Phenotype Library | phenotype: CCU002_01 Confirmed COVID-19 diagnoses

CCU002_01 Confirmed COVID-19 diagnoses

Rochelle Knight, Venexia Walker, Samantha Ip, Jennifer A Cooper, Thomas Bolton, Spencer Keene, Rachel Denholm, Ashley Akbari, Hoda Abbasizanjani, Fatemeh Torabi, Efosa Omigie, Sam Hollings, Teri-Louise North, Renin Toms, Emanuele Di Angelantonio, Spiros Denaxas, Johan H Thygesen, Christopher Tomlinson, Ben Bray, Craig J Smith, Mark Barber, George Davey Smith, Nishi Chaturvedi, Cathie Sudlow, William N Whiteley, Angela Wood, Jonathan A C Sterne

PH954

Version ID

2132

Type

Disease or Syndrome

Data Sources

GPES Data for Pandemic Planning and Research (COVID-19) , Hospital Episode Statistics Admitted Patient Care , Covid-19 Second Generation Surveillance System , Civil Registration - Deaths , Trusted Research Environments for CVD-COVID-UK / COVID-IMPACT , Secondary Uses Services Payment By Results

Valid event data range

01/01/1997 - 07/12/2020

Sex

♀ Female ♂ Male

Agreement Date

2021-11-24

Coding system

SNOMED CT codes

Collections

BHF Data Science Centre Phenotype Library

Definition

Publications

Rochelle Knight, Venexia Walker, Samantha Ip, Jennifer A Cooper, Thomas Bolton, Spencer Keene, Rachel Denholm, Ashley Akbari, Hoda Abbasizanjani, Fatemeh Torabi, Efosa Omigie, Sam Hollings, Teri-Louise North, Renin Toms, Emanuele Di Angelantonio, Spiros Denaxas, Johan H Thygesen, Christopher Tomlinson, Ben Bray, Craig J Smith, Mark Barber, George Davey Smith, Nishi Chaturvedi, Cathie Sudlow, William N Whiteley, Angela Wood, Jonathan A C Sterne, for the CVD-COVID-UK/COVID-IMPACT consortium and th

Clinical Code List

CSV

JSON

XML

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C2756/7277 CCU002_01 Confirmed COVID-19 diagnoses - Phenotypes - England primary care EHR: COVID-19 diagnosis - SNOMED CT codes

Rows: 43

Code	Description	terminology
1008541000000105	Coronavirus ribonucleic acid detection assay (observable entity)	SNOMEDCT
1029481000000103	Coronavirus nucleic acid detection assay (observable entity)	SNOMEDCT
120814005	Coronavirus antibody (substance)	SNOMEDCT
121973000	Measurement of coronavirus antibody (procedure)	SNOMEDCT
1240381000000105	Severe acute respiratory syndrome coronavirus 2 (organism)	SNOMEDCT
1240391000000107	Antigen of severe acute respiratory syndrome coronavirus 2 (substance)	SNOMEDCT
1240401000000105	Antibody to severe acute respiratory syndrome coronavirus 2 (substance)	SNOMEDCT
1240411000000107	Ribonucleic acid of severe acute respiratory syndrome coronavirus 2 (substance)	SNOMEDCT
1240421000000101	Serotype severe acute respiratory syndrome coronavirus 2 (qualifier value)	SNOMEDCT
1240511000000106	Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure)	SNOMEDCT
1240521000000100	Otitis media caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1240531000000103	Myocarditis caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1240541000000107	Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1240551000000105	Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1240561000000108	Encephalopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1240571000000101	Gastroenteritis caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1240581000000104	Severe acute respiratory syndrome coronavirus 2 ribonucleic acid detected (finding)	SNOMEDCT
1240741000000103	Severe acute respiratory syndrome coronavirus 2 serology (observable entity)	SNOMEDCT
1240751000000100	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1300631000000101	Coronavirus disease 19 severity score (observable entity)	SNOMEDCT
1300671000000104	Coronavirus disease 19 severity scale (assessment scale)	SNOMEDCT
1300681000000102	Assessment using coronavirus disease 19 severity scale (procedure)	SNOMEDCT
1300721000000109	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation)	SNOMEDCT
1300731000000106	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed using clinical diagnostic criteria (situation)	SNOMEDCT
1321181000000108	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 record extraction simple reference set (foundation metadata concept)	SNOMEDCT
1321191000000105	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 procedures simple reference set (foundation metadata concept)	SNOMEDCT
1321201000000107	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 health issues simple reference set (foundation metadata concept)	SNOMEDCT
1321211000000109	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 presenting complaints simple reference set (foundation metadata concept)	SNOMEDCT
1321241000000105	Cardiomyopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder)	SNOMEDCT
1321301000000101	Severe acute respiratory syndrome coronavirus 2 ribonucleic acid qualitative existence in specimen (observable entity)	SNOMEDCT
1321311000000104	Severe acute respiratory syndrome coronavirus 2 immunoglobulin M qualitative existence in specimen (observable entity)	SNOMEDCT
1321321000000105	Severe acute respiratory syndrome coronavirus 2 immunoglobulin G qualitative existence in specimen (observable entity)	SNOMEDCT
1321331000000107	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 total immunoglobulin in serum (observable entity)	SNOMEDCT
1321341000000103	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin G in serum (observable entity)	SNOMEDCT
1321351000000100	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin M in serum (observable entity)	SNOMEDCT
1321541000000108	Severe acute respiratory syndrome coronavirus 2 immunoglobulin G detected (finding)	SNOMEDCT
1321551000000106	Severe acute respiratory syndrome coronavirus 2 immunoglobulin M detected (finding)	SNOMEDCT
1321761000000103	Severe acute respiratory syndrome coronavirus 2 immunoglobulin A detected (finding)	SNOMEDCT
1321801000000108	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin A in serum (observable entity)	SNOMEDCT
1321811000000105	Severe acute respiratory syndrome coronavirus 2 immunoglobulin A qualitative existence in specimen (observable entity)	SNOMEDCT
1322781000000102	Severe acute respiratory syndrome coronavirus 2 antigen detection result positive (finding)	SNOMEDCT
1322871000000109	Severe acute respiratory syndrome coronavirus 2 antibody detection result positive (finding)	SNOMEDCT
186747009	Coronavirus infection (disorder)	SNOMEDCT

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH954/version/2132/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH954/version/2132/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('PH954', '2132', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH954/version/2132/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH954/version/2132/export/codes/?format=json
CSV	site_root/phenotypes/PH954/version/2132/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('PH954', '2132', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
2132	CCU002_01 Confirmed COVID-19 diagnoses	ieuan.scanlon	2022-05-17	currently shown
1987	CCU002_01 Confirmed COVID-19 diagnoses	ieuan.scanlon	2022-05-09