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Zheng L, Wang L. Comprehensive information management system for a medical research cohort biobank based on quality by design. BMC Med Inform Decis Mak 2023; 23:222. [PMID: 37845654 PMCID: PMC10580628 DOI: 10.1186/s12911-023-02318-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/30/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND With the development of big health and big data, cohort research has become a medical research hotspot. As an important repository of human genetic resources, biobanks must adapt to the requirements of large-scale and efficient operation. Thus, biobanks urgently need to design and build a legal, convenient, and efficient information management system. METHODS This study applies the concept of "quality by design" to build a comprehensive biobank information management system based on the analysis of user requirements, legal and regulatory risks, and industry-standard requirements. The system integrates the management of scientific research projects, biological specimens, clinical information, quality control, and multi-dimensional information query and development. After 10 months of its operation, the comprehensive management system was evaluated through statistical analysis of the efficiency of the construction of the pregnancy-birth cohort and the quality of genetic resources. RESULTS Since the system's launch, the statistics on cohort construction efficiency show that the enrollment rate of eligible pregnant women has increased, and the rate of missing volunteers has dropped. The time needed to establish a 1000-person cohort (with complete biological samples and clinical information in early, middle, and late pregnancy) was reduced, and the effective tracking rate of the samples was 77.42%. The error rate of the deep cryogenic refrigerator decreased, with a clinical information integrity rate of 96.47%. CONCLUSIONS The comprehensive biobank information management system constructed with the "quality by design" concept is well suited to meet the requirements of medical research. This study provides a solution for designing a comprehensive information system for medical institutions' biobanks.
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Affiliation(s)
- Lianshuai Zheng
- Biobank of Lianyungang Maternal and Child Health Hospital, Lianyungang Maternal and Child Health Hospital, Jiangsu, China
| | - Leilei Wang
- Biobank of Lianyungang Maternal and Child Health Hospital, Lianyungang Maternal and Child Health Hospital, Jiangsu, China.
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Brief Reports Prepared by Students and Graduates of Master of Science in Biobanking. Biopreserv Biobank 2023; 21:98-105. [PMID: 36169634 PMCID: PMC9963501 DOI: 10.1089/bio.2022.0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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3
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Ulrich H, Kock-Schoppenhauer AK, Deppenwiese N, Gött R, Kern J, Lablans M, Majeed RW, Stöhr MR, Stausberg J, Varghese J, Dugas M, Ingenerf J. Understanding the Nature of Metadata: Systematic Review. J Med Internet Res 2022; 24:e25440. [PMID: 35014967 PMCID: PMC8790684 DOI: 10.2196/25440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/28/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Background Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example, data identification and classification. However, a clear definition of metadata is crucial for further use. Unfortunately, extensive experience with the processing and management of metadata has shown that the term “metadata” and its use is not always unambiguous. Objective This study aimed to understand the definition of metadata and the challenges resulting from metadata reuse. Methods A systematic literature search was performed in this study following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines for reporting on systematic reviews. Five research questions were identified to streamline the review process, addressing metadata characteristics, metadata standards, use cases, and problems encountered. This review was preceded by a harmonization process to achieve a general understanding of the terms used. Results The harmonization process resulted in a clear set of definitions for metadata processing focusing on data integration. The following literature review was conducted by 10 reviewers with different backgrounds and using the harmonized definitions. This study included 81 peer-reviewed papers from the last decade after applying various filtering steps to identify the most relevant papers. The 5 research questions could be answered, resulting in a broad overview of the standards, use cases, problems, and corresponding solutions for the application of metadata in different research areas. Conclusions Metadata can be a powerful tool for identifying, describing, and processing information, but its meaningful creation is costly and challenging. This review process uncovered many standards, use cases, problems, and solutions for dealing with metadata. The presented harmonized definitions and the new schema have the potential to improve the classification and generation of metadata by creating a shared understanding of metadata and its context.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | | | - Noemi Deppenwiese
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Gött
- Department Epidemiology of Health Care and Community Health, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Raphael W Majeed
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Justus-Liebig-University, Giessen, Germany.,Institute of Medical Informatics, University Hospital RWTH Aachen, Aachen, Germany
| | - Mark R Stöhr
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
| | - Jürgen Stausberg
- Institute of Medical Informatics, Biometry and Epidemiology, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
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Nutrition Information in Oncology - Extending the Electronic Patient-Record Data Set. J Med Syst 2020; 44:191. [PMID: 32986139 PMCID: PMC7520877 DOI: 10.1007/s10916-020-01649-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
Electronic health records (EHRs) present extensive patient information and may be used as a tool to improve health care. However, the oncology context presents a complex content that increases the difficulties of EHR application. This study aimed at developing openEHR-archetypes representing clinical concepts in cancer nutrition-care, as well as to develop an openEHR-template including the aforementioned archetypes. The study involved the following stages: 1) a thorough literature review, followed by an expert’s (nutrition guideline authors) survey, aiming to identify the main statements of published clinical guidelines on nutrition in cancer patients that were not included on the Clinical Knowledge Manager (CKM) repository; 2) modelling of the archetypes using the Ocean Archetype Software and submission to the CKM repository; 3) creating an example template with Template Designer; and 4) automatic conversion of the openEHR-template into a readily usable EHR using VCIntegrator. The clinical concepts (among 17 clinical concepts not yet available in the CKM repository) chosen for further development were: body composition, diet plan, dietary nutrients, dietary supplements, dietary intake assessment, and Malnutrition Screening Tool (MST). So far, four archetypes were accepted for review in the CKM repository and a template was created and converted into an EHR. This study designed new openEHR-archetypes for nutrition management in cancer patients. These archetypes can be included in EHR. Future studies are needed to assess their applicability in other areas and their practical impact on data quality, system interoperability and, ultimately, on clinical practice and research.
