Studies in Health Technology and Informatics最新文献

{"title":"DE-Lemma: A Maximum-Entropy Based Lemmatizer for German Medical Text.","authors":"Martin Wiesner","doi":"10.3233/SHTI230712","DOIUrl":"https://doi.org/10.3233/SHTI230712","url":null,"abstract":"<p><p>When processing written German language, it is helpful, to use the base form (or: lemma) of possibly inflected words, such as verbs, nouns or named entities. However, for German text from the (bio)medical domain, e.g., discharge letters, or entries stored in electronic medical or health records (EMR, EHR), difficulties exist in finding the correct lemma, as, for instance, the medical language has roots in Latin or Greek. In such cases, stemming techniques might provide inaccurate results for text written in German. This study demonstrates a Machine Learning approach for training Apache OpenNLP-based lemmatizer models from publicly available German treebanks. The resulting four \"DE-Lemma\" models were evaluated against a sample of (bio)medical nouns, randomly selected from real-world discharge letters. The most promising DE-Lemma model achieved an accuracy of 88.0% (F1 = .936).</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"189-195"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Concept Graphs: A Novel Approach for Textual Analysis of Medical Documents.","authors":"Franz Matthies,&nbsp;Christoph Beger,&nbsp;Ralph Schäfermeier,&nbsp;Alexandr Uciteli","doi":"10.3233/SHTI230710","DOIUrl":"https://doi.org/10.3233/SHTI230710","url":null,"abstract":"<p><p>The task of automatically analyzing the textual content of documents faces a number of challenges in general but even more so when dealing with the medical domain. Here, we can't normally rely on specifically pre-trained NLP models or even, due to data privacy reasons, (massive) amounts of training material to generate said models. We, therefore, propose a method that utilizes general-purpose basic text analysis components and state-of-the-art transformer models to represent a corpus of documents as multiple graphs, wherein important conceptually related phrases from documents constitute the nodes and their semantic relation form the edges. This method could serve as a basis for several explorative procedures and is able to draw on a plethora of publicly available resources. We test it by comparing the effectiveness of these so-called Concept Graphs with another recently suggested approach for a common use case in information retrieval, document clustering.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"172-179"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards a Bavarian Oncology Real World Data Research Platform.","authors":"Jasmin Ziegler,&nbsp;Julian Gruendner,&nbsp;Lorenz Rosenau,&nbsp;Marcel Erpenbeck,&nbsp;Hans-Ulrich Prokosch,&nbsp;Noemi Deppenwiese","doi":"10.3233/SHTI230696","DOIUrl":"https://doi.org/10.3233/SHTI230696","url":null,"abstract":"<p><strong>Introduction: </strong>In the last decade numerous real-world data networks have been established in order to leverage the value of data from electronic health records for medical research. In Germany, a nation-wide network based on electronic health record data from all German university hospitals has been established within the Medical Informatics Initiative (MII) and recently opened for researcherst' access through the German Portal for Medical Research Data (FDPG). In Bavaria, the six university hospitals have joined forces within the Bavarian Cancer Research Center (BZKF). The oncology departments aim at establishing a federated observational research network based on the framework of the MII/FDPG and extending it with a clear focus on oncological clinical data, imaging data and molecular high throughput analysis data.</p><p><strong>Methods: </strong>We describe necessary adaptions and extensions of existing MII components with the goal of establishing a Bavarian oncology real world data research platform with its first use case of performing federated feasibility queries on clinical oncology data.</p><p><strong>Results: </strong>We share insights from developing a feasibility platform prototype and presenting it to end users. Our main discovery was that oncological data is characterized by a higher degree of interdependence and complexity compared to the MII core dataset that is already integrated into the FDPG.</p><p><strong>Discussion: </strong>The significance of our work lies in the requirements we formulated for extending already existing MII components to match oncology specific data and to meet oncology researchers needs while simultaneously transferring back our results and experiences into further developments within the MII.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"78-85"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10277572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How to Make Outpatient Healthcare Data in Germany Available for Research in the Dynamic Course of Digital Transformation.","authors":"Marius Koch,&nbsp;Jendrik Richter,&nbsp;Johannes Hauswaldt,&nbsp;Dagmar Krefting","doi":"10.3233/SHTI230688","DOIUrl":"https://doi.org/10.3233/SHTI230688","url":null,"abstract":"<p><strong>Introduction: </strong>There is increasing interest on re-use of outpatient healthcare data for research, as most medical diagnosis and treatment is provided in the ambulatory sector. One of the early projects to bring primary data from German ambulatory care into clinical research technically, organizationally and in compliance with legal demands has been the RADAR project, that is based on a broad consent and has used the then available practice information system's interfaces to extract and transfer data to a research repository. In course of the digital transformation of the German healthcare system, former standards are abandoned and new interoperability standards, interfaces and regulations on secondary use of patient data are defined, however with slow adoption by Health-IT systems. Therefore, it is of importance for all initiatives that aim at using ambulatory healthcare data for research, how to access this data in an efficient and effective way.