Heart failure - Secondary care

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

ID
C769
Version ID
2677
Coding system
SNOMED CT codes
Tags /Collections
Phenotype Library
Owner
ieuan.scanlon

Description

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

Primary publication DOI
10.1101/2020.04.24.20078006
Primary publication link
Secondary publication link
Paper published
Source reference
Citation requirements

Clinical Code List


Name Version Type Logical type  
carr_heartfailure_eJywGK6XvyoSe4SBhSexb3_SNOMEDCT - Expression Select Add codes
Code Description
42343007 Congestive heart failure (disorder)
426263006 Congestive heart failure due to left ventricular systolic dysfunction (disorder)
48447003 Chronic heart failure (disorder)
418304008 Diastolic heart failure (disorder)
10633002 Acute congestive heart failure (disorder)
...

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 Concept Details:

Format API
XML site_root/api/v1/public/concepts/C769/version/2677/detail/?format=xml
JSON site_root/api/v1/public/concepts/C769/version/2677/detail/?format=json
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get details of concept

details = get_concept_detail_by_version('C769', '2677', api_client=client)

To Export Concept Code List:

Format API
XML site_root/api/v1/public/concepts/C769/version/2677/export/codes/?format=xml
JSON site_root/api/v1/public/concepts/C769/version/2677/export/codes/?format=json
CSV site_root/concepts/C769/version/2677/export/codes/
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get codelist of concept

codelist = get_concept_code_list_by_version('C769', '2677', api_client=client)

Version History

Version
ID
Name Description Owner Publish date
2677 Heart failure - Secondary care

The data (demographics, emergency department lett…

ieuan.scanlon 2021-10-06 currently shown

Export - Export all codes into a csv file/JSON/XML for the current concept version.

Print - Print page.

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