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Kim HH, Park YR, Lee S, Kim JH. Composite CDE: modeling composite relationships between common data elements for representing complex clinical data. BMC Med Inform Decis Mak 2020; 20:147. [PMID: 32620117 PMCID: PMC7333279 DOI: 10.1186/s12911-020-01168-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Semantic interoperability is essential for improving data quality and sharing. The ISO/IEC 11179 Metadata Registry (MDR) standard has been highlighted as a solution for standardizing and registering clinical data elements (DEs). However, the standard model has both structural and semantic limitations, and the number of DEs continues to increase due to poor term reusability. Semantic types and constraints are lacking for comprehensively describing and evaluating DEs on real-world clinical documents. METHODS We addressed these limitations by defining three new types of semantic relationship (dependency, composite, and variable) in our previous studies. The present study created new and further extended existing semantic types (hybrid atomic and repeated and dictionary composite common data elements [CDEs]) with four constraints: ordered, operated, required, and dependent. For evaluation, we extracted all atomic and composite CDEs from five major clinical documents from five teaching hospitals in Korea, 14 Fast Healthcare Interoperability Resources (FHIR) resources from FHIR bulk sample data, and MIMIC-III (Medical Information Mart for Intensive Care) demo dataset. Metadata reusability and semantic interoperability in real clinical settings were comprehensively evaluated by applying the CDEs with our extended semantic types and constraints. RESULTS All of the CDEs (n = 1142) extracted from the 25 clinical documents were successfully integrated with a very high CDE reuse ratio (46.9%) into 586 CDEs (259 atomic and 20 unique composite CDEs), and all of CDEs (n = 238) extracted from the 14 FHIR resources of FHIR bulk sample data were successfully integrated with high CDE reuse ration (59.7%) into 96 CDEs (21 atomic and 28 unique composite CDEs), which improved the semantic integrity and interoperability without any semantic loss. Moreover, the most complex data structures from two CDE projects were successfully encoded with rich semantics and semantic integrity. CONCLUSION MDR-based extended semantic types and constraints can facilitate comprehensive representation of clinical documents with rich semantics, and improved semantic interoperability without semantic loss.
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Affiliation(s)
- Hye Hyeon Kim
- Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Yu Rang Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Suehyun Lee
- Department of Biomedical Informatics, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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Le Queau C, Ann Phillips W, Srinivasan A. [Practical use of biobank information management system (BIMS) for clinical-biological annotations in biobanks]. Med Sci (Paris) 2020; 36:285-288. [PMID: 32228852 DOI: 10.1051/medsci/2020044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Caroline Le Queau
- MSc biobanks and complex data management, Université Côte d'Azur, Centre hospitalier universitaire de Nice, Hôpital Pasteur, Biobanque BB-0033-00025, Nice, France
| | - Wendy Ann Phillips
- MSc biobanks and complex data management, Université Côte d'Azur, Centre hospitalier universitaire de Nice, Hôpital Pasteur, Biobanque BB-0033-00025, Nice, France
| | - Apoorva Srinivasan
- MSc biobanks and complex data management, Université Côte d'Azur, Centre hospitalier universitaire de Nice, Hôpital Pasteur, Biobanque BB-0033-00025, Nice, France
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Maia TA, De Muylder CF, Reis ZSN. Archetype Development Process: A Case Study of Support Interoperability among Electronic Health Record in the State of Minas Gerais, Brazil. J Med Syst 2019; 43:57. [PMID: 30706199 DOI: 10.1007/s10916-019-1179-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 01/22/2019] [Indexed: 11/25/2022]
Abstract
The interoperability among electronic medical records requires a standard that guarantees the semantic persistency of information. The study proposes an archetypes development process to support the Electronic Health Record (EHR) in the State of Minas Gerais, Brazil. It was case study with a qualitative analysis of applied nature with methodological exploratory purposes. For this, there was a literature review on archetypes development processes. The selected studies had their processes compared. Then, an own archetypes development process was proposed, also considering the legislation of Unified Health System in Brazil. The process was tested in a proof of concept, a practical test on a theoretical proposal. The proposed governance model was considered adequate for the organization of EHR at such scenario. It is expected that with its effective implementation, the proposed process supports the interoperability among clinical data arising from different levels of health care services.
