基于 OMOP 通用数据模型的时间序列数据中的患者队列识别。
Patient Cohort Identification on Time Series Data Using the OMOP Common Data Model.
机构信息
Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Bayern, Germany.
Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Bayern, Germany.
出版信息
Appl Clin Inform. 2021 Jan;12(1):57-64. doi: 10.1055/s-0040-1721481. Epub 2021 Jan 27.
BACKGROUND
The identification of patient cohorts for recruiting patients into clinical trials requires an evaluation of study-specific inclusion and exclusion criteria. These criteria are specified depending on corresponding clinical facts. Some of these facts may not be present in the clinical source systems and need to be calculated either in advance or at cohort query runtime (so-called feasibility query).
OBJECTIVES
We use the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) as the repository for our clinical data. However, Atlas, the graphical user interface of OMOP, does not offer the functionality to perform calculations on facts data. Therefore, we were in search for a different approach. The objective of this study is to investigate whether the Arden Syntax can be used for feasibility queries on the OMOP CDM to enable on-the-fly calculations at query runtime, to eliminate the need to precalculate data elements that are involved with researchers' criteria specification.
METHODS
We implemented a service that reads the facts from the OMOP repository and provides it in a form which an Arden Syntax Medical Logic Module (MLM) can process. Then, we implemented an MLM that applies the eligibility criteria to every patient data set and outputs the list of eligible cases (i.e., performs the feasibility query).
RESULTS
The study resulted in an MLM-based feasibility query that identifies cases of overventilation as an example of how an on-the-fly calculation can be realized. The algorithm is split into two MLMs to provide the reusability of the approach.
CONCLUSION
We found that MLMs are a suitable technology for feasibility queries on the OMOP CDM. Our method of performing on-the-fly calculations can be employed with any OMOP instance and without touching existing infrastructure like the Extract, Transform and Load pipeline. Therefore, we think that it is a well-suited method to perform on-the-fly calculations on OMOP.
背景
为了将患者招募到临床试验中，需要对特定研究的纳入和排除标准进行评估，以确定患者队列。这些标准是根据相应的临床事实来确定的。其中一些事实可能不在临床源系统中，需要在事先计算或在队列查询运行时（所谓的可行性查询）计算。
目的
我们使用观察性医学结局伙伴关系（OMOP）通用数据模型（CDM）作为我们的临床数据存储库。然而，OMOP 的图形用户界面 Atlas 没有提供在事实数据上执行计算的功能。因此，我们需要寻找一种不同的方法。本研究的目的是调查 Arden 语法是否可用于 OMOP CDM 的可行性查询，以实现查询运行时的实时计算，从而避免需要预先计算与研究人员标准规范相关的数据元素。
方法
我们实现了一项服务，该服务从 OMOP 存储库读取事实，并以 Arden 语法医疗逻辑模块（MLM）可以处理的形式提供。然后，我们实现了一个 MLM，该 MLM 将适用的标准应用于每个患者数据集，并输出合格病例列表（即执行可行性查询）。
结果
该研究产生了一个基于 MLM 的可行性查询，该查询以过度通气为例说明了如何实现实时计算。该算法分为两个 MLM，以提供方法的可重用性。
结论
我们发现 MLM 是 OMOP CDM 上可行性查询的合适技术。我们的实时计算方法可用于任何 OMOP 实例，而无需触及现有基础设施，如提取、转换和加载（Extract, Transform and Load，ETL）管道。因此，我们认为这是在 OMOP 上进行实时计算的一种合适方法。
Zotero 插件