Creating a next-generation phenotype library: the health data research UK Phenotype Library
File(s)Creating a next-generation phenotype library.pdf (1.17 MB)
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Author(s)
Type
Journal Article
Abstract
OBJECTIVE: To enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms. MATERIALS AND METHODS: We undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly. RESULTS: We created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and >200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups. DISCUSSION: This platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes. CONCLUSIONS: We have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.
Date Issued
2024-07
Date Acceptance
2024-05-20
Citation
JAMIA Open, 2024, 7 (2)
ISSN
2574-2531
Publisher
Oxford University Press
Journal / Book Title
JAMIA Open
Volume
7
Issue
2
Copyright Statement
© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/38895652
Subjects
algorithms
application programming interface
electronic health records
medical informatics
phenotyping
public health informatics
Publication Status
Published
Coverage Spatial
United States
Article Number
ooae049
Date Publish Online
2024-06-17