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Health Care Language Models and Their Fine-Tuning for Information Extraction: Scoping Review. 医疗保健语言模型及其用于信息提取的微调:范围审查。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-21 DOI: 10.2196/60164
Miguel Nunes, Joao Bone, Joao C Ferreira, Luis B Elvas
<p><strong>Background: </strong>In response to the intricate language, specialized terminology outside everyday life, and the frequent presence of abbreviations and acronyms inherent in health care text data, domain adaptation techniques have emerged as crucial to transformer-based models. This refinement in the knowledge of the language models (LMs) allows for a better understanding of the medical textual data, which results in an improvement in medical downstream tasks, such as information extraction (IE). We have identified a gap in the literature regarding health care LMs. Therefore, this study presents a scoping literature review investigating domain adaptation methods for transformers in health care, differentiating between English and non-English languages, focusing on Portuguese. Most specifically, we investigated the development of health care LMs, with the aim of comparing Portuguese with other more developed languages to guide the path of a non-English-language with fewer resources.</p><p><strong>Objective: </strong>This study aimed to research health care IE models, regardless of language, to understand the efficacy of transformers and what are the medical entities most commonly extracted.</p><p><strong>Methods: </strong>This scoping review was conducted using the PRISMA-ScR (Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews) methodology on Scopus and Web of Science Core Collection databases. Only studies that mentioned the creation of health care LMs or health care IE models were included, while large language models (LLMs) were excluded. The latest were not included since we wanted to research LMs and not LLMs, which are architecturally different and have distinct purposes.</p><p><strong>Results: </strong>Our search query retrieved 137 studies, 60 of which met the inclusion criteria, and none of them were systematic literature reviews. English and Chinese are the languages with the most health care LMs developed. These languages already have disease-specific LMs, while others only have general-health care LMs. European Portuguese does not have any public health care LM and should take examples from other languages to develop, first, general-health care LMs and then, in an advanced phase, disease-specific LMs. Regarding IE models, transformers were the most commonly used method, and named entity recognition was the most popular topic, with only a few studies mentioning Assertion Status or addressing medical lexical problems. The most extracted entities were diagnosis, posology, and symptoms.</p><p><strong>Conclusions: </strong>The findings indicate that domain adaptation is beneficial, achieving better results in downstream tasks. Our analysis allowed us to understand that the use of transformers is more developed for the English and Chinese languages. European Portuguese lacks relevant studies and should draw examples from other non-English languages to develop these models and drive pr
背景:针对医疗文本数据中固有的错综复杂的语言、日常生活之外的专业术语以及频繁出现的缩略语和首字母缩写词,领域适应技术已成为基于转换器的模型的关键。语言模型(LMs)知识的这种完善可以更好地理解医疗文本数据,从而改进医疗下游任务,如信息提取(IE)。我们发现有关医疗保健语言模型的文献存在空白。因此,本研究对医疗保健领域转换器的领域适应方法进行了文献综述,区分了英语和非英语语言,重点关注葡萄牙语。最具体地说,我们调查了医疗保健 LM 的发展情况,目的是将葡萄牙语与其他更发达的语言进行比较,以指导资源较少的非英语语言的发展道路:本研究旨在研究医疗保健 IE 模型(无论使用哪种语言),以了解转换器的功效以及最常提取的医疗实体:本范围综述采用 PRISMA-ScR(Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews)方法在 Scopus 和 Web of Science Core Collection 数据库中进行。只有提及创建医疗保健 LM 或医疗保健 IE 模型的研究才被纳入,而大型语言模型 (LLM) 则被排除在外。最新的研究未被包括在内,因为我们想研究的是 LM,而不是 LLM,它们在结构上不同,有不同的目的:我们的搜索查询检索到 137 项研究,其中 60 项符合纳入标准,但没有一项是系统性文献综述。英语和汉语是开发了最多医疗保健 LM 的语言。这些语言已经有了针对特定疾病的 LM,而其他语言只有普通保健 LM。欧洲葡萄牙语没有任何公共保健 LM,应借鉴其他语言的例子,首先开发普通保健 LM,然后在高级阶段开发特定疾病 LM。关于 IE 模型,转换器是最常用的方法,命名实体识别是最受欢迎的主题,只有少数研究提到了断言状态或解决医学词汇问题。提取最多的实体是诊断、姿势和症状:研究结果表明,领域适应是有益的,可以在下游任务中取得更好的结果。我们通过分析了解到,转换器的使用在英语和汉语中更为成熟。欧洲葡萄牙语缺乏相关研究,应借鉴其他非英语语言的例子来开发这些模型,推动人工智能的进步。突出显示医疗相关信息并优化文本数据的阅读,或将这些信息用于创建患者医疗时间表,从而进行特征分析,都能让医疗保健专业人员从中受益。
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引用次数: 0
A Generic Transformation Approach for Complex Laboratory Data Using the Fast Healthcare Interoperability Resources Mapping Language: Method Development and Implementation. 使用快速医疗保健互操作性资源映射语言的复杂实验室数据通用转换方法:方法开发与实施。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-18 DOI: 10.2196/57569
Jesse Kruse, Joshua Wiedekopf, Ann-Kristin Kock-Schoppenhauer, Andrea Essenwanger, Josef Ingenerf, Hannes Ulrich
<p><strong>Background: </strong>Reaching meaningful interoperability between proprietary health care systems is a ubiquitous task in medical informatics, where communication servers are traditionally used for referring and transforming data from the source to target systems. The Mirth Connect Server, an open-source communication server, offers, in addition to the exchange functionality, functions for simultaneous manipulation of data. The standard Fast Healthcare Interoperability Resources (FHIR) has recently become increasingly prevalent in national health care systems. FHIR specifies its own standardized mechanisms for transforming data structures using StructureMaps and the FHIR mapping language (FML).</p><p><strong>Objective: </strong>In this study, a generic approach is developed, which allows for the application of declarative mapping rules defined using FML in an exchangeable manner. A transformation engine is required to execute the mapping rules.</p><p><strong>Methods: </strong>FHIR natively defines resources to support the conversion of instance data, such as an FHIR StructureMap. This resource encodes all information required to transform data from a source system to a target system. In our approach, this information is defined in an implementation-independent manner using FML. Once the mapping has been defined, executable Mirth channels are automatically generated from the resources containing the mapping in JavaScript format. These channels can then be deployed to the Mirth Connect Server.