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Affiliation(s)
- Thais Abreu Maia
- State Health Secretariat of Minas Gerais, Rodovia Papa João Paulo II, 4.143, 12° andar, Bairro: Serra Verde, Belo Horizonte, MG, CEP: 31.630-900, Brazil.
| | | | - Zilma Silveira Nogueira Reis
- Center of Health Informatics, Federal University of Minas Gerais (UFMG), Avenida Professor Alfredo Balena, 190, Bairro: Santa Efigênia, Belo Horizonte, MG, CEP: 30130-100, Brazil
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Min L, Tian Q, Lu X, Duan H. Modeling EHR with the openEHR approach: an exploratory study in China. BMC Med Inform Decis Mak 2018; 18:75. [PMID: 30157838 PMCID: PMC6116359 DOI: 10.1186/s12911-018-0650-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 07/04/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The openEHR approach can improve the interoperability of electronic health record (EHR) through two-level modeling. Developing archetypes for the complete EHR dataset is essential for implementing a large-scale interoperable EHR system with the openEHR approach. Although the openEHR approach has been applied in different domains, the feasibility of archetyping a complete EHR dataset in a hospital has not been reported in academic literature, especially in a country where using openEHR is still in its infancy stage, like China. This paper presents a case study of modeling an EHR in China aiming to investigate the feasibility and challenges of archetyping a complete EHR dataset with the openEHR approach. METHODS We proposed an archetype modeling method including an iterative process of collecting requirements, normalizing data elements, organizing concepts, searching corresponding archetypes, editing archetypes and reviewing archetypes. Two representative EHR systems from Chinese vendors and the existing Chinese EHR standards have been used as resources to identify the requirements of EHR in China, and a case study of modeling EHR in China has been conducted. Based on the models developed in this case study, we have implemented a clinical data repository (CDR) to verify the feasibility of modeling EHR with archetypes. RESULTS Sixty four archetypes were developed to represent all requirements of a complete EHR dataset. 59 (91%) archetypes could be found in Clinical Knowledge Manager (CKM), of which 35 could be reused directly without change, and 23 required further development including two revisions, two new versions, 18 extensions and one specialization. Meanwhile, 6 (9%) archetypes were newly developed. The legacy data of the EHR system in hospitals could be integrated into the CDR developed with these archetypes successfully. CONCLUSIONS The existing archetypes in CKM can faithfully represent most of the EHR requirements in China except customizations for local hospital management. This case study verified the feasibility of modeling EHR with the openEHR approach and identified the fact that the challenges such as localization, tool support, and an agile publishing process still exist for a broader application of the openEHR approach.
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Affiliation(s)
- Lingtong Min
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road, Hangzhou, 310027, China
| | - Qi Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road, Hangzhou, 310027, China
| | - Xudong Lu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road, Hangzhou, 310027, China.
| | - Huilong Duan
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road, Hangzhou, 310027, China
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Li B, Li J, Lan X, An Y, Gao W, Jiang Y. Experiences of building a medical data acquisition system based on two-level modeling. Int J Med Inform 2018; 112:114-122. [DOI: 10.1016/j.ijmedinf.2018.01.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/19/2018] [Accepted: 01/20/2018] [Indexed: 01/08/2023]
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Min L, Tian Q, Lu X, An J, Duan H. An openEHR based approach to improve the semantic interoperability of clinical data registry. BMC Med Inform Decis Mak 2018; 18:15. [PMID: 29589572 PMCID: PMC5872380 DOI: 10.1186/s12911-018-0596-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Clinical data registry is designed to collect and manage information about the practices and outcomes of a patient population for improving the quality and safety of care and facilitating novel researches. Semantic interoperability is a challenge when integrating the data from more than one clinical data registry. The openEHR approach can represent the information and knowledge semantics by multi-level modeling, and it advocates the use of collaborative modeling to facilitate reusing existing archetypes with consistent semantics so as to be a potential solution to improve the semantic interoperability. Methods This paper proposed an openEHR based approach to improve the semantic interoperability of clinical data registry. The approach consists of five steps: clinical data registry meta-information collection, data element definition, archetype modeling, template editing, and implementation. Through collaborative modeling and maximum reusing of existing archetype at the archetype modeling step, the approach can improve semantic interoperability. To verify the feasibility of the approach, this paper conducted a case study of building a Coronary Computed Tomography Angiography (CCTA) registry that can interoperate with an existing Electronic Health Record (EHR) system. Results The CCTA registry includes 183 data elements, which involves 20 archetypes. A total number of 45 CCTA data elements and EHR data elements have semantic overlap. Among them, 38 (84%) CCTA data elements can be found in the 10 reused EHR archetypes. These corresponding clinical data can be collected from the EHR system directly without transformation. The other 7 (16%) CCTA data elements correspond to one coarse-grained EHR data elements, and these clinical data can be collected with mapping rules. The results show that the approach can improve semantic interoperability of clinical data registry. Conclusions Using an openEHR based approach to develop clinical data registry can improve the semantic interoperability. Meanwhile, some challenges for broader semantic interoperability are identified, including domain experts’ involvement, archetype sharing and reusing, and archetype semantic mapping. Collaborative modeling, easy-to-use tools, and semantic relationship establishment are potential solutions for these challenges. This study provides some experience and insight about clinical modeling and clinical data registry development.
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Affiliation(s)
- Lingtong Min
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Zheda Road, Hanghzou, 310027, China
| | - Qi Tian
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Zheda Road, Hanghzou, 310027, China
| | - Xudong Lu
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Zheda Road, Hanghzou, 310027, China.
| | - Jiye An
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Zheda Road, Hanghzou, 310027, China
| | - Huilong Duan
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Zheda Road, Hanghzou, 310027, China
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Eminaga O, Semjonow A, Oezguer E, Herden J, Akbarov I, Tok A, Engelmann U, Wille S. An Electronic Specimen Collection Protocol Schema (eSCPS). Methods Inf Med 2018; 53:29-38. [PMID: 24317441 DOI: 10.3414/me13-01-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 11/04/2013] [Indexed: 11/09/2022]
Abstract
SummaryBackground: The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols.Materials and Methods: The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Fi -nally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS.Results: We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002).Conclusion: The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.
