Desiderata for the development of next-generation electronic health record phenotype libraries
Year: 2021
Type: article
Abstract: BACKGROUND: High-quality phenotype definitions are desirable to enable the extraction of patient cohorts from large electronic health record repositories and are characterized by properties such as portability, reproducibility, and validity. Phenotype libraries, where definitions are stored, have the potential to contribute significantly to the quality of the definitions they host. In this work, we present a set of desiderata for the design of a next-generation phenotype library that is able to ensure the quality of hosted definitions by combining the functionality currently offered by disparate tooling. METHODS: A group of researchers examined work to date on phenotype models, implementation, and validation, as well as contemporary phenotype libraries developed as a part of their own phenomics communities. Existing phenotype frameworks were also examined. This work was translated and refined by all the authors into a set of best practices. RESULTS: We present 14 library desiderata that promote high-quality phenotype definitions, in the areas of modelling, logging, validation, and sharing and warehousing. CONCLUSIONS: There are a number of choices to be made when constructing phenotype libraries. Our considerations distil the best practices in the field and include pointers towards their further development to support portable, reproducible, and clinically valid phenotype design. The provision of high-quality phenotype definitions enables electronic health record data to be more effectively used in medical domains.
Source: GigaScience
Language: English
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,345
Funders: Wellcome Trust, Scottish Government, European Molecular Biology Laboratory, European Federation of Pharmaceutical Industries and Associations, National Institute for Health and Care Research, British Heart Foundation, Department of Health and Social Care, King's College London, European Commission, Public Health Agency, Surgical Reconstruction and Microbiology Research Centre, Horizon 2020 Framework Programme, Chief Scientist Office, Scottish Government Health and Social Care Directorate, Imperial Experimental Cancer Medicine Centre, Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Health and Social Care Research and Development Division, Birmingham Biomedical Research Centre, National Human Genome Research Institute, National Institute of General Medical Sciences
Awards: G1137571926, G1374303215, G2107972360, G2259971274, National Infrastructure for Standardized and Portable EHR Phenotyping Algorithms, G2844294282, The European Nanotechnology Community Informatics Platform: Bridging data and disciplinary gaps for industry and regulators (NanoCommons), Big Data 4 Better Hearts - Sofia ref.: 116074, G388764848, G5836017005, G6036059206, G6582518128, G7414939125, G7631291304, Semantic-based secure infrastructure for interoperable, in-depth biomedical data and analytics, G8585535233
OpenAlex ID: W3197590519