</p><p><strong>Results: </strong>The resulting tool is called FML2Mirth, a Java-based transformer that derives Mirth channels from detailed declarative mapping rules based on the underlying StructureMaps. Implementation of the translate functionality is provided by the integration of a terminology server, and to achieve conformity with existing profiles, validation via the FHIR validator is built in. The system was evaluated for its practical use by transforming Labordatenträger version 2 (LDTv.2) laboratory results into Medical Information Object (Medizinisches Informationsobjekt) laboratory reports in accordance with the National Association of Statutory Health Insurance Physicians' specifications and into the HL7 (Health Level Seven) Europe Laboratory Report. The system could generate complex structures, but LDTv.2 lacks some information to fully comply with the specification.</p><p><strong>Conclusions: </strong>The tool for the auto-generation of Mirth channels was successfully presented. Our tests reveal the feasibility of using the complex structures of the mapping language in combination with a terminology server to transform instance data. Although the Mirth Server and the FHIR are well established in medical informatics, the combination offers space for more research, especially with regard to FML. Simultaneously, it can be stated that the mapping language still has implementation-related shortcomings that can be compensated by Mirth Connec
背景:在专有医疗保健系统之间实现有意义的互操作性是医疗信息学中一项无处不在的任务,传统上通信服务器用于将数据从源系统转发和转换到目标系统。Mirth Connect 服务器是一个开源通信服务器,除交换功能外,还提供同步操作数据的功能。快速医疗互操作性资源(FHIR)标准近来在各国医疗系统中日益盛行。FHIR 规定了自己的标准化机制,用于使用结构图和 FHIR 映射语言(FML)转换数据结构:本研究开发了一种通用方法,允许以可交换的方式应用使用 FML 定义的声明式映射规则。执行映射规则需要一个转换引擎:方法:FHIR 本机定义了支持实例数据转换的资源,如 FHIR StructureMap。该资源编码了将数据从源系统转换到目标系统所需的所有信息。在我们的方法中,这些信息是使用 FML 以独立于实现的方式定义的。一旦定义了映射,可执行的 Mirth 通道就会从包含 JavaScript 格式映射的资源中自动生成。这些通道可以部署到 Mirth Connect Server.Results 上:由此产生的工具名为 FML2Mirth,它是一种基于 Java 的转换器,可根据底层结构图的详细声明性映射规则生成 Mirth 通道。翻译功能通过集成术语服务器来实现,为了与现有配置文件保持一致,还内置了 FHIR 验证器进行验证。通过将 Labordatenträger version 2 (LDTv.2) 实验室结果转化为符合国家法定医疗保险医师协会规范的医疗信息对象 (Medizinisches Informationsobjekt) 实验室报告和 HL7(健康七级)欧洲实验室报告,对该系统的实际使用情况进行了评估。该系统可以生成复杂的结构,但 LDTv.2 缺乏一些信息,无法完全符合规范要求:我们成功地展示了 Mirth 信道自动生成工具。我们的测试表明,将映射语言的复杂结构与术语服务器相结合来转换实例数据是可行的。尽管 Mirth 服务器和 FHIR 在医学信息学中已经得到广泛应用,但两者的结合仍为更多研究提供了空间,尤其是在 FML 方面。同时,可以说映射语言仍然存在与实施相关的缺陷,而这些缺陷可以通过作为基础技术的 Mirth Connect 得到弥补。
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引用次数: 0
Applying the Non-Adoption, Abandonment, Scale-up, Spread, and Sustainability Framework Across Implementation Stages to Identify Key Strategies to Facilitate Clinical Decision Support System Integration Within a Large Metropolitan Health Service: Interview and Focus Group Study. 在各实施阶段应用 "不采用、放弃、扩大规模、传播和可持续性 "框架,以确定促进大都市卫生服务机构内临床决策支持系统整合的关键策略:访谈与焦点小组研究。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-17 DOI: 10.2196/60402
Manasha Fernando, Bridget Abell, Steven M McPhail, Zephanie Tyack, Amina Tariq, Sundresan Naicker
<p><strong>Background: </strong>Computerized clinical decision support systems (CDSSs) enhance patient care through real-time, evidence-based guidance for health care professionals. Despite this, the effective implementation of these systems for health services presents multifaceted challenges, leading to inappropriate use and abandonment over the course of time. Using the Non-Adoption, Abandonment, Scale-Up, Spread, and Sustainability (NASSS) framework, this qualitative study examined CDSS adoption in a metropolitan health service, identifying determinants across implementation stages to optimize CDSS integration into health care practice.</p><p><strong>Objective: </strong>This study aims to identify the theory-informed (NASSS) determinants, which included multiple CDSS interventions across a 2-year period, both at the health-service level and at the individual hospital setting, that either facilitate or hinder the application of CDSSs within a metropolitan health service. In addition, this study aimed to map these determinants onto specific stages of the implementation process, thereby developing a system-level understanding of CDSS application across implementation stages.</p><p><strong>Methods: </strong>Participants involved in various stages of the implementation process were recruited (N=30). Participants took part in interviews and focus groups. We used a hybrid inductive-deductive qualitative content analysis and a framework mapping approach to categorize findings into barriers, enablers, or neutral determinants aligned to NASSS framework domains. These determinants were also mapped to implementation stages using the Active Implementation Framework stages approach.</p><p><strong>Results: </strong>Participants comprised clinical adopters (14/30, 47%), organizational champions (5/30, 16%), and those with roles in organizational clinical informatics (5/30, 16%). Most determinants were mapped to the organization level, technology, and adopter subdomains. However, the study findings also demonstrated a relative lack of long-term implementation planning. Consequently, determinants were not uniformly distributed across the stages of implementation, with 61.1% (77/126) identified in the exploration stage, 30.9% (39/126) in the full implementation stage, and 4.7% (6/126) in the installation stages. Stakeholders engaged in more preimplementation and full-scale implementation activities, with fewer cycles of monitoring and iteration activities identified.</p><p><strong>Conclusions: </strong>These findings addressed a substantial knowledge gap in the literature using systems thinking principles to identify the interdependent dynamics of CDSS implementation. A lack of sustained implementation strategies (ie, training and longer-term, adopter-level championing) weakened the sociotechnical network between developers and adopters, leading to communication barriers. More rigorous implementation planning, encompassing all 4 implementation stages, may, in a
