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Cystic Fibrosis

Tim Doran, Evangelos Kontopantelis, Jose M Valderas, Stephen Campbell, Martin Roland, Chris Salisbury, David Reeves

Type
Disease or Syndrome
ID
PH416
Version ID
832
Data Sources
Valid event data range
01/01/2000 - 31/12/2007
Sex
Female, Male
Agreement Date
2011-06-28
Coding system
Read codes v2 OXMIS codes
Tags /Collections
ClinicalCodes Repository Phenotype Library

Definition

Patient level data were extracted from the General Practice Research Database (GPRD), which contains anonymised, patient based data on morbidity, prescribing, treatment, and referral collected from over 500 general practices, covering about 7% of the UK population (4.4 million patients).14 Data are in Read code format—a hierarchical system used to code clinical data. Additional data on prescriptions and test results are available as free-text entries. We selected a sample of 148 practices that provided data to the GPRD continuously between January 2000 and December 2007, structured to include a range of list (patient panel) sizes. Selected practices were nationally representative in terms of patient sex and age distribution and area socioeconomic deprivation but had a relatively large average list size, reflecting a bias towards larger practices in the GPRD. Overall, the selected practices performed marginally better than national practices on the clinical indicators in the Quality and Outcomes Framework. A random selection of 4500 patients registered for at least one day between 1 January 2000 and 31 December 2007 was drawn from each practice. For practices with fewer than 4501 patients, all patients were selected. The final sample consisted of 653 500 patients. Patients with relevant conditions were identified from their diagnostic Read codes. Patients for whom targets were met were identified from the relevant Read codes and free-text terms.

Publications

  • Tim Doran, Evangelos Kontopantelis, Jose M Valderas, Stephen Campbell, Martin Roland, Chris Salisbury, David Reeves, Effect of financial incentives on incentivised and non-incentivised clinical activities: longitudinal analysis of data from the UK Quality and Outcomes Framework. BMJ, 342:d3590, 2011.

Clinical Code List

Rows: 10
Code Description Entity type Coding System (OXMIS Read) Category
C370.00 Cystic fibrosis cystic fibrosis Read diagnostic
C370.12 Mucoviscidosis cystic fibrosis Read diagnostic
C370000 Cystic fibrosis with no meconium ileus cystic fibrosis Read diagnostic
C370100 Cystic fibrosis with meconium ileus cystic fibrosis Read diagnostic
C370111 Meconium ileus in cystic fibrosis cystic fibrosis Read diagnostic
C370200 Cystic fibrosis with pulmonary manifestations cystic fibrosis Read diagnostic
C370300 Cystic fibrosis with intestinal manifestations cystic fibrosis Read diagnostic
C370y00 Cystic fibrosis with other manifestations cystic fibrosis Read diagnostic
C370y11 Cystic fibrosis with combined manifestations cystic fibrosis Read diagnostic
C370z00 Cystic fibrosis NOS cystic fibrosis Read diagnostic
Rows: 2
Code Description Entity type Coding System (OXMIS Read) Category
2730A FIBROSIS CYSTIC cystic fibrosis OXMIS diagnostic
7484F FIBROCYSTIC DISEASE LUNG cystic fibrosis OXMIS diagnostic

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH416/version/832/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH416/version/832/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('PH416', '832', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH416/version/832/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH416/version/832/export/codes/?format=json
CSV site_root/phenotypes/PH416/version/832/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('PH416', '832', api_client=client)

Version History

Version
ID
Name Owner Publish date
832 Cystic Fibrosis 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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