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
Overview
Phenotype TypeDisease or syndromeSexBothValid Event Date Range01/03/2020-05/04/2020Coding SystemSNOMED CT codesData SourcesKings College Hospital NHS Foundation TrustCollectionsPhenotype LibraryTagsNo dataDefinition
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
Implementation
Phenoflow IDImplementation
Clinical Code List
PUBLISHED - 1 Codes
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]
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH21/version/42/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH21',
version_id=42
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH21',
version_id=42
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH21/version/42/export/codes/?format=json CSV site_root/phenotypes/PH21/version/42/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH21',
version_id=42
)Py Package 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
)Version History