背景:计算机化临床决策支持系统(CDSS)通过为医护人员提供实时、循证的指导来加强对患者的护理。尽管如此,在医疗服务中有效实施这些系统仍面临着多方面的挑战,导致使用不当和随着时间的推移而被放弃。本定性研究采用 "不采用、放弃、扩大规模、传播和可持续性"(NASSS)框架,考察了一个大都市医疗服务机构采用 CDSS 的情况,确定了各实施阶段的决定因素,以优化 CDSS 与医疗实践的整合:本研究旨在确定促进或阻碍 CDSS 在大都市医疗服务机构中应用的理论依据(NASSS)决定因素,其中包括医疗服务机构和单个医院在两年时间内采取的多种 CDSS 干预措施。此外,本研究还旨在将这些决定因素映射到实施过程的具体阶段,从而从系统层面了解 CDSS 在各个实施阶段的应用情况:方法:招募了参与实施过程各个阶段的参与者(30 人)。参与者参加了访谈和焦点小组。我们采用了归纳-演绎混合定性内容分析和框架映射方法,将研究结果归类为与 NASSS 框架领域相一致的障碍、促进因素或中性决定因素。这些决定因素还使用积极实施框架阶段法映射到实施阶段:结果:参与者包括临床采用者(14/30,47%)、组织拥护者(5/30,16%)以及在组织临床信息学中发挥作用的人员(5/30,16%)。大多数决定因素被映射到组织层面、技术和采用者子域。然而,研究结果也表明,相对缺乏长期的实施规划。因此,决定因素在实施阶段的分布并不均匀,61.1%(77/126)的决定因素在探索阶段被发现,30.9%(39/126)的决定因素在全面实施阶段被发现,4.7%(6/126)的决定因素在安装阶段被发现。利益相关者参与了更多的实施前和全面实施活动,而确定的监测和迭代活动周期较少:这些研究结果弥补了文献中的重大知识空白,利用系统思维原则确定了 CDSS 实施过程中相互依存的动态关系。缺乏持续的实施策略(即培训和长期的、采用者层面的支持)削弱了开发者和采用者之间的社会技术网络,导致沟通障碍。在某种程度上,包括所有 4 个实施阶段在内的更严格的实施规划可能有助于消除已发现的障碍和增强促进因素。
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引用次数: 0
Evaluating Medical Entity Recognition in Health Care: Entity Model Quantitative Study. 评估医疗保健中的医疗实体识别:实体模型定量研究。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-17 DOI: 10.2196/59782
Shengyu Liu, Anran Wang, Xiaolei Xiu, Ming Zhong, Sizhu Wu
<p><strong>Background: </strong>Named entity recognition (NER) models are essential for extracting structured information from unstructured medical texts by identifying entities such as diseases, treatments, and conditions, enhancing clinical decision-making and research. Innovations in machine learning, particularly those involving Bidirectional Encoder Representations From Transformers (BERT)-based deep learning and large language models, have significantly advanced NER capabilities. However, their performance varies across medical datasets due to the complexity and diversity of medical terminology. Previous studies have often focused on overall performance, neglecting specific challenges in medical contexts and the impact of macrofactors like lexical composition on prediction accuracy. These gaps hinder the development of optimized NER models for medical applications.</p><p><strong>Objective: </strong>This study aims to meticulously evaluate the performance of various NER models in the context of medical text analysis, focusing on how complex medical terminology affects entity recognition accuracy. Additionally, we explored the influence of macrofactors on model performance, seeking to provide insights for refining NER models and enhancing their reliability for medical applications.</p><p><strong>Methods: </strong>This study comprehensively evaluated 7 NER models-hidden Markov models, conditional random fields, BERT for Biomedical Text Mining, Big Transformer Models for Efficient Long-Sequence Attention, Decoding-enhanced BERT with Disentangled Attention, Robustly Optimized BERT Pretraining Approach, and Gemma-across 3 medical datasets: Revised Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), BioCreative V CDR, and Anatomical Entity Mention (AnatEM). The evaluation focused on prediction accuracy, resource use (eg, central processing unit and graphics processing unit use), and the impact of fine-tuning hyperparameters. The macrofactors affecting model performance were also screened using the multilevel factor elimination algorithm.</p><p><strong>Results: </strong>The fine-tuned BERT for Biomedical Text Mining, with balanced resource use, generally achieved the highest prediction accuracy across the Revised JNLPBA and AnatEM datasets, with microaverage (AVG_MICRO) scores of 0.932 and 0.8494, respectively, highlighting its superior proficiency in identifying medical entities. Gemma, fine-tuned using the low-rank adaptation technique, achieved the highest accuracy on the BioCreative V CDR dataset with an AVG_MICRO score of 0.9962 but exhibited variability across the other datasets (AVG_MICRO scores of 0.9088 on the Revised JNLPBA and 0.8029 on AnatEM), indicating a need for further optimization. In addition, our analysis revealed that 2 macrofactors, entity phrase length and the number of entity words in each entity phrase, significantly influenced model performance.</p><p><strong>Conclusions: </strong>Th
背景:命名实体识别(NER)模型对于从非结构化医学文本中提取结构化信息至关重要,它可以识别疾病、治疗和病情等实体,从而加强临床决策和研究。机器学习领域的创新,尤其是基于双向编码器变换器表征(BERT)的深度学习和大型语言模型的创新,大大提高了 NER 的能力。然而,由于医学术语的复杂性和多样性,它们在不同医学数据集上的表现也不尽相同。以往的研究往往只关注整体性能,而忽视了医学语境中的特定挑战以及词法构成等宏观因素对预测准确性的影响。这些差距阻碍了针对医疗应用开发优化的 NER 模型:本研究旨在细致评估各种 NER 模型在医学文本分析中的性能,重点关注复杂的医学术语如何影响实体识别的准确性。此外,我们还探讨了宏观因素对模型性能的影响,力求为完善 NER 模型和提高其在医学应用中的可靠性提供见解:本研究在 3 个医学数据集上全面评估了 7 种 NER 模型--隐藏马尔可夫模型、条件随机场、生物医学文本挖掘 BERT、高效长序列注意的大变换器模型、解码增强型 BERT 与分离注意、稳健优化的 BERT 预训练方法和 Gemma:这些数据集包括:生物医学自然语言处理及其应用联合研讨会修订版(JNLPBA)、BioCreative V CDR 和 Anatomical Entity Mention (AnatEM)。评估的重点是预测准确性、资源使用(如中央处理单元和图形处理单元的使用)以及微调超参数的影响。此外,还使用多级因子消除算法筛选了影响模型性能的宏观因素:结果:经过微调的生物医学文本挖掘 BERT 在均衡使用资源的情况下,在修订版 JNLPBA 和 AnatEM 数据集上普遍获得了最高的预测准确率,微观平均(AVG_MICRO)得分分别为 0.932 和 0.8494,这突出表明它在识别医学实体方面具有卓越的能力。使用低秩适应技术进行微调的 Gemma 在 BioCreative V CDR 数据集上达到了最高的准确率,AVG_MICRO 得分为 0.9962,但在其他数据集上表现出了差异(在修订版 JNLPBA 上的 AVG_MICRO 得分为 0.9088,在 AnatEM 上的 AVG_MICRO 得分为 0.8029),这表明需要进一步优化。此外,我们的分析表明,实体短语长度和每个实体短语中的实体词数量这两个宏观因素对模型性能有显著影响:本研究突出了 NER 模型在医学信息学中的重要作用,强调了通过精确的数据定位和微调来优化模型的必要性。本研究的见解将显著改善临床决策,促进创建更复杂、更有效的医学 NER 模型。
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引用次数: 0
The Effects of Electronic Health Records on Medical Error Reduction: Extension of the DeLone and McLean Information System Success Model. 电子健康记录对减少医疗事故的影响:DeLone 和 McLean 信息系统成功模型的扩展。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-16 DOI: 10.2196/54572
Bester Chimbo, Lovemore Motsi

