Any malignancy - Charlson primary care

David Metcalfe, James Masters, Antonella Delmestri, Andrew Judge, Daniel Perry, Cheryl Zogg, Belinda Gabbe, Matthew Costa

PH1052 / 2307 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    No data
    Coding System
    Read codes v2
    Data Sources
    No data
    Collections
    Phenotype Library
    Tags
    Comorbidity Index
    Ontology
    No data

  2. Definition

    Any malignancy comorbidity category for Charlson index, defined in Read codes for primary care by David Metcalfe et. al. The Charlson comorbidity index score for this phenotype is 2.

  3. Implementation

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    Related publications

    • Metcalfe, D., Masters, J., Delmestri, A. et al. Coding algorithms for defining Charlson and Elixhauser co-morbidities in Read-coded databases. BMC Med Res Methodol 19, 115 (2019). https://doi.org/10.1186/s12874-019-0753-5

      (DOI: 10.1186/s12874-019-0753-5)

    • Charlson ME, Pompei P, Ales KL, et al. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. J Chronic Dis. 1987;40(5):373–83.

    • Lyons J, Akbari A, Agrawal U, et al Protocol for the development of the Wales Multimorbidity e-Cohort (WMC): data sources and methods to construct a population-based research platform to investigate multimorbidity BMJ Open 2021;11:e047101. doi: 10.1136/bmjopen-2020-047101

      (DOI: 10.1136/bmjopen-2020-047101)

    Citation Example

    David Metcalfe, James Masters, Antonella Delmestri, Andrew Judge, Daniel Perry, Cheryl Zogg, Belinda Gabbe, Matthew Costa. PH1052 / 2307 - Any malignancy - Charlson primary care. Phenotype Library [Online]. 13 February 2023. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH1052/version/2307/detail/. [Accessed 25 April 2025]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1052/version/2307/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(
     'PH1052',
     version_id=2307
    )

    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(
     'PH1052',
     version_id=2307
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1052/version/2307/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(
     'PH1052',
     version_id=2307
    )

    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(
     'PH1052',
     version_id=2307
    )

  7. Version History

    Version IDNameOwnerPublish date
    Any malignancy - Charlson primary care coldeaa2023-02-14 14:56