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Chronic Obstructive Pulmonary Disease (COPD)

Carr E, Bendayan R, Bean D, OGallagher K, Pickles A, Stahl D, Zakeri R, Searle T, Shek A, Kraljevic Z, Teo J, Shah A, Dobson R

Type
Disease or Syndrome
ID
PH23
Version ID
46
Data Sources
Kings College Hospital NHS Foundation Trust
Valid event data range
01/03/2020-05/04/2020
Sex
Female, Male
Agreement Date
Coding system
SNOMED CT codes
Tags /Collections
Phenotype Library

Definition

The data (demographics, emergency department letters, discharge summaries, clinical notes, lab results, vital signs) were retrieved and analyzed in near real-time from the structured and unstructured components of the electronic health record (EHR) using a variety of natural language processing (NLP) informatics tools belonging to the CogStack ecosystem, namely MedCAT and MedCATTrainer. The CogStack NLP pipeline captures negation, synonyms, and acronyms for medical SNOMED-CT concepts as well as surrounding linguistic context using deep learning and long short-term memory networks. MedCAT produces unsupervised annotations for all SNOMED-CT concepts under parent terms Clinical Finding, Disorder, Organism, and Event with disambiguation, pre-trained on MIMIC-III. The annotated SNOMED-CT terms are summarised below

Publications

  • Carr E, Bendayan R, Bean D, OGallagher K, Pickles A, Stahl D, Zakeri R, Searle T, Shek A, Kraljevic Z, Teo J, Shah A, Dobson R. (2020) Supplementing the National Early Warning Score (NEWS2) for anticipating early deterioration among patients with COVID-19 infection. medRxiv DOI: 10.1101/2020.04.24.20078006

Clinical Code List

Rows: 2
Code Description
13645005 Chronic obstructive lung disease (disorder)
313297008 Moderate chronic obstructive pulmonary disease (disorder)

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH23/version/46/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH23/version/46/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('PH23', '46', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH23/version/46/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH23/version/46/export/codes/?format=json
CSV site_root/phenotypes/PH23/version/46/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('PH23', '46', api_client=client)

Version History

Version
ID
Name Owner Publish date
46 Chronic Obstructive Pulmonary Disease (COPD) 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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