicators - patient unsuitable (finding) | ||
| 716881000000104 Excepted from chronic kidney disease quality indicators - informed dissent (finding) |
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