From 18ef81d6c23de94eb38194de81dd86a881436b14 Mon Sep 17 00:00:00 2001 From: tomlincr Date: Fri, 18 Mar 2022 15:11:34 +0000 Subject: [PATCH] remove redundant long covid phenotypes & codelists --- phenotypes/README.md | 37 ++----------------- .../long_covid.csv | 16 -------- ...ts-and-outcome-measures-for-long-covid.csv | 11 ------ ...ging-the-long-term-effects-of-covid-19.csv | 3 -- ...eferral-and-signposting-for-long-covid.csv | 4 -- 5 files changed, 4 insertions(+), 67 deletions(-) delete mode 100644 phenotypes/openSAFELY_long_covid_codelists/long_covid.csv delete mode 100644 phenotypes/openSAFELY_long_covid_codelists/opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv delete mode 100644 phenotypes/openSAFELY_long_covid_codelists/opensafely-nice-managing-the-long-term-effects-of-covid-19.csv delete mode 100644 phenotypes/openSAFELY_long_covid_codelists/opensafely-referral-and-signposting-for-long-covid.csv diff --git a/phenotypes/README.md b/phenotypes/README.md index 8bdffcd..d51f083 100644 --- a/phenotypes/README.md +++ b/phenotypes/README.md @@ -53,18 +53,9 @@ Figure 1 below show how these phenotypes and datasets were used in our manuscrip # Other phenotypes used within this work -1. `long-COVID` based on an aggregation across the following three [OpenSAFELY codelists](https://www.opencodelists.org/) these are best accessed on the [OpenSAFELY website](https://www.opencodelists.org/) however codelists and version ids used are committed to this repository for posterity: - 1. `opensafely-assessment-instruments-and-outcome-measures-for-long-covid` @ [OpenCodelists](https://www.opencodelists.org/codelist/opensafely/assessment-instruments-and-outcome-measures-for-long-covid/) - 2. `opensafely-nice-managing-the-long-term-effects-of-covid-19` @ [OpenCodelists](https://www.opencodelists.org/codelist/opensafely/nice-managing-the-long-term-effects-of-covid-19/) - 3. `opensafely-referral-and-signposting-for-long-covid` @ [OpenCodelists](https://www.opencodelists.org/codelist/opensafely/referral-and-signposting-for-long-covid/) +1. `high_risk` produced following [NHS-Digital Guidance on 'How to flag patients as high risk'](https://digital.nhs.uk/coronavirus/shielded-patient-list/guidance-for-general-practice#how-to-flag-patients-as-high-risk) - > Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY -The OpenSAFELY Collaborative, Alex J Walker, Brian MacKenna, Peter Inglesby, Christopher T Rentsch, Helen J Curtis, Caroline E Morton, Jessica Morley, Amir Mehrkar, Seb Bacon, George Hickman, Chris Bates, Richard Croker, David Evans, Tom Ward, Jonathan Cockburn, Simon Davy, Krishnan Bhaskaran, Anna Schultze, Elizabeth J Williamson, William J Hulme, Helen I McDonald, Laurie Tomlinson, Rohini Mathur, Rosalind M Eggo, Kevin Wing, Angel YS Wong, Harriet Forbes, John Tazare, John Parry, Frank Hester, Sam Harper, Shaun O’Hanlon, Alex Eavis, Richard Jarvis, Dima Avramov, Paul Griffiths, Aaron Fowles, Nasreen Parkes, Ian J Douglas, Stephen JW Evans, Liam Smeeth, Ben Goldacre -medRxiv 2021.05.06.21256755; doi: https://doi.org/10.1101/2021.05.06.21256755 - -2. `high_risk` produced following [NHS-Digital Guidance on 'How to flag patients as high risk'](https://digital.nhs.uk/coronavirus/shielded-patient-list/guidance-for-general-practice#how-to-flag-patients-as-high-risk) - -3. [CALIBER phenotypes for comorbidities](https://github.com/spiros/chronological-map-phenotypes) +2. [CALIBER phenotypes for comorbidities](https://github.com/spiros/chronological-map-phenotypes) > Kuan V., Denaxas S., Gonzalez-Izquierdo A. et al. _A chronological map of 308 physical and mental health conditions from 4 million individuals in the National Health Service_ published in the Lancet Digital Health - DOI 10.1016/S2589-7500(19)30012-3 @@ -155,28 +146,8 @@ medRxiv 2021.05.06.21256755; doi: https://doi.org/10.1101/2021.05.06.21256755