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Affiliation(s)
- O Eminaga
- Okyaz Eminaga, M.D., Department of Urology/Prostate Center, University Hospital Cologne, Kerpener Street 62, 50937 Cologne, Germany, E-mail:
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Kennell TI, Willig JH, Cimino JJ. Clinical Informatics Researcher's Desiderata for the Data Content of the Next Generation Electronic Health Record. Appl Clin Inform 2017; 8:1159-1172. [PMID: 29270955 DOI: 10.4338/aci-2017-06-r-0101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVE Clinical informatics researchers depend on the availability of high-quality data from the electronic health record (EHR) to design and implement new methods and systems for clinical practice and research. However, these data are frequently unavailable or present in a format that requires substantial revision. This article reports the results of a review of informatics literature published from 2010 to 2016 that addresses these issues by identifying categories of data content that might be included or revised in the EHR. MATERIALS AND METHODS We used an iterative review process on 1,215 biomedical informatics research articles. We placed them into generic categories, reviewed and refined the categories, and then assigned additional articles, for a total of three iterations. RESULTS Our process identified eight categories of data content issues: Adverse Events, Clinician Cognitive Processes, Data Standards Creation and Data Communication, Genomics, Medication List Data Capture, Patient Preferences, Patient-reported Data, and Phenotyping. DISCUSSION These categories summarize discussions in biomedical informatics literature that concern data content issues restricting clinical informatics research. These barriers to research result from data that are either absent from the EHR or are inadequate (e.g., in narrative text form) for the downstream applications of the data. In light of these categories, we discuss changes to EHR data storage that should be considered in the redesign of EHRs, to promote continued innovation in clinical informatics. CONCLUSION Based on published literature of clinical informaticians' reuse of EHR data, we characterize eight types of data content that, if included in the next generation of EHRs, would find immediate application in advanced informatics tools and techniques.
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Affiliation(s)
- Timothy I Kennell
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - James H Willig
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States.,Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - James J Cimino
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States.,Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
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Boussadi A, Zapletal E. A Fast Healthcare Interoperability Resources (FHIR) layer implemented over i2b2. BMC Med Inform Decis Mak 2017; 17:120. [PMID: 28806953 PMCID: PMC5557515 DOI: 10.1186/s12911-017-0513-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Standards and technical specifications have been developed to define how the information contained in Electronic Health Records (EHRs) should be structured, semantically described, and communicated. Current trends rely on differentiating the representation of data instances from the definition of clinical information models. The dual model approach, which combines a reference model (RM) and a clinical information model (CIM), sets in practice this software design pattern. The most recent initiative, proposed by HL7, is called Fast Health Interoperability Resources (FHIR). The aim of our study was to investigate the feasibility of applying the FHIR standard to modeling and exposing EHR data of the Georges Pompidou European Hospital (HEGP) integrating biology and the bedside (i2b2) clinical data warehouse (CDW). RESULTS We implemented a FHIR server over i2b2 to expose EHR data in relation with five FHIR resources: DiagnosisReport, MedicationOrder, Patient, Encounter, and Medication. The architecture of the server combines a Data Access Object design pattern and FHIR resource providers, implemented using the Java HAPI FHIR API. Two types of queries were tested: query type #1 requests the server to display DiagnosticReport resources, for which the diagnosis code is equal to a given ICD-10 code. A total of 80 DiagnosticReport resources, corresponding to 36 patients, were displayed. Query type #2, requests the server to display MedicationOrder, for which the FHIR Medication identification code is equal to a given code expressed in a French coding system. A total of 503 MedicationOrder resources, corresponding to 290 patients, were displayed. Results were validated by manually comparing the results of each request to the results displayed by an ad-hoc SQL query. CONCLUSION We showed the feasibility of implementing a Java layer over the i2b2 database model to expose data of the CDW as a set of FHIR resources. An important part of this work was the structural and semantic mapping between the i2b2 model and the FHIR RM. To accomplish this, developers must manually browse the specifications of the FHIR standard. Our source code is freely available and can be adapted for use in other i2b2 sites.
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Affiliation(s)
- Abdelali Boussadi
- INSERM UMR 1138, Equipe 22, Centre de Recherche des Cordeliers, Universités Paris 5 et 6, Paris, France. .,Département de Santé Publique et Informatique Médicale, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris, Paris, France.
| | - Eric Zapletal
- Département de Santé Publique et Informatique Médicale, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris, Paris, France
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Yang L, Chen Y, Yu C, Shen B. Biobanks and Their Clinical Application and Informatics Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 939:241-257. [PMID: 27807750 DOI: 10.1007/978-981-10-1503-8_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Biobanks are one of the most important biomedical research resources and contribute to the development of biomarker detection, molecular diagnosis, translational medicine, and multidisciplinary disease research, as well as studies of interactions between genetic and environmental or lifestyle factors. Aiming for the wide clinical application of biobanks, biobanking efforts have recently switched from a focus on accumulating samples to both formalizing and sustaining collections in light of the rapid progress in the fields of personalized medicine and bioinformatics analysis. With the emergence of novel molecular diagnostic technologies, although the bioinformatics platform of biobanks ensures reliable bioinformatics analysis of patient samples, there are a series of challenges facing biobanks in terms of the overall harmonization of policies, integrated processes, and local informatics solutions across the network. Further, there is a controversy regarding the increased role of ethical boards, governance, and accreditation bodies in ensuring that collected samples have sufficient informatics capabilities to be used in biobanks. In this volume, we present a selection of current issues on the inevitable challenges of the clinical application of biobanks in informatics.