Background: Medical errors are becoming a major problem for health care providers and those who design health policies. These errors cause patients' illnesses to worsen over time and can make recovery impossible. For the benefit of patients and the welfare of health care providers, a decrease in these errors is required to maintain safe, high-quality patient care.

Objective: This study aimed to improve the ability of health care professionals to diagnose diseases and reduce medical errors.

Methods: Data collection was performed at Dr George Mukhari Academic Hospital using convenience sampling. In total, 300 health care professionals were given a self-administered questionnaire, including doctors, dentists, pharmacists, physiologists, and nurses. To test the study hypotheses, multiple linear regression was used to evaluate empirical data.

Results: In the sample of 300 health care professionals, no significant correlation was found between medical error reduction (MER) and knowledge quality (KQ) (β=.043, P=.48). A nonsignificant negative relationship existed between MER and information quality (IQ) (β=-.080, P=.19). However, a significant positive relationship was observed between MER and electronic health records (EHR; β=.125, 95% CI 0.005-0.245, P=.042).

Conclusions: Increasing patient access to medical records for health care professionals may significantly improve patient health and well-being. The effectiveness of health care organizations' operations can also be increased through better health information systems. To lower medical errors and enhance patient outcomes, policy makers should provide financing and support for EHR adoption as a top priority. Health care administrators should also concentrate on providing staff with the training they need to operate these systems efficiently. Empirical surveys in other public and private hospitals can be used to further test the validated survey instrument.

背景:医疗失误正成为医疗服务提供者和医疗政策制定者面临的一个主要问题。这些错误会导致病人的病情长期恶化,甚至无法康复。为了病人的利益和医疗服务提供者的福利,必须减少这些错误,以保持安全、高质量的病人护理:本研究旨在提高医护人员诊断疾病的能力,减少医疗失误:方法:在乔治-穆哈里博士学术医院采用便利抽样法收集数据。共向 300 名医护人员发放了自填问卷,其中包括医生、牙医、药剂师、生理学家和护士。为了验证研究假设,采用了多元线性回归法来评估经验数据:在 300 名医护人员的样本中,发现减少医疗差错(MER)与知识质量(KQ)之间没有明显的相关性(β=.043,P=.48)。减少医疗差错(MER)与信息质量(IQ)之间存在不明显的负相关关系(β=-.080,P=.19)。然而,MER 与电子健康记录(EHR;β=.125,95% CI 0.005-0.245,P=.042)之间存在明显的正相关关系:增加患者对医疗保健专业人员医疗记录的访问可能会大大改善患者的健康和福祉。通过更好的医疗信息系统还可以提高医疗机构的运营效率。为了减少医疗失误并提高病人的治疗效果,政策制定者应优先为电子病历的采用提供资金和支持。医疗管理者也应集中精力为员工提供有效操作这些系统所需的培训。在其他公立和私立医院进行的经验性调查可用于进一步检验经过验证的调查工具。
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引用次数: 0
Application of Spatial Analysis on Electronic Health Records to Characterize Patient Phenotypes: Systematic Review. 应用电子健康记录空间分析来描述患者表型:系统综述。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-15 DOI: 10.2196/56343
Abolfazl Mollalo, Bashir Hamidi, Leslie A Lenert, Alexander V Alekseyenko

Background: Electronic health records (EHRs) commonly contain patient addresses that provide valuable data for geocoding and spatial analysis, enabling more comprehensive descriptions of individual patients for clinical purposes. Despite the widespread use of EHRs in clinical decision support and interventions, no systematic review has examined the extent to which spatial analysis is used to characterize patient phenotypes.

