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CCU013_01 COVID-19 infection

Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas

Type
Disease or Syndrome
ID
PH1020
Version ID
2198
Valid event data range
23/01/2020 - 31/05/2021
Sex
Female, Male
Agreement Date
2021-11-09
Coding system
ICD10 codes OPCS4 codes SNOMED CT codes
Tags /Collections
BHF Data Science Centre Phenotype Library

Definition

Publications

  • Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas m

Clinical Code List

Rows: 41
Code Description covid_status terminology covid_phenotype source
1008541000000105 Coronavirus ribonucleic acid detection assay (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1029481000000103 Coronavirus nucleic acid detection assay (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
120814005 Coronavirus antibody (substance) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240381000000105 Severe acute respiratory syndrome coronavirus 2 (organism) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240391000000107 Antigen of severe acute respiratory syndrome coronavirus 2 (substance) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240401000000105 Antibody to severe acute respiratory syndrome coronavirus 2 (substance) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240411000000107 Ribonucleic acid of severe acute respiratory syndrome coronavirus 2 (substance) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240421000000101 Serotype severe acute respiratory syndrome coronavirus 2 (qualifier value) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240511000000106 Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240521000000100 Otitis media caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240531000000103 Myocarditis caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240541000000107 Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240551000000105 Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240561000000108 Encephalopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240571000000101 Gastroenteritis caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240581000000104 Severe acute respiratory syndrome coronavirus 2 ribonucleic acid detected (finding) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240741000000103 Severe acute respiratory syndrome coronavirus 2 serology (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1240751000000100 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1300631000000101 Coronavirus disease 19 severity score (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1300671000000104 Coronavirus disease 19 severity scale (assessment scale) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1300681000000102 Assessment using coronavirus disease 19 severity scale (procedure) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1300721000000109 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1300731000000106 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed using clinical diagnostic criteria (situation) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321181000000108 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 record extraction simple reference set (foundation metadata concept) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321191000000105 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 procedures simple reference set (foundation metadata concept) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321201000000107 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 health issues simple reference set (foundation metadata concept) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321241000000105 Cardiomyopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321301000000101 Severe acute respiratory syndrome coronavirus 2 ribonucleic acid qualitative existence in specimen (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321311000000104 Severe acute respiratory syndrome coronavirus 2 immunoglobulin M qualitative existence in specimen (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321321000000105 Severe acute respiratory syndrome coronavirus 2 immunoglobulin G qualitative existence in specimen (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321331000000107 Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 total immunoglobulin in serum (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321341000000103 Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin G in serum (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321351000000100 Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin M in serum (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321541000000108 Severe acute respiratory syndrome coronavirus 2 immunoglobulin G detected (finding) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321551000000106 Severe acute respiratory syndrome coronavirus 2 immunoglobulin M detected (finding) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321761000000103 Severe acute respiratory syndrome coronavirus 2 immunoglobulin A detected (finding) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321801000000108 Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin A in serum (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1321811000000105 Severe acute respiratory syndrome coronavirus 2 immunoglobulin A qualitative existence in specimen (observable entity) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1322781000000102 Severe acute respiratory syndrome coronavirus 2 antigen detection result positive (finding) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
1322871000000109 Severe acute respiratory syndrome coronavirus 2 antibody detection result positive (finding) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
186747009 Coronavirus infection (disorder) confirmed SNOMEDCT 01_GP_covid_diagnosis GDPPR
Rows: 2
Code Description covid_status terminology covid_phenotype source
U07.1 Confirmed_COVID19 confirmed ICD10 02_Covid_admission HES APC
U07.2 Suspected_COVID19 suspected ICD10 02_Covid_admission HES APC
Rows: 1
Code Description covid_status terminology covid_phenotype source
X58.1 Extracorporeal membrane oxygenation confirmed OPCS 03_ECMO_treatment HES APC
Rows: 2
Code Description covid_status terminology covid_phenotype source
E85.1 Invasive ventilation confirmed OPCS 03_IMV_treatment HES APC
X56 Intubation of trachea confirmed OPCS 03_IMV_treatment HES APC
Rows: 2
Code Description covid_status terminology covid_phenotype source
E85.2 Non-invasive ventilation NEC confirmed OPCS 03_NIV_treatment HES APC
E85.6 Continuous positive airway pressure confirmed OPCS 03_NIV_treatment HES APC
Rows: 2
Code Description covid_status terminology covid_phenotype source
U071 confirmed ICD10 04_Fatal_with_covid_diagnosis deaths
U072 suspected ICD10 04_Fatal_with_covid_diagnosis deaths

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH1020/version/2198/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH1020/version/2198/detail/?format=json
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get details of phenotype

details = get_phenotype_detail_by_version('PH1020', '2198', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH1020/version/2198/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH1020/version/2198/export/codes/?format=json
CSV site_root/phenotypes/PH1020/version/2198/export/codes/
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get codelists of phenotype

codelists = get_phenotype_code_list('PH1020', '2198', api_client=client)

Version History

Version
ID
Name Owner Publish date
2198 CCU013_01 COVID-19 infection ieuan.scanlon 2022-05-17 currently shown
2119 CCU013_01 COVID-19 infection ieuan.scanlon 2022-05-09

Export - export all codes into a csv file/JSON/XML for the current phenotype version.

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