Severe Mental Illnesses

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.

PH940 / 2966 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Phenotype UUID
    excel-ADP-idS7NG1
    Sex
    Both
    Valid Event Date Range
    No data
    Coding System
    Read codes v2
    Data Sources
    Welsh Longitudinal GP Dataset - Welsh Primary Care (WLGP), Patient Episode Dataset for Wales (PEDW)
    Collections
    Adolescent Data Platform (ADP)DATAMINDPhenotype Library
    Tags
    No data

  2. Definition

    Severe mental illnesses (SMIs) refers to individuals with psychological problems that are so debilitating that their ability to engage in functional and occupational activities is severely impaired. In keeping with the literature (John et al., 2018), SMIs are divided into three categories: 1) schizophrenia-related disorders (schizophrenia) that include schizophrenia, schizotypal and delusional disorders, 2) bipolar disorder and other mood related disorders that include bipolar disorder, manic depressive episodes with psychotic symptoms, and 3) other psychotic disorders/SMIs. The attached lists of Read codes and ICD-10 for SMIs are based on John et al. (2018) and reviewed by two clinicians (Prof. Keith Lloyd and Prof. Ann John) in the study team. The codes in these lists exclude organic psychoses (e.g., drug and alcohol induced) and psychoses with origins in childhood. Additional Read codes for 'other psychotic disorders' that were mapped to the ICD-10 codes for acute and transient psychotic disorders (F23), depressive episodes/disorders with psychotic symptoms (F32.3 and F33.3) were added to the list as reviewed by two clinicians (Prof. Keith Lloyd and Prof. Ann John) in the study team and were used in published study (John et al., 2022). Information on algorithm construction are included in the following papers (Economou et. al. 2012; McGregor et. al. 2010).

  3. Implementation

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    • 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. (2018). Premature mortality among people with severe mental illness - New evidence from linked primary care data. Schizophrenia Research, 199, 154-162. https://doi.org/10.1016/j.schres.2018.04.009

      (DOI:10.1016/j.schres.2018.04.009)

    • John, A., Friedmann, Y., Delpozo-Banos, M., Frizzati, A., Ford, T., & Thapar, A. 2022. "Association of School Absence and Exclusion with Recorded Neurodevelopmental Disorders, Mental Disorders, or Self-Harm: A Nationwide, Retrospective, Electronic Cohort Study of Children and Young People in Wales, UK."

    • Economou, A. Michelle G. McGregor, J. Craddock, N. Lyons, R,A. Owen, M.J. Price, V. Thomson, S. Walters, J.T. & Lloyd, K. (2012). "The Health Informatics Cohort Enhancement Project (HICE): Using Routinely Collected Primary Care Data to Identify People with a Lifetime Diagnosis of Psychotic Disorder." BMC Research Notes 5(1):1-6.

    • McGregor, J. Brooks, C. Chalasani, P. Chukwuma, J. Hutchings, H. Lyons, R,A. & Lloyd, K. (2010). "The Health Informatics Trial Enhancement Project (HITE): Using Routinely Collected Primary Care Data to Identify Potential Participants for a Depression Trial." Trials 11(1):1-6.

    • Main reference link: https://www.sciencedirect.com/science/article/pii/S0920996418301981?via%3Dihub

    Citation Requirements

    John A, Friedmann Y, DelPozo-Banos M, Frizzati A, Ford T, Thapar A. Association of school absence and exclusion with recorded neurodevelopmental disorders, mental disorders, or self-harm: a nationwide, retrospective, electronic cohort study of children and young people in Wales, UK. Lancet Psychiatry. 2022 Jan;9(1):23-34. doi: 10.1016/S2215-0366(21)00367-9.

    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.. PH940 / 2966 - Severe Mental Illnesses. Phenotype Library [Online]. 13 November 2023. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH940/version/2966/detail/. [Accessed 26 April 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH940/version/2966/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(
     'PH940',
     version_id=2966
    )

    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(
     'PH940',
     version_id=2966
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH940/version/2966/export/codes/?format=json
    CSV site_root/phenotypes/PH940/version/2966/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(
     'PH940',
     version_id=2966
    )

    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(
     'PH940',
     version_id=2966
    )

  7. Version History

    Version IDNameOwnerPublish date
    2966 Severe Mental Illnesses ieuan.scanlon2023-11-13currently shown
    2962 Severe Mental Illnesses ieuan.scanlon2023-11-13
    2951 Bipolar Disorder, Schizophrenia and Other Psychotic Disorders Primary Care ieuan.scanlon2023-11-08
    1959 Bipolar Disorder, Schizophrenia and Other Psychotic Disorders Primary Care ieuan.scanlon2022-05-05