Objective: This study reviews advanced spatial analyses that used individual-level health data from EHRs within the United States to characterize patient phenotypes.

Methods: We systematically evaluated English-language, peer-reviewed studies from the PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar databases from inception to August 20, 2023, without imposing constraints on study design or specific health domains.

Results: A substantial proportion of studies (>85%) were limited to geocoding or basic mapping without implementing advanced spatial statistical analysis, leaving only 49 studies that met the eligibility criteria. These studies used diverse spatial methods, with a predominant focus on clustering techniques, while spatiotemporal analysis (frequentist and Bayesian) and modeling were less common. A noteworthy surge (n=42, 86%) in publications was observed after 2017. The publications investigated a variety of adult and pediatric clinical areas, including infectious disease, endocrinology, and cardiology, using phenotypes defined over a range of data domains such as demographics, diagnoses, and visits. The primary health outcomes investigated were asthma, hypertension, and diabetes. Notably, patient phenotypes involving genomics, imaging, and notes were limited.

Conclusions: This review underscores the growing interest in spatial analysis of EHR-derived data and highlights knowledge gaps in clinical health, phenotype domains, and spatial methodologies. We suggest that future research should focus on addressing these gaps and harnessing spatial analysis to enhance individual patient contexts and clinical decision support.

背景:电子健康记录(EHR)通常包含患者地址,这些地址为地理编码和空间分析提供了宝贵的数据,从而能够为临床目的提供更全面的个体患者描述。尽管电子病历广泛应用于临床决策支持和干预,但还没有系统性综述对空间分析用于描述患者表型的程度进行研究:本研究回顾了利用美国电子病历中的个人健康数据来描述患者表型的高级空间分析:我们系统评估了 PubMed/MEDLINE、Scopus、Web of Science 和 Google Scholar 数据库中从开始到 2023 年 8 月 20 日的英语同行评审研究,没有对研究设计或特定健康领域施加限制:相当一部分研究(>85%)仅限于地理编码或基本制图,没有实施高级空间统计分析,因此只有 49 项研究符合资格标准。这些研究使用了不同的空间方法,主要侧重于聚类技术,而时空分析(频数分析和贝叶斯分析)和建模则不太常见。值得注意的是,2017 年后发表的论文激增(42 篇,占 86%)。这些出版物调查了各种成人和儿科临床领域,包括传染病学、内分泌学和心脏病学,使用了在人口统计学、诊断和就诊等一系列数据域中定义的表型。调查的主要健康结果是哮喘、高血压和糖尿病。值得注意的是,涉及基因组学、影像学和笔记的患者表型有限:本综述强调了人们对电子病历衍生数据空间分析日益增长的兴趣,并突出了临床健康、表型领域和空间方法学方面的知识差距。我们建议,未来的研究应侧重于解决这些差距,并利用空间分析来增强患者个体情况和临床决策支持。
{"title":"Application of Spatial Analysis on Electronic Health Records to Characterize Patient Phenotypes: Systematic Review.","authors":"Abolfazl Mollalo, Bashir Hamidi, Leslie A Lenert, Alexander V Alekseyenko","doi":"10.2196/56343","DOIUrl":"10.2196/56343","url":null,"abstract":"<p><strong>Background: </strong>Electronic health records (EHRs) commonly contain patient addresses that provide valuable data for geocoding and spatial analysis, enabling more comprehensive descriptions of individual patients for clinical purposes. Despite the widespread use of EHRs in clinical decision support and interventions, no systematic review has examined the extent to which spatial analysis is used to characterize patient phenotypes.</p><p><strong>Objective: </strong>This study reviews advanced spatial analyses that used individual-level health data from EHRs within the United States to characterize patient phenotypes.</p><p><strong>Methods: </strong>We systematically evaluated English-language, peer-reviewed studies from the PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar databases from inception to August 20, 2023, without imposing constraints on study design or specific health domains.</p><p><strong>Results: </strong>A substantial proportion of studies (>85%) were limited to geocoding or basic mapping without implementing advanced spatial statistical analysis, leaving only 49 studies that met the eligibility criteria. These studies used diverse spatial methods, with a predominant focus on clustering techniques, while spatiotemporal analysis (frequentist and Bayesian) and modeling were less common. A noteworthy surge (n=42, 86%) in publications was observed after 2017. The publications investigated a variety of adult and pediatric clinical areas, including infectious disease, endocrinology, and cardiology, using phenotypes defined over a range of data domains such as demographics, diagnoses, and visits. The primary health outcomes investigated were asthma, hypertension, and diabetes. Notably, patient phenotypes involving genomics, imaging, and notes were limited.</p><p><strong>Conclusions: </strong>This review underscores the growing interest in spatial analysis of EHR-derived data and highlights knowledge gaps in clinical health, phenotype domains, and spatial methodologies. We suggest that future research should focus on addressing these gaps and harnessing spatial analysis to enhance individual patient contexts and clinical decision support.</p>","PeriodicalId":56334,"journal":{"name":"JMIR Medical Informatics","volume":"12 ","pages":"e56343"},"PeriodicalIF":3.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bridging Data Models in Health Care With a Novel Intermediate Query Format for Feasibility Queries: Mixed Methods Study. 利用用于可行性查询的新型中间查询格式连接医疗保健数据模型:混合方法研究。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-14 DOI: 10.2196/58541
Lorenz Rosenau, Julian Gruendner, Alexander Kiel, Thomas Köhler, Bastian Schaffer, Raphael W Majeed

