Phenotype Library | phenotype: Mycoses

Mycoses

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

PH214

Version ID

428

Type

Disease or Syndrome

Data Sources

HES Admitted Patient Care data for CPRD GOLD

Valid event data range

01/01/1999 - 01/07/2016

Sex

♀ Female ♂ Male

Agreement Date

2019-05-20

Coding system

ICD10 codes

Collections

CALIBER Phenotype Library

Definition

At the specified date, a patient is defined as having had Mycoses 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:

Secondary care

ALL diagnoses of Mycoses or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/619

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

CSV

JSON

XML

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C1295/3729 Mycoses - Secondary care - Diagnoses - ICD10 codes

Rows: 23

Code	Description	Disease	Category
B20.4	HIV disease resulting in candidiasis	Mycoses	Diagnosis of mycoses
B20.5	HIV disease resulting in other mycoses	Mycoses	Diagnosis of mycoses
B20.6	HIV disease resulting in Pneumocystis jirovecii pneumonia	Mycoses	Diagnosis of mycoses
B35	Dermatophytosis	Mycoses	Diagnosis of mycoses
B36	Other superficial mycoses	Mycoses	Diagnosis of mycoses
B37	Candidiasis	Mycoses	Diagnosis of mycoses
B38	Coccidioidomycosis	Mycoses	Diagnosis of mycoses
B39	Histoplasmosis	Mycoses	Diagnosis of mycoses
B40	Blastomycosis	Mycoses	Diagnosis of mycoses
B41	Paracoccidioidomycosis	Mycoses	Diagnosis of mycoses
B42	Sporotrichosis	Mycoses	Diagnosis of mycoses
B43	Chromomycosis and phaeomycotic abscess	Mycoses	Diagnosis of mycoses
B44	Aspergillosis	Mycoses	Diagnosis of mycoses
B45	Cryptococcosis	Mycoses	Diagnosis of mycoses
B46	Zygomycosis	Mycoses	Diagnosis of mycoses
B47	Mycetoma	Mycoses	Diagnosis of mycoses
B48	Other mycoses, not elsewhere classified	Mycoses	Diagnosis of mycoses
B49	Unspecified mycosis	Mycoses	Diagnosis of mycoses
B59	Pneumocystosis	Mycoses	Diagnosis of mycoses
G02.1	Meningitis in mycoses	Mycoses	Diagnosis of mycoses
H62.2	Otitis externa in mycoses	Mycoses	Diagnosis of mycoses
J17.2	Pneumonia in mycoses	Mycoses	Diagnosis of mycoses
M01.6	Arthritis in mycoses	Mycoses	Diagnosis of mycoses

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH214/version/428/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH214/version/428/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('PH214', '428', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH214/version/428/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH214/version/428/export/codes/?format=json
CSV	site_root/phenotypes/PH214/version/428/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('PH214', '428', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
428	Mycoses	ieuan.scanlon	2021-10-06	currently shown