Deaths by certain infectious and parasitic diseases (natural cause)

John, A, McGregor, J., Jones, I., Lee, S. C., Walters, J. T. R., Owen, M. J., O'Donovan, M., DelPozo-Banos, M., Berridge, D., & Lloyd, K.

PH1472 / 2987 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    No data
    Coding System
    ICD10 codes
    Data Sources
    No data
    Collections
    Adolescent Data Platform (ADP)DATAMINDPhenotype Library
    Tags
    No data

  2. Definition

    Causes of deaths are ICD-10 codes associated with the “underlying cause of death” from the Office for National Statistics death registry. Based on a previous study (John et al., 2018), causes of deaths are first grouped into natural and unnatural main categories and then further grouped in accordance with the respective chapters of ICD-10:

    Natural causes

    Unnatural causes

    As discussed with a clinician in the study team (Prof Ann John), all codes related to deaths by suicide but with age of death not complying with the corresponding age criteria should be regarded as deaths by unknown causes. References John, A., McGregor, J., Jones, I., Lee, S.C., Walters, J.T., Owen, M.J., O'Donovan, M., DelPozo-Banos, M., Berridge, D. & Lloyd, K. (2018). Premature mortality among people with severe mental illness — New evidence from linked primary care data. Schizophrenia Research, 199, 154-162.

  3. Implementation

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    Citation Example

    John, A, McGregor, J., Jones, I., Lee, S. C., Walters, J. T. R., Owen, M. J., O'Donovan, M., DelPozo-Banos, M., Berridge, D., & Lloyd, K.. PH1472 / 2987 - Deaths by certain infectious and parasitic diseases (natural cause). Phenotype Library [Online]. 13 November 2023. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH1472/version/2987/detail/. [Accessed 23 November 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1472/version/2987/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(
     'PH1472',
     version_id=2987
    )

    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(
     'PH1472',
     version_id=2987
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1472/version/2987/export/codes/?format=json
    CSV site_root/phenotypes/PH1472/version/2987/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(
     'PH1472',
     version_id=2987
    )

    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(
     'PH1472',
     version_id=2987
    )

  7. Version History

    Version IDNameOwnerPublish date
    2987 Deaths by certain infectious and parasitic diseases (natural cause) lees2023-11-28currently shown