基于多种数据源的 COVID-19 流行病学情况报告自动化，荷兰，2020 年至 2023 年。

IF 4.9 2区医学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer methods and programs in biomedicine Pub Date : 2024-09-20 DOI:10.1016/j.cmpb.2024.108436

Priscila de Oliveira Bressane Lima , Jan van de Kassteele , Maarten Schipper , Naomi Smorenburg , Martijn S․ van Rooijen , Janneke Heijne , Rolina D․ van Gaalen

{"title":"基于多种数据源的 COVID-19 流行病学情况报告自动化，荷兰，2020 年至 2023 年。","authors":"Priscila de Oliveira Bressane Lima , Jan van de Kassteele , Maarten Schipper , Naomi Smorenburg , Martijn S․ van Rooijen , Janneke Heijne , Rolina D․ van Gaalen","doi":"10.1016/j.cmpb.2024.108436","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><div>During the COVID-19 pandemic, the National Institute for Public Health and the Environment in the Netherlands developed a pipeline of scripts to automate and streamline the production of epidemiological situation reports (epi‑sitrep). The pipeline was developed for the Automation of Data Import, Summarization, and Communication (hereafter called the A-DISC pipeline).</div></div><div><h3>Objective</h3><div>This paper describes the A-DISC pipeline and provides a customizable scripts template that may be useful for other countries wanting to automate their infectious disease surveillance processes.</div></div><div><h3>Methods</h3><div>The A-DISC pipeline was developed using the open-source statistical software R. It is organized in four modules: <em>Prepare, Process data, Produce report</em>, and <em>Communicate.</em> The <em>Prepare</em> scripts set the working environment (e.g., load packages). The (data-specific) <em>Process data</em> scripts import, validate, verify, transform, save, analyze, and summarize data as tables and figures and store these data summaries. The <em>Produce report</em> scripts gather summaries from multiple data sources and integrate them into a RMarkdown document – the epi‑sitrep. The <em>Communicate</em> scripts send e-mails to stakeholders with the epi‑sitrep.</div></div><div><h3>Results</h3><div>As of March 2023, up to ten data sources were automatically summarized into tables and figures by A-DISC. These data summaries were featured in routine extensive COVID-19 epi‑sitreps, shared as open data, plotted on RIVM's website, sent to stakeholders and submitted to European Centre for Disease Prevention and Control via the European Surveillance System -TESSy [<span><span>38</span></span>].</div></div><div><h3>Discussion</h3><div>In the face of an unprecedented high number of cases being reported during the COVID-19 pandemic, the A-DISC pipeline was essential to produce frequent and comprehensive epi‑sitreps. A-DISC's modular and intuitive structure allowed for the integration of data sources of varying complexities, encouraged collaboration among people with various R-scripting capabilities, and improved data lineage. The A-DISC pipeline remains under active development and is currently being used in modified form for the automatization and professionalization of various other disease surveillance processes at the RIVM, with high acceptance from the participant epidemiologists.</div></div><div><h3>Conclusion</h3><div>The A-DISC pipeline is an open-source, robust, and customizable tool for automating epi‑sitreps based on multiple data sources.</div></div>","PeriodicalId":10624,"journal":{"name":"Computer methods and programs in biomedicine","volume":"257 ","pages":"Article 108436"},"PeriodicalIF":4.9000,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Automating COVID-19 epidemiological situation reports based on multiple data sources, the Netherlands, 2020 to 2023\",\"authors\":\"Priscila de Oliveira Bressane Lima , Jan van de Kassteele , Maarten Schipper , Naomi Smorenburg , Martijn S․ van Rooijen , Janneke Heijne , Rolina D․ van Gaalen\",\"doi\":\"10.1016/j.cmpb.2024.108436\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><div>During the COVID-19 pandemic, the National Institute for Public Health and the Environment in the Netherlands developed a pipeline of scripts to automate and streamline the production of epidemiological situation reports (epi‑sitrep). The pipeline was developed for the Automation of Data Import, Summarization, and Communication (hereafter called the A-DISC pipeline).</div></div><div><h3>Objective</h3><div>This paper describes the A-DISC pipeline and provides a customizable scripts template that may be useful for other countries wanting to automate their infectious disease surveillance processes.</div></div><div><h3>Methods</h3><div>The A-DISC pipeline was developed using the open-source statistical software R. It is organized in four modules: <em>Prepare, Process data, Produce report</em>, and <em>Communicate.</em> The <em>Prepare</em> scripts set the working environment (e.g., load packages). The (data-specific) <em>Process data</em> scripts import, validate, verify, transform, save, analyze, and summarize data as tables and figures and store these data summaries. The <em>Produce report</em> scripts gather summaries from multiple data sources and integrate them into a RMarkdown document – the epi‑sitrep. The <em>Communicate</em> scripts send e-mails to stakeholders with the epi‑sitrep.</div></div><div><h3>Results</h3><div>As of March 2023, up to ten data sources were automatically summarized into tables and figures by A-DISC. These data summaries were featured in routine extensive COVID-19 epi‑sitreps, shared as open data, plotted on RIVM's website, sent to stakeholders and submitted to European Centre for Disease Prevention and Control via the European Surveillance System -TESSy [<span><span>38</span></span>].</div></div><div><h3>Discussion</h3><div>In the face of an unprecedented high number of cases being reported during the COVID-19 pandemic, the A-DISC pipeline was essential to produce frequent and comprehensive epi‑sitreps. A-DISC's modular and intuitive structure allowed for the integration of data sources of varying complexities, encouraged collaboration among people with various R-scripting capabilities, and improved data lineage. The A-DISC pipeline remains under active development and is currently being used in modified form for the automatization and professionalization of various other disease surveillance processes at the RIVM, with high acceptance from the participant epidemiologists.</div></div><div><h3>Conclusion</h3><div>The A-DISC pipeline is an open-source, robust, and customizable tool for automating epi‑sitreps based on multiple data sources.</div></div>\",\"PeriodicalId\":10624,\"journal\":{\"name\":\"Computer methods and programs in biomedicine\",\"volume\":\"257 \",\"pages\":\"Article 108436\"},\"PeriodicalIF\":4.9000,\"publicationDate\":\"2024-09-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computer methods and programs in biomedicine\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0169260724004292\",\"RegionNum\":2,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computer methods and programs in biomedicine","FirstCategoryId":"5","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0169260724004292","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}

