Phenotype Library | phenotype: Chronic Kidney Disease (CKD)

Chronic Kidney Disease (CKD)

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

PH22

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

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

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C766/2671 Chronic Kidney Disease (CKD) - Secondary care - SNOMED CT codes

Rows: 3

Code	Description
433144002	Chronic kidney disease stage 3 (disorder)
709044004	Chronic kidney disease (disorder)
90688005	Chronic renal failure syndrome (disorder)

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH22/version/44/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH22/version/44/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('PH22', '44', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH22/version/44/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH22/version/44/export/codes/?format=json
CSV	site_root/phenotypes/PH22/version/44/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('PH22', '44', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
44	Chronic Kidney Disease (CKD)	ieuan.scanlon	2021-10-06	currently shown