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Affiliation(s)
- Lan Yang
- Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China
| | - Yalan Chen
- Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China.,Department of Medical Informatics, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Chunjiang Yu
- Suzhou Industrial Park Institute of Services Outsourcing, No. 99 Ruoshui Road, Suzhou Industrial Park, Suzhou, 215123, Jiangsu, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China.
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Ellouze AS, Bouaziz R, Ghorbel H. Integrating semantic dimension into openEHR archetypes for the management of cerebral palsy electronic medical records. J Biomed Inform 2016; 63:307-324. [PMID: 27568295 DOI: 10.1016/j.jbi.2016.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
PURPOSE Integrating semantic dimension into clinical archetypes is necessary once modeling medical records. First, it enables semantic interoperability and, it offers applying semantic activities on clinical data and provides a higher design quality of Electronic Medical Record (EMR) systems. However, to obtain these advantages, designers need to use archetypes that cover semantic features of clinical concepts involved in their specific applications. In fact, most of archetypes filed within open repositories are expressed in the Archetype Definition Language (ALD) which allows defining only the syntactic structure of clinical concepts weakening semantic activities on the EMR content in the semantic web environment. This paper focuses on the modeling of an EMR prototype for infants affected by Cerebral Palsy (CP), using the dual model approach and integrating semantic web technologies. Such a modeling provides a better delivery of quality of care and ensures semantic interoperability between all involved therapies' information systems. METHODS First, data to be documented are identified and collected from the involved therapies. Subsequently, data are analyzed and arranged into archetypes expressed in accordance of ADL. During this step, open archetype repositories are explored, in order to find the suitable archetypes. Then, ADL archetypes are transformed into archetypes expressed in OWL-DL (Ontology Web Language - Description Language). Finally, we construct an ontological source related to these archetypes enabling hence their annotation to facilitate data extraction and providing possibility to exercise semantic activities on such archetypes. RESULTS Semantic dimension integration into EMR modeled in accordance to the archetype approach. The feasibility of our solution is shown through the development of a prototype, baptized "CP-SMS", which ensures semantic exploitation of CP EMR. This prototype provides the following features: (i) creation of CP EMR instances and their checking by using a knowledge base which we have constructed by interviews with domain experts, (ii) translation of initially CP ADL archetypes into CP OWL-DL archetypes, (iii) creation of an ontological source which we can use to annotate obtained archetypes and (vi) enrichment and supply of the ontological source and integration of semantic relations by providing hence fueling the ontology with new concepts, ensuring consistency and eliminating ambiguity between concepts. CONCLUSIONS The degree of semantic interoperability that could be reached between EMR systems depends strongly on the quality of the used archetypes. Thus, the integration of semantic dimension in archetypes modeling process is crucial. By creating an ontological source and annotating archetypes, we create a supportive platform ensuring semantic interoperability between archetypes-based EMR-systems.
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Affiliation(s)
- Afef Samet Ellouze
- Mir@cl Laboratory, Tunisia; Higher Institute of Technological Studies, Sfax, Tunisia.
| | - Rafik Bouaziz
- Mir@cl Laboratory, Tunisia; Faculty of Economic Sciences and Management, Sfax University, Tunisia.
| | - Hanen Ghorbel
- Mir@cl Laboratory, Tunisia; Higher Institute of Management, Sousse, Tunisia.
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Moreno-Conde A, Austin T, Moreno-Conde J, Parra-Calderón CL, Kalra D. Evaluation of clinical information modeling tools. J Am Med Inform Assoc 2016; 23:1127-1135. [DOI: 10.1093/jamia/ocw018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/20/2016] [Accepted: 01/27/2016] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objective Clinical information models are formal specifications for representing the structure and semantics of the clinical content within electronic health record systems. This research aims to define, test, and validate evaluation metrics for software tools designed to support the processes associated with the definition, management, and implementation of these models.
Methodology The proposed framework builds on previous research that focused on obtaining agreement on the essential requirements in this area. A set of 50 conformance criteria were defined based on the 20 functional requirements agreed by that consensus and applied to evaluate the currently available tools.
Results Of the 11 initiative developing tools for clinical information modeling identified, 9 were evaluated according to their performance on the evaluation metrics. Results show that functionalities related to management of data types, specifications, metadata, and terminology or ontology bindings have a good level of adoption. Improvements can be made in other areas focused on information modeling and associated processes. Other criteria related to displaying semantic relationships between concepts and communication with terminology servers had low levels of adoption.
Conclusions The proposed evaluation metrics were successfully tested and validated against a representative sample of existing tools. The results identify the need to improve tool support for information modeling and software development processes, especially in those areas related to governance, clinician involvement, and optimizing the technical validation of testing processes. This research confirmed the potential of these evaluation metrics to support decision makers in identifying the most appropriate tool for their organization.