Background: To advance research with clinical data, it is essential to make access to the available data as fast and easy as possible for researchers, which is especially challenging for data from different source systems within and across institutions. Over the years, many research repositories and data standards have been created. One of these is the Fast Healthcare Interoperability Resources (FHIR) standard, used by the German Medical Informatics Initiative (MII) to harmonize and standardize data across university hospitals in Germany. One of the first steps to make these data available is to allow researchers to create feasibility queries to determine the data availability for a specific research question. Given the heterogeneity of different query languages to access different data across and even within standards such as FHIR (eg, CQL and FHIR Search), creating an intermediate query syntax for feasibility queries reduces the complexity of query translation and improves interoperability across different research repositories and query languages.

Objective: This study describes the creation and implementation of an intermediate query syntax for feasibility queries and how it integrates into the federated German health research portal (Forschungsdatenportal Gesundheit) and the MII.

Methods: We analyzed the requirements for feasibility queries and the feasibility tools that are currently available in research repositories. Based on this analysis, we developed an intermediate query syntax that can be easily translated into different research repository-specific query languages.

Results: The resulting Clinical Cohort Definition Language (CCDL) for feasibility queries combines inclusion criteria in a conjunctive normal form and exclusion criteria in a disjunctive normal form, allowing for additional filters like time or numerical restrictions. The inclusion and exclusion results are combined via an expression to specify feasibility queries. We defined a JSON schema for the CCDL, generated an ontology, and demonstrated the use and translatability of the CCDL across multiple studies and real-world use cases.

Conclusions: We developed and evaluated a structured query syntax for feasibility queries and demonstrated its use in a real-world example as part of a research platform across 39 German university hospitals.

背景:要推进临床数据研究,就必须让研究人员尽可能快速、方便地访问可用数据,这对于来自机构内部和机构间不同源系统的数据来说尤其具有挑战性。多年来,许多研究资料库和数据标准应运而生。其中之一就是快速医疗互操作性资源(FHIR)标准,该标准由德国医疗信息学倡议(MII)使用,用于统一和标准化德国各大学医院的数据。提供这些数据的第一步是允许研究人员创建可行性查询,以确定特定研究问题的数据可用性。鉴于不同的查询语言在 FHIR(如 CQL 和 FHIR Search)等标准之间甚至标准内部访问不同数据的异质性,为可行性查询创建中间查询语法可降低查询翻译的复杂性,提高不同研究资料库和查询语言之间的互操作性:本研究描述了可行性查询中间查询语法的创建和实施,以及如何将其集成到联合的德国健康研究门户网站(Forschungsdatenportal Gesundheit)和 MII 中:我们分析了可行性查询的要求以及目前研究资料库中可用的可行性工具。在分析的基础上,我们开发了一种中间查询语法,该语法可以很容易地翻译成不同研究资料库的特定查询语言:结果:由此产生的用于可行性查询的临床队列定义语言(CCDL)结合了连接正则表达式中的包含标准和非连接正则表达式中的排除标准,并允许使用时间或数字限制等附加筛选条件。包含和排除结果通过表达式结合起来,以指定可行性查询。我们为 CCDL 定义了一个 JSON 模式,生成了一个本体,并演示了 CCDL 在多项研究和真实世界用例中的使用和可转换性:我们开发并评估了用于可行性查询的结构化查询语法,并在一个实际案例中演示了其在德国 39 家大学医院研究平台中的应用。
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引用次数: 0
Case Identification of Depression in Inpatient Electronic Medical Records: Scoping Review. 住院病人电子病历中的抑郁症病例识别:范围审查。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-14 DOI: 10.2196/49781
Allison Grothman, William J Ma, Kendra G Tickner, Elliot A Martin, Danielle A Southern, Hude Quan

Background: Electronic medical records (EMRs) contain large amounts of detailed clinical information. Using medical record review to identify conditions within large quantities of EMRs can be time-consuming and inefficient. EMR-based phenotyping using machine learning and natural language processing algorithms is a continually developing area of study that holds potential for numerous mental health disorders.

Objective: This review evaluates the current state of EMR-based case identification for depression and provides guidance on using current algorithms and constructing new ones.

Methods: A scoping review of EMR-based algorithms for phenotyping depression was completed. This research encompassed studies published from January 2000 to May 2023. The search involved 3 databases: Embase, MEDLINE, and APA PsycInfo. This was carried out using selected keywords that fell into 3 categories: terms connected with EMRs, terms connected to case identification, and terms pertaining to depression. This study adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines.

Results: A total of 20 papers were assessed and summarized in the review. Most of these studies were undertaken in the United States, accounting for 75% (15/20). The United Kingdom and Spain followed this, accounting for 15% (3/20) and 10% (2/20) of the studies, respectively. Both data-driven and clinical rule-based methodologies were identified. The development of EMR-based phenotypes and algorithms indicates the data accessibility permitted by each health system, which led to varying performance levels among different algorithms.

Conclusions: Better use of structured and unstructured EMR components through techniques such as machine learning and natural language processing has the potential to improve depression phenotyping. However, more validation must be carried out to have confidence in depression case identification algorithms in general.

