Primary Malignancy_colorectal and anus

Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A

PH250 / 500 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/1999 - 01/07/2016
    Coding System
    Read codes v2Med codesICD10 codes
    Data Sources
    CPRD GOLD , HES Admitted Patient Care data for CPRD GOLD
    Collections
    CALIBERPhenotype Library
    Tags
    No data

  2. Definition

    At the specified date, a patient is defined as having had Primary Malignancy colorectal and anus IF they meet the criteria for any of the following on or before the specified date. The earliest date on which the individual meets any of the following criteria on or before the specified date is defined as the first event date:

    Primary care

    1. Primary Malignancy colorectal and anus diagnosis or history of diagnosis during a consultation

    OR Secondary care

    1. ALL diagnoses of Primary Malignancy colorectal and anus or history of diagnosis during a hospitalization

  3. Implementation

    Phenoflow ID
    https://kclhi.org/phenoflow/phenotype/download/727

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    • Kuan V., Denaxas S., Gonzalez-Izquierdo A. et al. A chronological map of 308 physical and mental health conditions from 4 million individuals in the National Health Service. The Lancet Digital Health - DOI 10.1016/S2589-7500(19)30012-3

      (DOI:10.1016/S2589-7500(19)30012-3)

    Citation Requirements

    No data

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH250/version/500/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(
     'PH250',
     version_id=500
    )

    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(
     'PH250',
     version_id=500
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH250/version/500/export/codes/?format=json
    CSV site_root/phenotypes/PH250/version/500/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(
     'PH250',
     version_id=500
    )

    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(
     'PH250',
     version_id=500
    )

  7. Version History

    Version IDNameOwnerPublish date
    500 Primary Malignancy_colorectal and anus ieuan.scanlon2021-10-06currently shown