Asthma

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

PH21 / 42 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/03/2020-05/04/2020
    Coding System
    SNOMED CT codes
    Data Sources
    Kings College Hospital NHS Foundation Trust
    Collections
    Phenotype Library
    Tags
    No data

  2. 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

  3. Implementation

    Phenoflow ID
    https://kclhi.org/phenoflow/phenotype/download/43

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    • 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

      (DOI:10.1101/2020.04.24.20078006)

    Citation Example

    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. PH21 / 42 - Asthma. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH21/version/42/detail/. [Accessed 30 October 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH21/version/42/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH21',
     version_id=42
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_detail(
     'PH21',
     version_id=42
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH21/version/42/export/codes/?format=json
    CSV site_root/phenotypes/PH21/version/42/export/codes/
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH21',
     version_id=42
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH21',
     version_id=42
    )

  7. Version History

    Version IDNameOwnerPublish date
    42 Asthma ieuan.scanlon2021-10-06currently shown