背景:电子病历(EMR)包含大量详细的临床信息:电子病历(EMR)包含大量详细的临床信息。使用病历审查来识别大量 EMR 中的病症既耗时又低效。使用机器学习和自然语言处理算法进行基于 EMR 的表型分析是一个不断发展的研究领域,对许多心理健康疾病都有潜在的帮助:本综述评估了基于 EMR 的抑郁症病例识别的现状,并为使用现有算法和构建新算法提供指导:方法:我们完成了对基于电子病历的抑郁症表型算法的范围综述。这项研究涵盖了 2000 年 1 月至 2023 年 5 月期间发表的研究。检索涉及 3 个数据库:Embase、MEDLINE 和 APA PsycInfo。检索时使用的关键词分为三类:与 EMR 相关的术语、与病例识别相关的术语以及与抑郁症相关的术语。这项研究遵循了 PRISMA-ScR(系统性综述和元分析的首选报告项目,范围综述的扩展)指南:本综述共评估和总结了 20 篇论文。这些研究大多在美国进行,占 75%(15/20)。英国和西班牙紧随其后,分别占 15%(3/20)和 10%(2/20)。研究发现了数据驱动和基于临床规则的方法。基于EMR的表型和算法的发展表明了每个医疗系统允许的数据可访问性,这导致不同算法的性能水平各不相同:结论:通过机器学习和自然语言处理等技术更好地利用结构化和非结构化的 EMR 组件有可能改善抑郁症的表型。然而,要对抑郁症病例识别算法有信心,还必须进行更多的验证。
{"title":"Case Identification of Depression in Inpatient Electronic Medical Records: Scoping Review.","authors":"Allison Grothman, William J Ma, Kendra G Tickner, Elliot A Martin, Danielle A Southern, Hude Quan","doi":"10.2196/49781","DOIUrl":"10.2196/49781","url":null,"abstract":"<p><strong>Background: </strong>Electronic medical records (EMRs) contain large amounts of detailed clinical information. Using medical record review to identify conditions within large quantities of EMRs can be time-consuming and inefficient. EMR-based phenotyping using machine learning and natural language processing algorithms is a continually developing area of study that holds potential for numerous mental health disorders.</p><p><strong>Objective: </strong>This review evaluates the current state of EMR-based case identification for depression and provides guidance on using current algorithms and constructing new ones.</p><p><strong>Methods: </strong>A scoping review of EMR-based algorithms for phenotyping depression was completed. This research encompassed studies published from January 2000 to May 2023. The search involved 3 databases: Embase, MEDLINE, and APA PsycInfo. This was carried out using selected keywords that fell into 3 categories: terms connected with EMRs, terms connected to case identification, and terms pertaining to depression. This study adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines.</p><p><strong>Results: </strong>A total of 20 papers were assessed and summarized in the review. Most of these studies were undertaken in the United States, accounting for 75% (15/20). The United Kingdom and Spain followed this, accounting for 15% (3/20) and 10% (2/20) of the studies, respectively. Both data-driven and clinical rule-based methodologies were identified. The development of EMR-based phenotypes and algorithms indicates the data accessibility permitted by each health system, which led to varying performance levels among different algorithms.</p><p><strong>Conclusions: </strong>Better use of structured and unstructured EMR components through techniques such as machine learning and natural language processing has the potential to improve depression phenotyping. However, more validation must be carried out to have confidence in depression case identification algorithms in general.</p>","PeriodicalId":56334,"journal":{"name":"JMIR Medical Informatics","volume":"12 ","pages":"e49781"},"PeriodicalIF":3.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Application of Information Link Control in Surgical Specimen Near-Miss Events in a South China Hospital: Nonrandomized Controlled Study. 信息链接控制在华南某医院手术标本近失事件中的应用:非随机对照研究
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-14 DOI: 10.2196/52722
Tingting Chen, Xiaofen Tang, Min Xu, Yue Jiang, Fengyan Zheng

Background: Information control is a promising approach for managing surgical specimens. However, there is limited research evidence on surgical near misses. This is particularly true in the closed loop of information control for each link.

Objective: A new model of surgical specimen process management is further constructed, and a safe operating room nursing practice environment is created by intercepting specimen near-miss events through information safety barriers.

Methods: In a large hospital in China, 84,289 surgical specimens collected in the conventional information specimen management mode from January to December 2021 were selected as the control group, and 99,998 surgical specimens collected in the information safety barrier control surgical specimen management mode from January to December 2022 were selected as the improvement group. The incidence of near misses, the qualified rate of pathological specimen fixation, and the average time required for specimen fixation were compared under the 2 management modes. The causes of 2 groups of near misses were analyzed and the near misses of information safety barrier control surgical specimens were studied.

Results: Under the information-based safety barrier control surgical specimen management model, the incidence of adverse events in surgical specimens was reduced, the reporting of near-miss events in surgical specimens was improved by 100%, the quality control quality management of surgical specimens was effectively improved, the pass rate of surgical pathology specimen fixation was improved, and the meantime for surgical specimen fixation was shortened, with differences considered statistically significant at P<.05.

Conclusions: Our research has developed a new mode of managing the surgical specimen process. This mode can prevent errors in approaching specimens by implementing information security barriers, thereby enhancing the quality of specimen management, ensuring the safety of medical procedures, and improving the quality of hospital services.

