Chronic Obstructive Pulmonary Disease (COPD) - 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
C767
Version ID
2673
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_copd_Cx5tTPaZno6hhcp4Psq5Er_SNOMEDCT - Expression Select Add codes
Code Description
13645005 Chronic obstructive lung disease (disorder)
313297008 Moderate chronic obstructive pulmonary disease (disorder)
...

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

API

To Export Concept Details:

Format API
XML site_root/api/v1/public/concepts/C767/version/2673/detail/?format=xml
JSON site_root/api/v1/public/concepts/C767/version/2673/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('C767', '2673', api_client=client)

To Export Concept Code List:

Format API
XML site_root/api/v1/public/concepts/C767/version/2673/export/codes/?format=xml
JSON site_root/api/v1/public/concepts/C767/version/2673/export/codes/?format=json
CSV site_root/concepts/C767/version/2673/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('C767', '2673', api_client=client)

Version History

Version
ID
Name Description Owner Publish date
2673 Chronic Obstructive Pulmonary Disease (COPD) - 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.