引用次数: 0

摘要

背景：在 COVID-19 大流行期间，荷兰国家公共卫生与环境研究所（National Institute for Public Health and the Environment in the Netherlands）开发了一个脚本管道，用于自动化和简化流行病学情况报告（epi-sitrep）的制作。该管道是为数据导入、汇总和交流自动化（以下简称 A-DISC 管道）而开发的：本文介绍了 A-DISC 管道，并提供了一个可定制的脚本模板，该模板可能对希望实现传染病监测过程自动化的其他国家有用：A-DISC 管道是使用开源统计软件 R 开发的：准备、处理数据、生成报告和交流。准备脚本设置工作环境（如加载软件包）。特定数据）处理数据脚本将数据导入、验证、校验、转换、保存、分析和汇总为表格和数字，并存储这些数据汇总。制作报告脚本从多个数据源收集摘要，并将其整合到 RMarkdown 文档--epi-sitrep。交流脚本会向利益相关者发送带有 epi-sitrep.Results 的电子邮件：截至 2023 年 3 月，A-DISC 系统已将多达十个数据源自动汇总为表格和图表。这些数据摘要在 COVID-19 广泛的 epi-sitreps 中进行了例行介绍，作为开放数据进行了共享，在 RIVM 网站上进行了绘制，发送给了利益相关者，并通过欧洲监测系统 -TESSy [38]提交给了欧洲疾病预防与控制中心：在 COVID-19 大流行期间，面对前所未有的大量病例报告，A-DISC 管道对于频繁、全面地制作外观病例报告至关重要。A-DISC 的模块化和直观结构允许整合不同复杂程度的数据源，鼓励具有不同 R 脚本能力的人员进行协作，并改善了数据序列。A-DISC 管道仍在积极开发中，目前正以修改后的形式用于 RIVM 其他各种疾病监测流程的自动化和专业化，并得到了参与流行病学家的高度认可：结论：A-DISC 管道是一个开源、强大且可定制的工具，可用于基于多种数据源的表观病例自动监测。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