背景:信息控制是一种很有前景的手术标本管理方法。然而,有关手术险情的研究证据却很有限。在每个环节的信息控制闭环中尤其如此:进一步构建手术标本流程管理的新模式,通过信息安全屏障拦截标本近失事件,创造安全的手术室护理实践环境:在国内某大型医院选取2021年1月至12月常规信息标本管理模式下采集的84289例手术标本作为对照组,2022年1月至12月信息安全屏障控制手术标本管理模式下采集的99998例手术标本作为改进组。比较两种管理模式下的险情发生率、病理标本固定合格率和标本固定平均所需时间。分析了两组险情发生的原因,并对信息化安全屏障控制手术标本的险情进行了研究:结果:在信息化安全屏障控制手术标本管理模式下,手术标本不良事件发生率降低,手术标本近失事件报告率提高了100%,手术标本质控质量管理水平得到有效提高,手术病理标本固定合格率提高,手术标本固定时间缩短,PConclusions认为差异有统计学意义:我们的研究开发了一种新的手术标本流程管理模式。这种模式可以通过实施信息安全屏障来防止标本接近中的错误,从而提高标本管理的质量,确保医疗过程的安全,改善医院的服务质量。
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引用次数: 0
Health Care Worker Usage of Large-Scale Health Information Exchanges in Japan: User-Level Audit Log Analysis Study. 日本医护人员使用大规模医疗信息交换的情况:用户级审计日志分析研究》。
IF 3.1 3区 医学 Q2 MEDICAL INFORMATICS Pub Date : 2024-10-09 DOI: 10.2196/56263
Jun Suzumoto, Yukiko Mori, Tomohiro Kuroda

Background: Over 200 health information exchanges (HIEs) are currently operational in Japan. The most common feature of HIEs is remote on-demand viewing or searching of aggregated patient health data from multiple institutions. However, the usage of this feature by individual users and institutions remains unknown.

Objective: This study aims to understand usage of the on-demand patient data viewing feature of large-scale HIEs by individual health care workers and institutions in Japan.

Methods: We conducted audit log analyses of large-scale HIEs. The research subjects were HIEs connected to over 100 institutions and with over 10,000 patients. Each health care worker's profile and audit log data for HIEs were collected. We conducted four types of analyses on the extracted audit log. First, we calculated the ratio of the number of days of active HIE use for each hospital-affiliated doctor account. Second, we calculated cumulative monthly usage days of HIEs by each institution in financial year (FY) 2021/22. Third, we calculated each facility type's monthly active institution ratio in FY2021/22. Fourth, we compared the monthly active institution ratio by medical institution for each HIE and the proportion of cumulative usage days by user type for each HIE.

Results: We identified 24 HIEs as candidates for data collection and we analyzed data from 7 HIEs. Among hospital doctors, 93.5% (7326/7833) had never used HIEs during the available period in FY2021/22, while 19 doctors used them at least 30% of days. The median (IQR) monthly active institution ratios were 0.482 (0.470-0.487) for hospitals, 0.243 (0.230-0.247) for medical clinics, and 0.030 (0.024-0.048) for dental clinics. In 51.9% (1781/3434) of hospitals, the cumulative monthly usage days of HIEs was 0, while in 26.8% (921/3434) of hospitals, it was between 1 and 10, and in 3% (103/3434) of hospitals, it was 100 or more. The median (IQR) monthly active institution ratio in medical institutions was 0.511 (0.487-0.529) for the most used HIE and 0.109 (0.0927-0.117) for the least used. The proportion of cumulative usage days of HIE by user type was complex for each HIE, and no consistent trends could be discerned.

Conclusions: In the large-scale HIEs surveyed in this study, the overall usage of the on-demand patient data viewing feature was low, consistent with past official reports. User-level analyses of audit logs revealed large disparities in the number of days of HIE use among health care workers and institutions. There were also large disparities in HIE use by facility type or HIE; the percentage of cumulative HIE usage days by user type also differed by HIE. This study indicates the need for further research into why there are large disparities in demand for HIEs in Japan as well as the need to design comprehensive audit logs that can be matched with other official datasets.

背景:日本目前有 200 多个健康信息交换系统(HIE)在运行。HIE 最常见的功能是远程按需查看或搜索来自多个机构的汇总病人健康数据。然而,个人用户和医疗机构对这一功能的使用情况仍不得而知:本研究旨在了解日本医护人员个人和机构对大型 HIE 的按需查看患者数据功能的使用情况:我们对大型 HIE 进行了审计日志分析。研究对象是与 100 多家机构连接、拥有 10,000 多名患者的 HIE。我们收集了每位医护人员的个人资料和 HIE 的审计日志数据。我们对提取的审计日志进行了四种分析。首先,我们计算了每个医院附属医生账户的 HIE 有效使用天数比率。其次,我们计算了 2021/22 财政年度(FY)各机构每月使用 HIE 的累计天数。第三,我们计算了 2021/22 财政年度各设施类型的每月活跃机构比率。第四,我们比较了各医疗机构在每个医疗信息基础设施中的每月活跃机构比率和各医疗信息基础设施中按用户类型划分的累计使用天数比例:我们确定了 24 个 HIE 作为数据收集的候选机构,并对 7 个 HIE 的数据进行了分析。在医院医生中,93.5%(7326/7833)的医生在 2021/22 财政年度的可用期间从未使用过 HIE,而 19 名医生至少有 30% 的天数使用过 HIE。医院每月活跃机构比率的中位数(IQR)为 0.482(0.470-0.487),医疗诊所为 0.243(0.230-0.247),牙科诊所为 0.030(0.024-0.048)。51.9%(1781/3434)的医院每月使用HIE的累计天数为0,26.8%(921/3434)的医院为1至10天,3%(103/3434)的医院为100天或以上。在医疗机构中,使用最多的 HIE 每月活跃机构比例的中位数(IQR)为 0.511(0.487-0.529),使用最少的为 0.109(0.0927-0.117)。按用户类型划分的 HIE 累计使用天数比例在每个 HIE 中都很复杂,无法发现一致的趋势:在本研究调查的大型 HIE 中,按需查看病人数据功能的总体使用率较低,这与过去的官方报告一致。对审计日志进行的用户层面分析表明,医护人员和医疗机构在使用 HIE 的天数上存在巨大差异。不同机构类型或 HIE 在使用 HIE 方面也存在巨大差异;不同 HIE 的用户类型在累计 HIE 使用天数中所占的百分比也不尽相同。这项研究表明,有必要进一步研究日本对 HIE 的需求存在巨大差异的原因,以及设计可与其他官方数据集进行匹配的全面审计日志的必要性。
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JMIR Medical Informatics
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