OBJECTIVO Los Modelos de Información Clínica son especificaciones para representar la estructura y características semánticas del contenido clínico en los sistemas de Historia Clínica Electrónica. Esta investigación define, prueba y valida un marco para la evaluación de herramientas informáticas diseñadas para dar soporte en la en los procesos de definición, gestión e implementación de estos modelos.
METODOLOGIA El marco de evaluación propuesto se basa en una investigación previa para obtener consenso en la definición de requisitos esenciales en esta área. A partir de los 20 requisitos funcionales acordados, un conjunto de 50 criterios de conformidad fueron definidos y aplicados en la evaluación de las herramientas existentes.
RESULTADOS Un total de 9 de las 11 iniciativas identificadas desarrollando herramientas para el modelado de información clínica fueron evaluadas. Los resultados muestran que las funcionalidades relacionadas con la gestión de tipos de datos, especificaciones, metadatos y mapeo con terminologías u ontologías tienen un buen nivel de adopción. Se identifican posibles mejoras en áreas relacionadas con los procesos de modelado de información. Otros criterios relacionados con presentar las relaciones semánticas entre conceptos y la comunicación con servidores de terminología tienen un bajo nivel de adopción.
CONCLUSIONES El marco de evaluación propuesto fue probado y validado satisfactoriamente contra un conjunto representativo de las herramientas existentes. Los resultados identifican la necesidad de mejorar el soporte de herramientas a los procesos de modelado de información y desarrollo de software, especialmente en las áreas relacionadas con gobernanza, participación de profesionales clínicos y la optimización de la validación técnica en los procesos de pruebas técnicas. Esta investigación ha confirmado el potencial de este marco de evaluación para dar soporte a los usuarios en la toma de decisiones sobre que herramienta es más apropiadas para su organización.
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Affiliation(s)
- Alberto Moreno-Conde
- Centre for Health Informatics and Multiprofessional Education, University College London, London, UK
- Technological Innovation Group, Virgen del Rocío University Hospital, Seville, Spain
| | | | - Jesús Moreno-Conde
- Technological Innovation Group, Virgen del Rocío University Hospital, Seville, Spain
| | | | - Dipak Kalra
- Centre for Health Informatics and Multiprofessional Education, University College London, London, UK
- European Institute for Health Records (EuroRec), Sint-Martens-Latem, Belgium
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Park HS, Cho H, Kim HS. Development of an Integrated Biospecimen Database among the Regional Biobanks in Korea. Healthc Inform Res 2016; 22:129-41. [PMID: 27200223 PMCID: PMC4871843 DOI: 10.4258/hir.2016.22.2.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/19/2016] [Accepted: 04/22/2016] [Indexed: 11/23/2022] Open
Abstract
Objectives This study developed an integrated database for 15 regional biobanks that provides large quantities of high-quality bio-data to researchers to be used for the prevention of disease, for the development of personalized medicines, and in genetics studies. Methods We collected raw data, managed independently by 15 regional biobanks, for database modeling and analyzed and defined the metadata of the items. We also built a three-step (high, middle, and low) classification system for classifying the item concepts based on the metadata. To generate clear meanings of the items, clinical items were defined using the Systematized Nomenclature of Medicine Clinical Terms, and specimen items were defined using the Logical Observation Identifiers Names and Codes. To optimize database performance, we set up a multi-column index based on the classification system and the international standard code. Results As a result of subdividing 7,197,252 raw data items collected, we refined the metadata into 1,796 clinical items and 1,792 specimen items. The classification system consists of 15 high, 163 middle, and 3,588 low class items. International standard codes were linked to 69.9% of the clinical items and 71.7% of the specimen items. The database consists of 18 tables based on a table from MySQL Server 5.6. As a result of the performance evaluation, the multi-column index shortened query time by as much as nine times. Conclusions The database developed was based on an international standard terminology system, providing an infrastructure that can integrate the 7,197,252 raw data items managed by the 15 regional biobanks. In particular, it resolved the inevitable interoperability issues in the exchange of information among the biobanks, and provided a solution to the synonym problem, which arises when the same concept is expressed in a variety of ways.
