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 / 3522 Clinical-Coded Phenotype
Overview
Phenotype TypeDisease or syndromePhenotype UUIDexcel-ADP-idS7NG1SexBothValid Event Date RangeNo dataCoding SystemSNOMED CT codesICD10 codesRead codes v2Read codes v3CollectionsAdolescent Data Platform (ADP)DATAMINDPhenotype LibraryTagsNo dataDefinition
Severe mental illnesses (SMIs) refer 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:
Schizophrenia: Include schizophrenia, schizotypal and delusional disorders.
Bipolar disorder and other mood related disorders: Include bipolar disorder, manic depressive episodes with psychotic symptoms.
This phenotype excludes organic psychoses (e.g., drug and alcohol induced) and psychoses with origins in childhood.
Read code, SNOMED CT and ICD-10 definitions
Details about each of these definitions can be found in the respective phenotypes for schizophrenia, bipolar disorder and other mood related disorders, and other psychotic disorders and severe mental illnesses.
References
Economou, A., Grey, M., McGregor, J., Craddock, N., Lyons, R. A., Owen, M. J., ... & 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, 1-6.
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, 1-6.
Implementation
Implementation
Information on algorithm construction are included in the following papers (Economou et. al. 2012; McGregor et. al. 2010).
References
John, A., McGregor, J., Jones, I., Lee, S. C., Walters, J. T., Owen, M. J., ... & Lloyd, K. (2018). Premature mortality among people with severe mental illness—New evidence from linked primary care data. Schizophrenia research, 199, 154-162.
Clinical Code List
PUBLISHED - 97 Codes
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PUBLISHED - 80 Codes
PUBLISHED - 928 Codes
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PUBLISHED - 34 Codes
PUBLISHED - 404 Codes
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. The Lancet Psychiatry, 9(1), 23-34. https://doi.org/10.1016/S2215-0366(21)00367-9
(DOI:10.1016/S2215-0366(21)00367-9)Economou, A., Grey, M., McGregor, J., Craddock, N., Lyons, R. A., Owen, M. J., ... & 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, 1-6. https://link.springer.com/article/10.1186/1756-0500-5-95
(DOI:10.1186/1756-0500-5-95)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, 1-6. https://link.springer.com/article/10.1186/1745-6215-11-39
(DOI:10.1186/1745-6215-11-39)
Citation Requirements
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
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 / 3522 - Severe Mental Illnesses. Phenotype Library [Online]. 22 July 2024. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH940/version/3522/detail/. [Accessed 27 July 2024]
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH940/version/3522/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH940',
version_id=3522
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH940',
version_id=3522
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH940/version/3522/export/codes/?format=json CSV site_root/phenotypes/PH940/version/3522/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH940',
version_id=3522
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_codelist(
'PH940',
version_id=3522
)Version History