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Primary Malignancy_Mesothelioma

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

Type
Disease or Syndrome
ID
PH258
Version ID
516
Valid event data range
01/01/1999 - 01/07/2016
Sex
Female, Male
Agreement Date
2019-05-20
Coding system
Read codes v2 ICD10 codes Med codes
Tags /Collections
CALIBER Phenotype Library

Definition

At the specified date, a patient is defined as having had Primary Malignancy Mesothelioma 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_Mesothelioma diagnosis or history of diagnosis during a consultation

OR Secondary care

  1. ALL diagnoses of Primary Malignancy_Mesothelioma or history of diagnosis during a hospitalization

Implementation


Publications

  • 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

Clinical Code List

Rows: 4
Code Description Disease Medcode Category
BBP1.00 [M]Mesothelioma, malignant Primary Malignancy_Mesothelioma 27509.0 Diagnosis of Primary Malignancy_Mesothelioma
BBP3.11 [M]Sarcomatoid mesothelioma Primary Malignancy_Mesothelioma 104720.0 Diagnosis of Primary Malignancy_Mesothelioma
BBP5.00 [M]Epithelioid mesothelioma, malignant Primary Malignancy_Mesothelioma 47734.0 Diagnosis of Primary Malignancy_Mesothelioma
BBP7.00 [M]Mesothelioma, biphasic type, malignant Primary Malignancy_Mesothelioma 86820.0 Diagnosis of Primary Malignancy_Mesothelioma
Rows: 4
Code Description Disease ReadcodeDescr Readcode
104720.0 Diagnosis of Primary Malignancy_Mesothelioma Primary Malignancy_Mesothelioma [M]Sarcomatoid mesothelioma BBP3.11
27509.0 Diagnosis of Primary Malignancy_Mesothelioma Primary Malignancy_Mesothelioma [M]Mesothelioma, malignant BBP1.00
47734.0 Diagnosis of Primary Malignancy_Mesothelioma Primary Malignancy_Mesothelioma [M]Epithelioid mesothelioma, malignant BBP5.00
86820.0 Diagnosis of Primary Malignancy_Mesothelioma Primary Malignancy_Mesothelioma [M]Mesothelioma, biphasic type, malignant BBP7.00
Rows: 1
Code Description Disease Category
C45 Mesothelioma Primary Malignancy_Mesothelioma Diagnosis of Primary Malignancy_Mesothelioma

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH258/version/516/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH258/version/516/detail/?format=json
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get details of phenotype

details = get_phenotype_detail_by_version('PH258', '516', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH258/version/516/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH258/version/516/export/codes/?format=json
CSV site_root/phenotypes/PH258/version/516/export/codes/
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get codelists of phenotype

codelists = get_phenotype_code_list('PH258', '516', api_client=client)

Version History

Version
ID
Name Owner Publish date
516 Primary Malignancy_Mesothelioma ieuan.scanlon 2021-10-06 currently shown

Export - export all codes into a csv file/JSON/XML for the current phenotype version.

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