# Other phenotype codelists -## 1. `long_covid` phenotype codelists - - -| **phenotype** | **code** | **term** | **terminology** | **organisation** | **codelist_id** | **id** | **version** | -|---------------|------------------|---------------------------------------------------------------------------------------|-----------------|------------------|-----------------------------------------------------------------------|----------|-------------| -| long_covid | 1325031000000108 | Referral to post-COVID assessment clinic | SNOMED CT | OpenSAFELY | opensafely/referral-and-signposting-for-long-covid | 12d06dc0 | 12d06dc0 | -| long_covid | 1325051000000101 | Newcastle post-COVID syndrome Follow-up Screening Questionnaire | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325081000000107 | Assessment using COVID-19 Yorkshire Rehabilitation Screening tool | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325161000000102 | Post-COVID-19 syndrome | SNOMED CT | OpenSAFELY | opensafely/nice-managing-the-long-term-effects-of-covid-19 | 64f1ae69 | 64f1ae69 | -| long_covid | 1325041000000104 | Referral to Your COVID Recovery rehabilitation platform | SNOMED CT | OpenSAFELY | opensafely/referral-and-signposting-for-long-covid | 12d06dc0 | 12d06dc0 | -| long_covid | 1325101000000101 | Assessment using Post-COVID-19 Functional Status Scale patient self-report | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325121000000105 | Post-COVID-19 Functional Status Scale patient self-report final scale grade | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325141000000103 | Assessment using Post-COVID-19 Functional Status Scale structured interview | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325151000000100 | Post-COVID-19 Functional Status Scale structured interview | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325021000000106 | Signposting to Your COVID Recovery | SNOMED CT | OpenSAFELY | opensafely/referral-and-signposting-for-long-covid | 12d06dc0 | 12d06dc0 | -| long_covid | 1325181000000106 | Ongoing symptomatic disease caused by severe acute respiratory syndrome coronavirus 2 | SNOMED CT | OpenSAFELY | opensafely/nice-managing-the-long-term-effects-of-covid-19 | 64f1ae69 | 64f1ae69 | -| long_covid | 1325071000000105 | COVID-19 Yorkshire Rehabilitation Screening tool | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325061000000103 | Assessment using Newcastle post-COVID syndrome Follow-up Screening Questionnaire | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325131000000107 | Post-COVID-19 Functional Status Scale structured interview final scale grade | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | -| long_covid | 1325091000000109 | Post-COVID-19 Functional Status Scale patient self-report | SNOMED CT | OpenSAFELY | opensafely/assessment-instruments-and-outcome-measures-for-long-covid | 79c0fa8a | 79c0fa8a | - -## 2. `high_risk` phenotype codelists + +## 1. `high_risk` phenotype codelists | **code** | **term** | **terminology** | **organisation** | |------------------|------------------------------------------------------------------------------------------------------------------------------------------------|-----------------|------------------| | 1300561000000107 | High risk category for developing complication from coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 infection | SNOMED CT | NHS Digital | diff --git a/phenotypes/openSAFELY_long_covid_codelists/long_covid.csv b/phenotypes/openSAFELY_long_covid_codelists/long_covid.csv deleted file mode 100644 index f1bc373..0000000 --- a/phenotypes/openSAFELY_long_covid_codelists/long_covid.csv +++ /dev/null @@ -1,16 +0,0 @@ -phenotype,code,term,terminology,organisation,codelist_id,id,version -long_covid,1325031000000108,Referral to post-COVID assessment clinic,SNOMED CT,OpenSAFELY,opensafely/referral-and-signposting-for-long-covid,12d06dc0,12d06dc0 -long_covid,1325051000000101,Newcastle post-COVID syndrome Follow-up Screening Questionnaire,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325081000000107,Assessment using COVID-19 Yorkshire Rehabilitation Screening tool,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325161000000102,Post-COVID-19 syndrome,SNOMED CT,OpenSAFELY,opensafely/nice-managing-the-long-term-effects-of-covid-19,64f1ae69,64f1ae69 -long_covid,1325041000000104,Referral to Your COVID Recovery rehabilitation platform,SNOMED CT,OpenSAFELY,opensafely/referral-and-signposting-for-long-covid,12d06dc0,12d06dc0 -long_covid,1325101000000101,Assessment using Post-COVID-19 Functional Status Scale patient self-report,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325121000000105,Post-COVID-19 Functional Status Scale patient self-report final scale grade,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325141000000103,Assessment using Post-COVID-19 Functional Status Scale structured interview,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325151000000100,Post-COVID-19 Functional Status Scale structured interview,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325021000000106,Signposting to Your COVID