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Initial commit of COVID-19 codes #19

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5c5e510
Dataset namining cleanup
susheel Feb 7, 2021
6830955
Initial commit of WHO ICD10 COVID-19 Codes
susheel Feb 7, 2021
c48ea0a
Adding SNOMEDCT codes
susheel Feb 7, 2021
eaaa8ad
Minor edit
susheel Feb 9, 2021
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5 changes: 5 additions & 0 deletions _data/codelists/susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_ICD10.csv
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System,Code,Description
icd10,U071,COVID-19 has been confirmed by laboratory testing irrespective of severity of clinical signs or symptoms
icd10,U07.1,COVID-19 has been confirmed by laboratory testing irrespective of severity of clinical signs or symptoms
icd10,U072,COVID-19 is diagnosed clinically or epidemiologically but laboratory testing is inconclusive or not available
icd10,U07.2,COVID-19 is diagnosed clinically or epidemiologically but laboratory testing is inconclusive or not available
24 changes: 24 additions & 0 deletions _data/codelists/susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_SNOMEDCT.csv
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System,Code,Description,Category
snomedct,1240581000000104,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result positive,Detection of current infection - Virus
snomedct,1240591000000102,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result negative,Detection of current infection - Virus
snomedct,1321691000000102,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result unknown,Detection of current infection - Virus
snomedct,1322781000000102,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antigen detection result positive,Detection of current infection - Antigen
snomedct,1322791000000100,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antigen detection result negative,Detection of current infection - Antigen
snomedct,1322801000000101,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antigen detection result indeterminate,Detection of current infection - Antigen
snomedct,1322821000000105,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antigen detection result unknown,Detection of current infection - Antigen
snomedct,1322871000000109,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antibody detection result positive,Detection of Antibody - General
snomedct,1322891000000108,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antibody detection result negative,Detection of Antibody - General
snomedct,1322901000000109,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antibody detection result indeterminate,Detection of Antibody - General
snomedct,1322911000000106,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antibody detection result unknown,Detection of Antibody - General
snomedct,1321541000000108,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgG detection result positive,Detection of Antibody - IgG
snomedct,1321571000000102,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgG detection result negative,Detection of Antibody - IgG
snomedct,1322831000000107,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgG detection result indeterminate,Detection of Antibody - IgG
snomedct,1321641000000107,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgG detection result unknown,Detection of Antibody - IgG
snomedct,1321551000000106,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgM detection result positive,Detection of Antibody - IgM
snomedct,1321561000000109,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgM detection result negative,Detection of Antibody - IgM
snomedct,1322851000000100,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgM detection result indeterminate,Detection of Antibody - IgM
snomedct,1321581000000100,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgM detection result unknown,Detection of Antibody - IgM
snomedct,1321761000000103,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgA detection result positive,Detection of Antibody - IgA
snomedct,1321791000000109,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgA detection result negative,Detection of Antibody - IgA
snomedct,1322841000000103,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgA detection result indeterminate,Detection of Antibody - IgA
snomedct,1321781000000107,SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgA detection result unknown,Detection of Antibody - IgA
4 changes: 4 additions & 0 deletions _data/data_sources.yml
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Expand Up @@ -22,6 +22,10 @@ Practice postcode linked deprivation measures for CPRD GOLD:
name: Practice postcode linked deprivation measures for CPRD GOLD
id: 3326d554-ca11-4dc6-aff0-c5b314442d27
url: https://web.www.healthdatagateway.org/dataset/3326d554-ca11-4dc6-aff0-c5b314442d27
Patient postcode linked deprivation measures for CPRD Aurum:
name: Patient postcode linked deprivation measures for CPRD GOLD
id: f5c9ba01-a9cb-4a85-9850-d9466b2ff4fb
url: https://web.www.healthdatagateway.org/dataset/f5c9ba01-a9cb-4a85-9850-d9466b2ff4fb
Scottish Birth Record (SBR):
name: Scottish Birth Record (SBR)
id: 81c53293-ef64-4507-8fcf-2a254dc19936
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2 changes: 1 addition & 1 deletion _phenotypes/alcohol-consumption.md
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Expand Up @@ -6,7 +6,7 @@ name: Alcohol Consumption
type: Lifestyle Risk Factor
group: Lifestyle Risk Factor
data_sources:
- Primary care (Clinical Practice Research Datalink GOLD)
- Clinical Practice Research Datalink GOLD
clinical_terminologies:
- Read Version 2
validation: prognosis
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33 changes: 33 additions & 0 deletions _phenotypes/covid-19.md
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---
layout: phenotype
title: COVID-19
phenotype_id: Q9nBeqkXWqwqtNpcq3XFKd
name: COVID-19
type: Disease or Syndrome
group: Respiratory
data_sources:
-
validation: aetiology, prognosis
codelists:
- susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_ICD10.csv
- susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_SNOMEDCT.csv
clinical_terminologies:
- ICD10
- SNOMED CT
sex:
- Female
- Male
author: Susheel Varma
status: DRAFT
date: 2021-02-07
modified_date: 2021-02-07
version: Revision 1
---

