COVID-19 infection

PH1 / 2

BHF CVD COVID UK Consortium

Oct 6, 2021

BHF Data Science Centre Phenotype

  1. Overview

    Project Name
    None
    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
    Civil Registration - Deaths
    Covid-19 Second Generation Surveillance System
    Ontology
    No data
    Collections
    BHF Data Science CentrePhenotype Library
    Tags
    No data

  2. Definition

    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.

    Clinical Trials

    No Trials

    Endorsements

    No endorsement

  3. Implementation

    Phenoflow ID

    Please see the PhenoFLOW website here for more information on workflow-based Phenotypes.

    PhenoFLOW Reference: https://kclhi.org/phenoflow/workflows/github.com/phenoflow/COVID-19-infection---0ad8bf70-16ea-11ef-9de4-4d4ea830ad16/blob/read-potential-cases-fhir/COVID-19-infection.cwl

    Implementation

    No data

  4. Clinical Codelist

  5. Publication

    Related publications

    No known 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 27 January 2026]

  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 details of Phenotype

    phenotype_detail = 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
    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
    COVID-19 infection ieuan.scanlon2021-10-06 15:58