Automating COVID-19 epidemiological situation reports based on multiple data sources, the Netherlands, 2020 to 2023

Background

During the COVID-19 pandemic, the National Institute for Public Health and the Environment in the Netherlands developed a pipeline of scripts to automate and streamline the production of epidemiological situation reports (epi‑sitrep). The pipeline was developed for the Automation of Data Import, Summarization, and Communication (hereafter called the A-DISC pipeline).

Objective

This paper describes the A-DISC pipeline and provides a customizable scripts template that may be useful for other countries wanting to automate their infectious disease surveillance processes.

Methods

The A-DISC pipeline was developed using the open-source statistical software R. It is organized in four modules: Prepare, Process data, Produce report, and Communicate. The Prepare scripts set the working environment (e.g., load packages). The (data-specific) Process data scripts import, validate, verify, transform, save, analyze, and summarize data as tables and figures and store these data summaries. The Produce report scripts gather summaries from multiple data sources and integrate them into a RMarkdown document – the epi‑sitrep. The Communicate scripts send e-mails to stakeholders with the epi‑sitrep.

Results

As of March 2023, up to ten data sources were automatically summarized into tables and figures by A-DISC. These data summaries were featured in routine extensive COVID-19 epi‑sitreps, shared as open data, plotted on RIVM's website, sent to stakeholders and submitted to European Centre for Disease Prevention and Control via the European Surveillance System -TESSy [38].

Discussion

In the face of an unprecedented high number of cases being reported during the COVID-19 pandemic, the A-DISC pipeline was essential to produce frequent and comprehensive epi‑sitreps. A-DISC's modular and intuitive structure allowed for the integration of data sources of varying complexities, encouraged collaboration among people with various R-scripting capabilities, and improved data lineage. The A-DISC pipeline remains under active development and is currently being used in modified form for the automatization and professionalization of various other disease surveillance processes at the RIVM, with high acceptance from the participant epidemiologists.

Conclusion

The A-DISC pipeline is an open-source, robust, and customizable tool for automating epi‑sitreps based on multiple data sources.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Computer methods and programs in biomedicine 工程技术-工程：生物医学

CiteScore

12.30

自引率

6.60%

发文量

601

审稿时长

135 days

期刊介绍： To encourage the development of formal computing methods, and their application in biomedical research and medical practice, by illustration of fundamental principles in biomedical informatics research; to stimulate basic research into application software design; to report the state of research of biomedical information processing projects; to report new computer methodologies applied in biomedical areas; the eventual distribution of demonstrable software to avoid duplication of effort; to provide a forum for discussion and improvement of existing software; to optimize contact between national organizations and regional user groups by promoting an international exchange of information on formal methods, standards and software in biomedicine. Computer Methods and Programs in Biomedicine covers computing methodology and software systems derived from computing science for implementation in all aspects of biomedical research and medical practice. It is designed to serve: biochemists; biologists; geneticists; immunologists; neuroscientists; pharmacologists; toxicologists; clinicians; epidemiologists; psychiatrists; psychologists; cardiologists; chemists; (radio)physicists; computer scientists; programmers and systems analysts; biomedical, clinical, electrical and other engineers; teachers of medical informatics and users of educational software.