### Primary Care

{% include csv.html csvdata=site.data.codelists.susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_ICD10 %}

### Secondary Care

{% include csv.html csvdata=site.data.codelists.susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_SNOMEDCT %}
4 changes: 2 additions & 2 deletions _phenotypes/ethnic-status.md
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Expand Up @@ -6,8 +6,8 @@ name: Ethnic Status
type: Lifestyle Risk Factor
group: Demographics
data_sources:
- Primary care (Clinical Practice Research Datalink GOLD)
- Hospital Episode Statistics (HES)
- Clinical Practice Research Datalink GOLD
- Hospital Episode Statistics Admitted Patient Care
validation: aetiology, prognosis
codelists:
- caliber_ethnic_status_PMD762GQ76BscDn5YK3Mwe_Read2.csv
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2 changes: 1 addition & 1 deletion _phenotypes/lewer_HUPIO_mZXE2uZxDzVYBsAbTjbhrK.md
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Expand Up @@ -7,7 +7,7 @@ type: Lifestyle Risk Factor
group: Lifestyle Risk Factor
data_sources:
- Clinical Practice Research Datalink GOLD
- Clinical Practice Research Datalink AURUM
- Clinical Practice Research Datalink Aurum
clinical_terminologies:
- SNOMED-CT
- Read Version 2
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2 changes: 1 addition & 1 deletion _phenotypes/pregnancy.md
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Expand Up @@ -6,7 +6,7 @@ name: Pregnancy
type: Lifestyle Risk Factor
group:
data_sources:
- Primary care (Clinical Practice Research Datalink GOLD)
- Clinical Practice Research Datalink GOLD
clinical_terminologies: Read Version 2
validation: aetiology, prognosis
codelists:
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2 changes: 1 addition & 1 deletion _phenotypes/smoking-status.md
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Expand Up @@ -6,7 +6,7 @@ name: Smoking Status
type: Lifestyle Risk Factor
group:
data_sources:
- Primary care (Clinical Practice Research Datalink GOLD)
- Clinical Practice Research Datalink GOLD
clinical_terminologies:
- Read Version 2
validation: casenote, aetiology, prognosis
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2 changes: 1 addition & 1 deletion _phenotypes/socioeconomic-deprevation.md
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Expand Up @@ -6,7 +6,7 @@ name: Socioeconomic Deprevation
type: Lifestyle Risk Factor
group:
data_sources:
- Practice postcode linked deprivation measures for CPRD GOLD
- Patient postcode linked deprivation measures for CPRD GOLD
clinical_terminologies:
validation: prognosis
primary_care_code_lists:
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33 changes: 33 additions & 0 deletions _phenotypes/susheel_Q9nBeqkXWqwqtNpcq3XFKd_covid-19.md
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---
layout: phenotype
title: COVID-19
phenotype_id: Q9nBeqkXWqwqtNpcq3XFKd
name: COVID-19
type: Disease or Syndrome
group: Respiratory
data_sources:
-
validation: aetiology, prognosis
codelists:
- susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_ICD10.csv
- susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_SNOMEDCT.csv
clinical_terminologies:
- ICD10
- SNOMED CT
sex:
- Female
- Male
author: Susheel Varma
status: DRAFT
date: 2021-02-07
modified_date: 2021-02-07
version: Revision 1
---

### Primary Care

{% include csv.html csvdata=site.data.codelists.susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_ICD10 %}

### Secondary Care

{% include csv.html csvdata=site.data.codelists.susheel_covid_Q9nBeqkXWqwqtNpcq3XFKd_SNOMEDCT %}