COVID-19 infection

BHF CVD COVID UK Consortium

PH1 / 2 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2020 - 31/10/2020
    Coding System
    ICD10 codesSNOMED CT 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
    Collections
    BHF Data Science CentrePhenotype Library
    Tags
    No data

  2. Definition

    We ascertained people with a confirmed or suspected Covid-19 diagnosis as follows:

    1) a positive PCR or antigen test from the Covid-19 laboratory test data, with specimen date on or before 31 October 2020; or

    2) a Covid-19 diagnosis SNOMED-CT concept code appearing in the primary care data, with event date on or before 31 October; or

    3) a diagnosis ICD-10 code appearing in the hospital episodes (main or secondary diagnostic code position in the admitted patient care component of the hospital episode statistics), with admission date on or before 31 October or

    4) death registration with a mention (as underlying on contributing cause) of a diagnosis ICD-10 code , with death registration date on or before 31 October 2020.

  3. Implementation

    Phenoflow ID
    https://kclhi.org/phenoflow/phenotype/download/1

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    No publications

    Citation Example

    BHF CVD COVID UK Consortium. PH1 / 2 - COVID-19 infection. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH1/version/2/detail/. [Accessed 21 November 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1/version/2/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(
     'PH1',
     version_id=2
    )

    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(
     'PH1',
     version_id=2
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1/version/2/export/codes/?format=json
    CSV site_root/phenotypes/PH1/version/2/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(
     'PH1',
     version_id=2
    )

    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(
     'PH1',
     version_id=2
    )

  7. Version History

    Version IDNameOwnerPublish date
    2 COVID-19 infection ieuan.scanlon2021-10-06currently shown