Phenotypes > Infections of the digestive system

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Infections of the digestive system

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

ID
PH153
Version ID
306
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
Tags
No tags

Definition

At the specified date, a patient is defined as having had Infections of the digestive system 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

  1. ALL diagnoses of Infections of the digestive system or history of diagnosis during a hospitalization

Implementation


https://kclhi.org/phenoflow/phenotype/download/442

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

Expand All  /  Collapse All
Rows: 26
Code Description Disease Category
A00 Cholera Infections of the digestive system Diagnosis of Infections of the digestive system
A01 Typhoid and paratyphoid fevers Infections of the digestive system Diagnosis of Infections of the digestive system
A02.0 Salmonella enteritis Infections of the digestive system Diagnosis of Infections of the digestive system
A03 Shigellosis Infections of the digestive system Diagnosis of Infections of the digestive system
A04 Other bacterial intestinal infections Infections of the digestive system Diagnosis of Infections of the digestive system
A05 Other bacterial foodborne intoxications, not elsewhere classified Infections of the digestive system Diagnosis of Infections of the digestive system
A06.0 Acute amoebic dysentery Infections of the digestive system Diagnosis of Infections of the digestive system
A06.1 Chronic intestinal amoebiasis Infections of the digestive system Diagnosis of Infections of the digestive system
A06.2 Amoebic nondysenteric colitis Infections of the digestive system Diagnosis of Infections of the digestive system
A06.3 Amoeboma of intestine Infections of the digestive system Diagnosis of Infections of the digestive system
A07 Other protozoal intestinal diseases Infections of the digestive system Diagnosis of Infections of the digestive system
A08 Viral and other specified intestinal infections Infections of the digestive system Diagnosis of Infections of the digestive system
A09 Other gastroenteritis and colitis of infectious and unspecified origin Infections of the digestive system Diagnosis of Infections of the digestive system
A18.3 Tuberculosis of intestines, peritoneum and mesenteric glands Infections of the digestive system Diagnosis of Infections of the digestive system
A21.3 Gastrointestinal tularaemia Infections of the digestive system Diagnosis of Infections of the digestive system
A22.2 Gastrointestinal anthrax Infections of the digestive system Diagnosis of Infections of the digestive system
B05.4 Measles with intestinal complications Infections of the digestive system Diagnosis of Infections of the digestive system
B46.2 Gastrointestinal mucormycosis Infections of the digestive system Diagnosis of Infections of the digestive system
B78.0 Intestinal strongyloidiasis Infections of the digestive system Diagnosis of Infections of the digestive system
B81 Other intestinal helminthiases, not elsewhere classified Infections of the digestive system Diagnosis of Infections of the digestive system
B82 Unspecified intestinal parasitism Infections of the digestive system Diagnosis of Infections of the digestive system
B98.0 Helicobacter pylori [H.pylori] as the cause of diseases classified to other chapters Infections of the digestive system Diagnosis of Infections of the digestive system
K23.0 Tuberculous oesophagitis Infections of the digestive system Diagnosis of Infections of the digestive system
K23.1 Megaoesophagus in Chagas' disease Infections of the digestive system Diagnosis of Infections of the digestive system
K63.0 Abscess of intestine Infections of the digestive system Diagnosis of Infections of the digestive system
K93.0 Tuberculous disorders of intestines, peritoneum and mesenteric glands Infections of the digestive system Diagnosis of Infections of the digestive system

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH153/version/306/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH153/version/306/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('PH153', '306', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH153/version/306/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH153/version/306/export/codes/?format=json
CSV site_root/phenotypes/PH153/version/306/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('PH153', '306', api_client=client)

Version History

Version
ID		 Name Owner Publish date
306 Infections of the digestive system 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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