</p><p><strong>Methods: </strong>Currently defined healthcare standards are compared regarding coverage of data relevant for research as defined by the RADAR project. We compare four architectural options to access ambulatory health data through different components of healthcare and health research data infrastructures along the technical, organizational and regulatory conditions, the timetable of dissemination and the researcher's perspective.</p><p><strong>Results: </strong>A high-level comparison showed a high degree of semantic overlap in the information models used. Electronic patient records and practice information systems are alternative data sources for ambulatory health data - but differ strongly in data richness and accessibility.</p><p><strong>Conclusion: </strong>Considering the compared dimensions of architectural routes to access health data for secondary research use we conclude that data extraction from practice information systems is currently the most promising way due to data availability on a mid-term perspective. Integration of routine data into the national research data infrastructures might be enforced by convergence of to date different information models.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"12-21"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10277573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demand Analysis of a German Emergency Medical Service Feedback System.","authors":"Marina Keimer,&nbsp;Marten Villis,&nbsp;Jan Christoph,&nbsp;Wolfgang Rödle","doi":"10.3233/SHTI230700","DOIUrl":"https://doi.org/10.3233/SHTI230700","url":null,"abstract":"<p><strong>Background: </strong>The number of emergency medical service (EMS) calls in Germany is continuously increasing. The initial assessment, the pre-hospital care and the choice of hospital for further care by the EMS influences the patient's outcome and are the basis for further care in hospital. However, the EMS does not receive any official feedback on its decisions.</p><p><strong>Objectives: </strong>This study evaluates the demand for a feedback system from the emergency department (ED) to the EMS, what it should contain, and how it could be integrated in the electronic clinical systems.</p><p><strong>Methods: </strong>A semi-structured interview guideline for expert interviews with members of EMS staff (n = 6) and ED staff (n = 17) was developed. A mockup to visualise a possible implementation was designed and included in the interview.</p><p><strong>Results: </strong>There is a significant demand for feedback on pre-diagnosis, pre-hospital care and handover of patients from the EMS to the ED. The EDs are very interested in improving the collaboration with the paramedic services through feedback.</p><p><strong>Conclusion: </strong>A feedback system is strongly desired by various EMS stakeholders and, according to them, could improve both EMS and ED collaboration and overall patient care.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"102-109"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10277574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Usability Analysis of a Medication Visualization Tool for Decision Support.","authors":"Leon Schmidtchen,&nbsp;Marten Villis,&nbsp;Jan Christoph,&nbsp;Wolfgang Rödle","doi":"10.3233/SHTI230701","DOIUrl":"https://doi.org/10.3233/SHTI230701","url":null,"abstract":"<p><strong>Background: </strong>In Germany, patients are entitled to a medication plan. While the overview is useful, it does not contain explicit information on various potential adverse drug events (ADEs). Therefore, physicians must continue to seek information from various sources to ensure medication safety.</p><p><strong>Objective: </strong>In this project a first functional prototype of a medication therapy tool was developed that focuses on visualizing and highlighting potential ADEs. A usability analysis about the tool's functionality, design and usability was conducted.</p><p><strong>Methods: </strong>A web application tool was developed using the MMI Pharmindex as database. ADEs are color coded and can be displayed in three different ways - as a list, a table, or a graph. To test the tool, an online survey was conducted amongst healthcare professionals (n = 9). The test included two real medication plans to check ADEs through the tool.</p><p><strong>Results: </strong>The survey results indicated that the web tool was clear and self-explanatory. It scored overall \"good\" (score: 76.5) on the System Usability Scale questionnaire. Due to the free-text information of the database used, there were some inconsistencies in the visualized ADEs.</p><p><strong>Conclusion: </strong>There is a demand for a visualization tool for medications. The high quality of the database is crucial in order to correctly visualize all necessary information, such as drug-drug interactions and inclusion of patient data. This is essential to provide a trustworthy tool for medical professionals.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"110-116"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10277575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ECG Matching: An Approach to Synchronize ECG Datasets for Data Quality Comparisons.","authors":"Mohamed Alhaskir,&nbsp;Matteo Tschesche,&nbsp;Florian Linke,&nbsp;Elisabeth Schriewer,&nbsp;Yvonne Weber,&nbsp;Stefan Wolking,&nbsp;Rainer Röhrig,&nbsp;Henner Koch,&nbsp;Ekaterina Kutafina","doi":"10.3233/SHTI230718","DOIUrl":"https://doi.org/10.3233/SHTI230718","url":null,"abstract":"<p><p>Clinical assessment of newly developed sensors is important for ensuring their validity. Comparing recordings of emerging electrocardiography (ECG) systems to a reference ECG system requires accurate synchronization of data from both devices. Current methods can be inefficient and prone to errors. To address this issue, three algorithms are presented to synchronize two ECG time series from different recording systems: Binned R-peak Correlation, R-R Interval Correlation, and Average R-peak Distance. These algorithms reduce ECG data to their cyclic features, mitigating inefficiencies and minimizing discrepancies between different recording systems. We evaluate the performance of these algorithms using high-quality data and then assess their robustness after manipulating the R-peaks. Our results show that R-R Interval Correlation was the most efficient, whereas the Average R-peak Distance and Binned R-peak Correlation were more robust against noisy data.