Recovery,SNOMED CT,OpenSAFELY,opensafely/referral-and-signposting-for-long-covid,12d06dc0,12d06dc0 -long_covid,1325181000000106,Ongoing symptomatic disease caused by severe acute respiratory syndrome coronavirus 2,SNOMED CT,OpenSAFELY,opensafely/nice-managing-the-long-term-effects-of-covid-19,64f1ae69,64f1ae69 -long_covid,1325071000000105,COVID-19 Yorkshire Rehabilitation Screening tool,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325061000000103,Assessment using Newcastle post-COVID syndrome Follow-up Screening Questionnaire,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325131000000107,Post-COVID-19 Functional Status Scale structured interview final scale grade,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -long_covid,1325091000000109,Post-COVID-19 Functional Status Scale patient self-report,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a diff --git a/phenotypes/openSAFELY_long_covid_codelists/opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv b/phenotypes/openSAFELY_long_covid_codelists/opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv deleted file mode 100644 index 1dab7f3..0000000 --- a/phenotypes/openSAFELY_long_covid_codelists/opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv +++ /dev/null @@ -1,11 +0,0 @@ -code,term,terminology,organisation,codelist_id,id,version -1325051000000101,Newcastle post-COVID syndrome Follow-up Screening Questionnaire,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325061000000103,Assessment using Newcastle post-COVID syndrome Follow-up Screening Questionnaire,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325071000000105,COVID-19 Yorkshire Rehabilitation Screening tool,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325081000000107,Assessment using COVID-19 Yorkshire Rehabilitation Screening tool,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325091000000109,Post-COVID-19 Functional Status Scale patient self-report,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325101000000101,Assessment using Post-COVID-19 Functional Status Scale patient self-report,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325121000000105,Post-COVID-19 Functional Status Scale patient self-report final scale grade,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325131000000107,Post-COVID-19 Functional Status Scale structured interview final scale grade,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325141000000103,Assessment using Post-COVID-19 Functional Status Scale structured interview,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a -1325151000000100,Post-COVID-19 Functional Status Scale structured interview,SNOMED CT,OpenSAFELY,opensafely/assessment-instruments-and-outcome-measures-for-long-covid,79c0fa8a,79c0fa8a diff --git a/phenotypes/openSAFELY_long_covid_codelists/opensafely-nice-managing-the-long-term-effects-of-covid-19.csv b/phenotypes/openSAFELY_long_covid_codelists/opensafely-nice-managing-the-long-term-effects-of-covid-19.csv deleted file mode 100644 index 3118dd2..0000000 --- a/phenotypes/openSAFELY_long_covid_codelists/opensafely-nice-managing-the-long-term-effects-of-covid-19.csv +++ /dev/null @@ -1,3 +0,0 @@ -code,term,terminology,organisation,codelist_id,id,version -1325161000000102,Post-COVID-19 syndrome,SNOMED CT,OpenSAFELY,opensafely/nice-managing-the-long-term-effects-of-covid-19,64f1ae69,64f1ae69 -1325181000000106,Ongoing symptomatic disease caused by severe acute respiratory syndrome coronavirus 2,SNOMED CT,OpenSAFELY,opensafely/nice-managing-the-long-term-effects-of-covid-19,64f1ae69,64f1ae69 diff --git a/phenotypes/openSAFELY_long_covid_codelists/opensafely-referral-and-signposting-for-long-covid.csv b/phenotypes/openSAFELY_long_covid_codelists/opensafely-referral-and-signposting-for-long-covid.csv deleted file mode 100644 index 5206a1e..0000000 --- a/phenotypes/openSAFELY_long_covid_codelists/opensafely-referral-and-signposting-for-long-covid.csv +++ /dev/null @@ -1,4 +0,0 @@ -code,term,terminology,organisation,codelist_id,id,version -1325021000000106,Signposting to Your COVID Recovery,SNOMED CT,OpenSAFELY,opensafely/referral-and-signposting-for-long-covid,12d06dc0,12d06dc0 -1325031000000108,Referral to post-COVID assessment clinic,SNOMED CT,OpenSAFELY,opensafely/referral-and-signposting-for-long-covid,12d06dc0,12d06dc0 -1325041000000104,Referral to Your COVID Recovery rehabilitation platform,SNOMED CT,OpenSAFELY,opensafely/referral-and-signposting-for-long-covid,12d06dc0,12d06dc0