Pneumonia - UK Biobank

Eleanor L Axson, Jennifer K Quint

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Clinical Code List

Name Version Type Logical type  
axson_pneumonia_GL46c8PLQMdPuj7QuPtEh9_SNOMEDCT - Expression Select Add codes
Code Description

Rows: 58
Code Description Hospital-Acquired Description Community-Acquired Read Codes used by Braeken et al. 2017 Read v2 Code
1033111000000104 Influenza with pneumonia due to seasonal influenza virus
111900000 Pneumonia with aspergillosis Y H246.00
191727003 Postmeasles pneumonia Y A551.00
195878008 Chest infection- influenza with pneumonia Y H270.11
195881003 Pneumonia due to respiratory syncytial virus Y H201.00
195886008 Pneumonia due to streptococcus, group B Y H223000
195888009 Pneumonia due to proteus Y H22y100
195889001 Pneumonia- legionella Y H22y200
195896004 Pneumonia due to pleuropneumonia like organisms Y H232.00
195900001 Measles pneumonia H240.99
195908008 Pneumonia with actinomycosis Y H24y000
195911009 Pneumonia with varicella Y H24y700
196112005 Abscess of lung with pneumonia Y H530300
205237003 Pneumonitis Y H263.00
22754005 Pneumonia due to staphylococcus Y H224.00
233606009 Atypical pneumonia Y H28..00
233609002 Chlamydial pneumonia Y H233.00
233624006 Herpes simplex pneumonia Y A54x400
2523007 Salmonella pneumonia Y A022200
266350000 Chest infection- pneumococcal pneumonia Y H21..11
278516003 Lobar pneumonia
300999006 Basal pneumonia
301000005 Left lower zone pneumonia
301001009 Right lower zone pneumonia
301002002 Left upper zone pneumonia
301003007 Right middle zone pneumonia
301004001 Right upper zone pneumonia
312342009 [X]Other pneumonia, organism unspecified Hyu0H00
314978007 Postoperative pneumonia H262.00
34020007 Pneumonia due to streptococcus Y H223.00
385093006 Community acquired pneumonia Y Y H2B..00
396285007 Bronchopneumonia
406595002 [X]Mycoplasma pneumoniae [PPLO]cause/dis classifd/oth chaptr AyuK900
40733004 [X]Klebsiella pneumoniae/cause/disease classifd/oth chapters AyuKA00
41207000 Pneumonia due to adenovirus Y H200.00
41269000 Influenza with bronchopneumonia H270000
41381004 Pneumonia due to pseudomonas Y H221.00
415125002 Pneumonia with pneumocystis carinii Y H24y200
425464007 Y Hospital acquired pneumonia H2C..00
425996009 Bilateral basal pneumonia
426696003 Lingular pneumonia
440990006 Mycoplasma pneumoniae detected 4JUK.00
46970008 Mycoplasma pneumonia H231.99
51530003 E.coli pneumonia Y H22y011
53084003 [X]Other bacterial pneumonia Y Hyu0A00
540151000000108 Bilateral pneumonia H2z..98
59475000 Pneumonia with pertussis Y H243.11
64479007 Pneumonia due to Klebsiella pneumoniae Y H220.00
64667001 Interstitial pneumonia Y H56y100
64917006 Pneumonia due to parainfluenza virus Y H202.00
689401000000108 Bronchopneumonia H25..99
70036007 Pneumonia due to Haemophilus influenzae Y H222.00
7548000 Rheumatic pneumonia H571.00
75570004 [X]Other viral pneumonia Y Hyu0800
80003002 Tuberculous pneumonia A116.00
87628006 Other specified bacterial infection Y A3By.00
95436008 Lung consolidation Y H260000
9861002 Streptococcus pneumoniae


To Export Concept Details:

Format API
XML site_root/api/v1/public/concepts/C754/version/2647/detail/?format=xml
JSON site_root/api/v1/public/concepts/C754/version/2647/detail/?format=json
R Package

# Download here


# Connect to API

client = connect_to_API(public=TRUE)

# Get details of concept

details = get_concept_detail_by_version('C754', '2647', api_client=client)

To Export Concept Code List:

Format API
XML site_root/api/v1/public/concepts/C754/version/2647/export/codes/?format=xml
JSON site_root/api/v1/public/concepts/C754/version/2647/export/codes/?format=json
CSV site_root/concepts/C754/version/2647/export/codes/
R Package

# Download here


# Connect to API

client = connect_to_API(public=TRUE)

# Get codelist of concept

codelist = get_concept_code_list_by_version('C754', '2647', api_client=client)

Version History

Name Description Owner Publish date
2647 Pneumonia - UK Biobank ieuan.scanlon 2021-10-06 currently shown

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Components are individual rules matching a set of codes. One or more components are used to define the codes contained within a concept.