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"225-232"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptability of Existing Feasibility Tools for Clinical Study Research Data Platforms.","authors":"Marie-Louise Witte,&nbsp;Anne Schoneberg,&nbsp;Sabine Hanss,&nbsp;Martin Lablans,&nbsp;Janne Vehreschild,&nbsp;Dagmar Krefting","doi":"10.3233/SHTI230691","DOIUrl":"https://doi.org/10.3233/SHTI230691","url":null,"abstract":"<p><strong>Introduction: </strong>The increasing need for secondary use of clinical study data requires FAIR infrastructures, i.e. provide findable, accessible, interoperable and reusable data. It is crucial for data scientists to assess the number and distribution of cohorts that meet complex combinations of criteria defined by the research question. This so-called feasibility test is increasingly offered as a self-service, where scientists can filter the available data according to specific parameters. Early feasibility tools have been developed for biosamples or image collections. They are of high interest for clinical study platforms that federate multiple studies and data types, but they pose specific requirements on the integration of data sources and data protection.</p><p><strong>Methods: </strong>Mandatory and desired requirements for such tools were acquired from two user groups - primary users and staff managing a platform's transfer office. Open Source feasibility tools were sought by different literature search strategies and evaluated on their adaptability to the requirements.</p><p><strong>Results: </strong>We identified seven feasibility tools that we evaluated based on six mandatory properties.</p><p><strong>Discussion: </strong>We determined five feasibility tools to be most promising candidates for adaption to a clinical study research data platform, the Clinical Communication Platform, the German Portal for Medical Research Data, the Feasibility Explorer, Medical Controlling, and the Sample Locator.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"39-48"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10224078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"odML-Tables as a Metadata Standard in Microneurography.","authors":"Alina Troglio, Aidan Nickerson, Fabian Schlebusch, Rainer Röhrig, James Dunham, Barbara Namer, Ekaterina Kutafina","doi":"10.3233/SHTI230687","DOIUrl":"10.3233/SHTI230687","url":null,"abstract":"<p><p>Metadata is essential for handling medical data according to FAIR principles. Standards are well-established for many types of electrophysiological methods but are still lacking for microneurographic recordings of peripheral sensory nerve fibers in humans. Developing a new concept to enhance laboratory workflows is a complex process. We propose a standard for structuring and storing microneurography metadata based on odML and odML-tables. Further, we present an extension to the odML-tables GUI that enables user-friendly search functionality of the database. With our open-source repository, we encourage other microneurography labs to incorporate odML-based metadata into their experimental routines.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"3-11"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10277570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating REDCap as the Central Data Collection Tool for the Hamburg City Health Study.","authors":"Nils Schönbeck,&nbsp;Yassin Hussein,&nbsp;Alena Haack,&nbsp;Axel Schmager,&nbsp;Ulrike Harney,&nbsp;Leona Trübe,&nbsp;Frank Ückert,&nbsp;Karl Gottfried","doi":"10.3233/SHTI230693","DOIUrl":"https://doi.org/10.3233/SHTI230693","url":null,"abstract":"<p><strong>Introduction: </strong>The collection of examination data for large clinical studies is often done with proprietary systems, which are accompanied by several disadvantages such as high cost and low flexibility. With the use of open-source tools, these disadvantages can be overcome and thereby improve data collection as well as data quality. Here we exemplary use the data collection process of the Hamburg City Health Study (HCHS), carried out at the University Medical Center Hamburg-Eppendorf (UKE). We evaluated how the recording of the examination data can be converted from an established, proprietary electronic healthcare record (EHR) system to the free-to-use Research Electronic Data Capture (REDCap) software.</p><p><strong>Methods: </strong>For this purpose, a technical conversion of the EHR system is described first. Metafiles derived from the EHR system were used for REDCap electronic case report form (eCRF) building. The REDCap system was tested by HCHS study assistants via completion of self-developed tasks mimicking their everyday study life. Usability was quantitatively evaluated via the IBM Computer System Usability Questionnaire (CSUQ) and qualitatively assessed with a semi-structured interview.</p><p><strong>Results: </strong>With the IBM CSUQ, the study assistants rated the usage of the basic REDCap system for HCHS examination data collection with an overall score of 4.39, which represents a medium acceptance. The interview feedback was used to formulate user stories to subsequently increase the administrative sovereignty and to conceptualize a REDCap HCHS information technology (IT) infrastructure.</p><p><strong>Conclusion: </strong>Our work aims to serve as a template for evaluating the feasibility of a conversion from a proprietary to a free-to-use data collection tool for large clinical studies such as the HCHS. REDCap has great potential, but extensions and an integration to the current IT infrastructure are required.</p>","PeriodicalId":39242,"journal":{"name":"Studies in Health Technology and Informatics","volume":"307 ","pages":"51-59"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10277577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}