Desiderata for the development of next-generation electronic health record phenotype libraries.
Desiderata for the development of next-generation electronic health record phenotype libraries.
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为开发下一代电子健康记录表型库的发展。
DOI：
10.1093/gigascience/giab059
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发表时间：
2021-09-11
期刊：
影响因子：
9.2
通讯作者：
Curcin V
中科院分区：
文献类型：
--
作者：
Chapman M;Mumtaz S;Rasmussen LV;Karwath A;Gkoutos GV;Gao C;Thayer D;Pacheco JA;Parkinson H;Richesson RL;Jefferson E;Denaxas S;Curcin V
高质量的表型定义是理想的，以使患者队列的提取从大型电子健康记录库，其特征在于，如便携性，再现性和有效性的属性。表型库，定义存储，有可能大大有助于他们主机的定义的质量。在这项工作中，我们提出了一套desiderata的设计下一代表型库，能够确保托管定义的质量相结合的功能，目前提供的不同的工具。一组研究人员检查了迄今为止关于表型模型，实施和验证的工作，以及作为他们自己的表型组学社区的一部分开发的当代表型库。还检查了现有的表型框架。所有作者都将这项工作转化和完善为一套最佳做法。我们提出了14个图书馆的需求，促进高质量的表型定义，在建模，记录，验证，共享和仓储领域。在构建表型文库时有许多选择。我们的考虑是在该领域的最佳实践，并包括他们的进一步发展，以支持便携式，可重复性和临床有效的表型设计的指针。提供高质量的表型定义使得电子健康记录数据能够更有效地用于医学领域。
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. 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. We present 14 library desiderata that promote high-quality phenotype definitions, in the areas of modelling, logging, validation, and sharing and warehousing. 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.
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DOI：
10.1146/annurev-biodatasci-080917-013315
发表时间：
2018-01-01
期刊：
ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE, VOL 1
影响因子：
--
作者：
Banda, Juan M.;Seneviratne, Martin;Shah, Nigam H.
通讯作者：
Shah, Nigam H.
影响因子：
3.1
作者：
Brandt PS;Kiefer RC;Pacheco JA;Adekkanattu P;Sholle ET;Ahmad FS;Xu J;Xu Z;Ancker JS;Wang F;Luo Y;Jiang G;Pathak J;Rasmussen LV
通讯作者：
Rasmussen LV
影响因子：
9.5
作者：
Gkoutos GV;Schofield PN;Hoehndorf R
通讯作者：
Hoehndorf R
影响因子：
3.1
作者：
Alper BS;Flynn A;Bray BE;Conte ML;Eldredge C;Gold S;Greenes RA;Haug P;Jacoby K;Koru G;McClay J;Sainvil ML;Sottara D;Tuttle M;Visweswaran S;Yurk RA
通讯作者：
Yurk RA
DOI：
10.1093/bioinformatics/btq126
发表时间：
2010-05-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Denny JC;Ritchie MD;Basford MA;Pulley JM;Bastarache L;Brown-Gentry K;Wang D;Masys DR;Roden DM;Crawford DC
通讯作者：
Crawford DC