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Affiliation(s)
- Hyun Sang Park
- Department of Medical Informatics, Kyungpook National University, Daegu, Korea
| | - Hune Cho
- Department of Medical Informatics, Kyungpook National University, Daegu, Korea
| | - Hwa Sun Kim
- Faculty of Medical Industry Convergence, Daegu Haany University, Gyeongsan, Korea
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Christensen B, Ellingsen G. Evaluating Model-Driven Development for large-scale EHRs through the openEHR approach. Int J Med Inform 2016; 89:43-54. [DOI: 10.1016/j.ijmedinf.2016.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 02/14/2016] [Accepted: 02/15/2016] [Indexed: 10/22/2022]
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Lin CH, Fann YC, Liou DM. An exploratory study using an openEHR 2-level modeling approach to represent common data elements. J Am Med Inform Assoc 2016; 23:956-67. [PMID: 26911823 DOI: 10.1093/jamia/ocv137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/28/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND AND OBJECTIVE In order to facilitate clinical research across multiple institutions, data harmonization is a critical requirement. Common data elements (CDEs) collect data uniformly, allowing data interoperability between research studies. However, structural limitations have hindered the application of CDEs. An advanced modeling structure is needed to rectify such limitations. The openEHR 2-level modeling approach has been widely implemented in the medical informatics domain. The aim of our study is to explore the feasibility of applying an openEHR approach to model the CDE concept. MATERIALS AND METHODS Using the National Institute of Neurological Disorders and Stroke General CDEs as material, we developed a semiautomatic mapping tool to assist domain experts mapping CDEs to existing openEHR archetypes in order to evaluate their coverage and to allow further analysis. In addition, we modeled a set of CDEs using the openEHR approach to evaluate the ability of archetypes to structurally represent any type of CDE content. RESULTS Among 184 CDEs, 28% (51) of the archetypes could be directly used to represent CDEs, while 53% (98) of the archetypes required further development (extension or specialization). A comprehensive comparison between CDEs and openEHR archetypes was conducted based on the lessons learnt from the practical modeling. DISCUSSION CDEs and archetypes have dissimilar modeling approaches, but the data structure of both models are essentially similar. This study proposes to develop a comprehensive structure to model CDE concepts instead of improving the structure of CED. CONCLUSION The findings from this research show that the openEHR archetype has structural coverage for the CDEs, namely the openEHR archetype is able to represent the CDEs and meet the functional expectations of the CDEs. This work can be used as a reference when improving CDE structure using an advanced modeling approach.
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Affiliation(s)
- Ching-Heng Lin
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Yang-Cheng Fann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Der-Ming Liou
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
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Wang L, Min L, Wang R, Lu X, Duan H. Archetype relational mapping - a practical openEHR persistence solution. BMC Med Inform Decis Mak 2015; 15:88. [PMID: 26541142 PMCID: PMC4636072 DOI: 10.1186/s12911-015-0212-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the primary obstacles to the widespread adoption of openEHR methodology is the lack of practical persistence solutions for future-proof electronic health record (EHR) systems as described by the openEHR specifications. This paper presents an archetype relational mapping (ARM) persistence solution for the archetype-based EHR systems to support healthcare delivery in the clinical environment. METHODS First, the data requirements of the EHR systems are analysed and organized into archetype-friendly concepts. The Clinical Knowledge Manager (CKM) is queried for matching archetypes; when necessary, new archetypes are developed to reflect concepts that are not encompassed by existing archetypes. Next, a template is designed for each archetype to apply constraints related to the local EHR context. Finally, a set of rules is designed to map the archetypes to data tables and provide data persistence based on the relational database. RESULTS A comparison study was conducted to investigate the differences among the conventional database of an EHR system from a tertiary Class A hospital in China, the generated ARM database, and the Node + Path database. Five data-retrieving tests were designed based on clinical workflow to retrieve exams and laboratory tests. Additionally, two patient-searching tests were designed to identify patients who satisfy certain criteria. The ARM database achieved better performance than the conventional database in three of the five data-retrieving tests, but was less efficient in the remaining two tests. The time difference of query executions conducted by the ARM database and the conventional database is less than 130 %. The ARM database was approximately 6-50 times more efficient than the conventional database in the patient-searching tests, while the Node + Path database requires far more time than the other two databases to execute both the data-retrieving and the patient-searching tests. CONCLUSIONS The ARM approach is capable of generating relational databases using archetypes and templates for archetype-based EHR systems, thus successfully adapting to changes in data requirements. ARM performance is similar to that of conventionally-designed EHR systems, and can be applied in a practical clinical environment. System components such as ARM can greatly facilitate the adoption of openEHR architecture within EHR systems.
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Affiliation(s)
- Li Wang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Room 512, Zhouyiqing Building, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China
| | - Lingtong Min
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Room 512, Zhouyiqing Building, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China
| | - Rui Wang
- Department of Information Technology, Shanxi Dayi Hospital, Taiyuan, Shanxi, China
| | - Xudong Lu
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Room 512, Zhouyiqing Building, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
| | - Huilong Duan
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Room 512, Zhouyiqing Building, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China
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Eguzkiza A, Trigo JD, Martínez-Espronceda M, Serrano L, Andonegui J. Formalize clinical processes into electronic health information systems: Modelling a screening service for diabetic retinopathy. J Biomed Inform 2015; 56:112-26. [DOI: 10.1016/j.jbi.2015.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 10/23/2022]
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Moreno-Conde A, Moner D, Cruz WDD, Santos MR, Maldonado JA, Robles M, Kalra D. Clinical information modeling processes for semantic interoperability of electronic health records: systematic review and inductive analysis. J Am Med Inform Assoc 2015; 22:925-34. [PMID: 25796595 DOI: 10.1093/jamia/ocv008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/24/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE This systematic review aims to identify and compare the existing processes and methodologies that have been published in the literature for defining clinical information models (CIMs) that support the semantic interoperability of electronic health record (EHR) systems. MATERIAL AND METHODS Following the preferred reporting items for systematic reviews and meta-analyses systematic review methodology, the authors reviewed published papers between 2000 and 2013 that covered that semantic interoperability of EHRs, found by searching the PubMed, IEEE Xplore, and ScienceDirect databases. Additionally, after selection of a final group of articles, an inductive content analysis was done to summarize the steps and methodologies followed in order to build CIMs described in those articles. RESULTS Three hundred and seventy-eight articles were screened and thirty six were selected for full review. The articles selected for full review were analyzed to extract relevant information for the analysis and characterized according to the steps the authors had followed for clinical information modeling. DISCUSSION Most of the reviewed papers lack a detailed description of the modeling methodologies used to create CIMs. A representative example is the lack of description related to the definition of terminology bindings and the publication of the generated models. However, this systematic review confirms that most clinical information modeling activities follow very similar steps for the definition of CIMs. Having a robust and shared methodology could improve their correctness, reliability, and quality. CONCLUSION Independently of implementation technologies and standards, it is possible to find common patterns in methods for developing CIMs, suggesting the viability of defining a unified good practice methodology to be used by any clinical information modeler.
