将伤口相关数据转换为标准化公共数据模型的etl流程的设计与实现。

Q3 Health Professions
Mareike Przysucha, Jens Hüsers, Daniil Liberman, Oliver Kersten, Aphrodite Schlüter, Sebastian Fraas, Dorothee Busch, Maurice Moelleken, Cornelia Erfurt-Berge, Joachim Dissemond, Ursula Hübner
{"title":"将伤口相关数据转换为标准化公共数据模型的etl流程的设计与实现。","authors":"Mareike Przysucha,&nbsp;Jens Hüsers,&nbsp;Daniil Liberman,&nbsp;Oliver Kersten,&nbsp;Aphrodite Schlüter,&nbsp;Sebastian Fraas,&nbsp;Dorothee Busch,&nbsp;Maurice Moelleken,&nbsp;Cornelia Erfurt-Berge,&nbsp;Joachim Dissemond,&nbsp;Ursula Hübner","doi":"10.3233/SHTI230723","DOIUrl":null,"url":null,"abstract":"<p><p>For observational studies, which are relevant especially for chronic conditions like chronic wounds, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) offers a standardized database schema. In this study an ETL process for the transition of wound related data was developed. After understanding the data in general and mapping the relevant codes to concepts available in OMOP, the ETL process was implemented. In a first step, a generic algorithm to convert data to a csv format was implemented in Java. The resulting csv file was then processed within KNIME to be loaded into an OMOP CDM conformant database. During the whole ETL process, HL7 FHIR CodeSystem and ConceptMap resources were used for coding and mapping. First clinical test cases to retrieve data were successfully processed as an example to demonstrate the feasibility and usefulness. They concerned wound size at the first visit and the main issues of patients in the wound quality of life questionnaire (n = 24). In general, the ETL process worked well, yet some challenges arose, like post coordinated SNOMED codes or conditions, which might occur more than once.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Design and Implementation of an ETL-Process to Transfer Wound-Related Data into a Standardized Common Data Model.\",\"authors\":\"Mareike Przysucha,&nbsp;Jens Hüsers,&nbsp;Daniil Liberman,&nbsp;Oliver Kersten,&nbsp;Aphrodite Schlüter,&nbsp;Sebastian Fraas,&nbsp;Dorothee Busch,&nbsp;Maurice Moelleken,&nbsp;Cornelia Erfurt-Berge,&nbsp;Joachim Dissemond,&nbsp;Ursula Hübner\",\"doi\":\"10.3233/SHTI230723\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>For observational studies, which are relevant especially for chronic conditions like chronic wounds, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) offers a standardized database schema. In this study an ETL process for the transition of wound related data was developed. After understanding the data in general and mapping the relevant codes to concepts available in OMOP, the ETL process was implemented. In a first step, a generic algorithm to convert data to a csv format was implemented in Java. The resulting csv file was then processed within KNIME to be loaded into an OMOP CDM conformant database. During the whole ETL process, HL7 FHIR CodeSystem and ConceptMap resources were used for coding and mapping. First clinical test cases to retrieve data were successfully processed as an example to demonstrate the feasibility and usefulness. They concerned wound size at the first visit and the main issues of patients in the wound quality of life questionnaire (n = 24). In general, the ETL process worked well, yet some challenges arose, like post coordinated SNOMED codes or conditions, which might occur more than once.</p>\",\"PeriodicalId\":39242,\"journal\":{\"name\":\"Studies in Health Technology and Informatics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2023-09-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Studies in Health Technology and Informatics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3233/SHTI230723\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Health Professions\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Studies in Health Technology and Informatics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3233/SHTI230723","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Health Professions","Score":null,"Total":0}
引用次数: 0

摘要

对于观察性研究,特别是与慢性疾病(如慢性伤口)相关的观察性研究,观察性医疗结果伙伴关系(OMOP)公共数据模型(CDM)提供了一个标准化的数据库模式。本研究开发了创伤相关数据转换的ETL流程。在大致理解数据并将相关代码映射到OMOP中可用的概念之后,就实现了ETL流程。在第一步中,用Java实现了将数据转换为csv格式的通用算法。然后在KNIME中处理生成的csv文件,将其加载到OMOP CDM一致性数据库中。在整个ETL过程中,使用HL7 FHIR CodeSystem和ConceptMap资源进行编码和映射。以临床试验用例检索数据为例,验证了该方法的可行性和有效性。在伤口生活质量问卷中对首次就诊时的伤口大小和患者的主要问题进行调查(n = 24)。总的来说,ETL过程工作得很好,但也出现了一些挑战,比如后期协调的SNOMED代码或条件,这些问题可能不止一次出现。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Design and Implementation of an ETL-Process to Transfer Wound-Related Data into a Standardized Common Data Model.

For observational studies, which are relevant especially for chronic conditions like chronic wounds, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) offers a standardized database schema. In this study an ETL process for the transition of wound related data was developed. After understanding the data in general and mapping the relevant codes to concepts available in OMOP, the ETL process was implemented. In a first step, a generic algorithm to convert data to a csv format was implemented in Java. The resulting csv file was then processed within KNIME to be loaded into an OMOP CDM conformant database. During the whole ETL process, HL7 FHIR CodeSystem and ConceptMap resources were used for coding and mapping. First clinical test cases to retrieve data were successfully processed as an example to demonstrate the feasibility and usefulness. They concerned wound size at the first visit and the main issues of patients in the wound quality of life questionnaire (n = 24). In general, the ETL process worked well, yet some challenges arose, like post coordinated SNOMED codes or conditions, which might occur more than once.

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
Studies in Health Technology and Informatics
Studies in Health Technology and Informatics Health Professions-Health Information Management
CiteScore
1.20
自引率
0.00%
发文量
1463
期刊介绍: This book series was started in 1990 to promote research conducted under the auspices of the EC programmes’ Advanced Informatics in Medicine (AIM) and Biomedical and Health Research (BHR) bioengineering branch. A driving aspect of international health informatics is that telecommunication technology, rehabilitative technology, intelligent home technology and many other components are moving together and form one integrated world of information and communication media.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信