Phenotype Library | phenotype: Heart failure

Heart failure

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

PH25

Version ID

Type

Disease or Syndrome

Data Sources

Kings College Hospital NHS Foundation Trust

Valid event data range

01/03/2020-05/04/2020

Sex

♀ Female ♂ Male

Agreement Date

2020-05-03

Coding system

SNOMED CT codes

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

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/87

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

CSV

JSON

XML

Expand All / Collapse All

C769/2677 Heart failure - Secondary care - SNOMED CT codes

Rows: 5

Code	Description
10633002	Acute congestive heart failure (disorder)
418304008	Diastolic heart failure (disorder)
42343007	Congestive heart failure (disorder)
426263006	Congestive heart failure due to left ventricular systolic dysfunction (disorder)
48447003	Chronic heart failure (disorder)

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH25/version/50/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH25/version/50/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('PH25', '50', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH25/version/50/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH25/version/50/export/codes/?format=json
CSV	site_root/phenotypes/PH25/version/50/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('PH25', '50', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
50	Heart failure	ieuan.scanlon	2021-10-06	currently shown