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

PH1020 / 2198 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    23/01/2020 - 31/05/2021
    Coding System
    SNOMED CT codesICD10 codesOPCS4 codes
    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 , COVID-19 SARI-Watch (formerly CHESS)
    Collections
    BHF Data Science CentrePhenotype Library
    Tags
    No data

  2. Definition

  3. Implementation

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    • 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

    Citation Requirements

    No data

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1020/version/2198/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH1020',
     version_id=2198
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_detail(
     'PH1020',
     version_id=2198
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/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 = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH1020',
     version_id=2198
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH1020',
     version_id=2198
    )

  7. Version History

    Version IDNameOwnerPublish date
    2198 CCU013_01 COVID-19 infection ieuan.scanlon2022-05-17currently shown
    2119 CCU013_01 COVID-19 infection ieuan.scanlon2022-05-09