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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

ID
PH954
Version ID
2132
Type
Disease or Syndrome
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
Tags
No tags

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

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

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

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