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Affiliation(s)
- Alberto Moreno-Conde
- Centre for Health Informatics and Multiprofessional Education, University College London, London, UK Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - David Moner
- Instituto de Aplicaciones de las Tecnologías de la Información y de las Comunicaciones Avanzadas, Universitat Politècnica de València, Valencia, Spain
| | | | - Marcelo R Santos
- Centro de Informática em Saúde (CINS), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José Alberto Maldonado
- Instituto de Aplicaciones de las Tecnologías de la Información y de las Comunicaciones Avanzadas, Universitat Politècnica de València, Valencia, Spain VeraTech for Health SL, Valencia, Spain
| | - Montserrat Robles
- Instituto de Aplicaciones de las Tecnologías de la Información y de las Comunicaciones Avanzadas, Universitat Politècnica de València, Valencia, Spain
| | - Dipak Kalra
- Centre for Health Informatics and Multiprofessional Education, University College London, London, UK
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Nogueira JRM, Cook TW, Cavalini LT. Mapping a Nursing Terminology Subset to openEHR Archetypes. A Case Study of the International Classification for Nursing Practice. Methods Inf Med 2015; 54:271-5. [PMID: 25609209 DOI: 10.3414/me14-01-0053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022]
Abstract
BACKGROUND Healthcare information technologies have the potential to transform nursing care. However, healthcare information systems based on conventional software architecture are not semantically interoperable and have high maintenance costs. Health informatics standards, such as controlled terminologies, have been proposed to improve healthcare information systems, but their implementation in conventional software has not been enough to overcome the current challenge. Such obstacles could be removed by adopting a multilevel model-driven approach, such as the openEHR specifications, in nursing information systems. OBJECTIVES To create an openEHR archetype model for the Functional Status concepts as published in Nursing Outcome Indicators Catalog of the International Classification for Nursing Practice (NOIC-ICNP). METHODS Four methodological steps were followed: 1) extraction of terms from the NOIC-ICNP terminology; 2) identification of previously published openEHR archetypes; 3) assessment of the adequacy of those openEHR archetypes to represent the terms; and 4) development of new openEHR archetypes when required. RESULTS The "Barthel Index" archetype was retrieved and mapped to the 68 NOIC-ICNP Functional Status terms. There were 19 exact matches between a term and the correspondent archetype node and 23 archetype nodes that matched to one or more NOIC-INCP. No matches were found between the archetype and 14 of the NOIC-ICNP terms, and nine archetype nodes did not match any of the NOIC-ICNP terms. CONCLUSIONS The openEHR model was sufficient to represent the semantics of the Functional Status concept according to the NOIC-ICNP, but there were differences in data granularity between the terminology and the archetype, thus producing a significantly complex mapping, which could be difficult to implement in real healthcare information systems. However, despite the technological complexity, the present study demonstrated the feasibility of mapping nursing terminologies to openEHR archetypes, which emphasizes the importance of adopting the multilevel model-driven approach for the achievement of semantic interoperability between healthcare information systems.
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Affiliation(s)
- J R M Nogueira
- Joyce Rocha de Matos Nogueira, Avenida Professor Manoel de Abreu, 444 - 2nd floor - Vila Isabel, Rio de Janeiro, RJ, 20550-170, Brazil, E-mail:
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Braun M, Brandt AU, Schulz S, Boeker M. Validating archetypes for the Multiple Sclerosis Functional Composite. BMC Med Inform Decis Mak 2014; 14:64. [PMID: 25087081 PMCID: PMC4131486 DOI: 10.1186/1472-6947-14-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/22/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Numerous information models for electronic health records, such as openEHR archetypes are available. The quality of such clinical models is important to guarantee standardised semantics and to facilitate their interoperability. However, validation aspects are not regarded sufficiently yet. The objective of this report is to investigate the feasibility of archetype development and its community-based validation process, presuming that this review process is a practical way to ensure high-quality information models amending the formal reference model definitions. METHODS A standard archetype development approach was applied on a case set of three clinical tests for multiple sclerosis assessment: After an analysis of the tests, the obtained data elements were organised and structured. The appropriate archetype class was selected and the data elements were implemented in an iterative refinement process. Clinical and information modelling experts validated the models in a structured review process. RESULTS Four new archetypes were developed and publicly deployed in the openEHR Clinical Knowledge Manager, an online platform provided by the openEHR Foundation. Afterwards, these four archetypes were validated by domain experts in a team review. The review was a formalised process, organised in the Clinical Knowledge Manager. Both, development and review process turned out to be time-consuming tasks, mostly due to difficult selection processes between alternative modelling approaches. The archetype review was a straightforward team process with the goal to validate archetypes pragmatically. CONCLUSIONS The quality of medical information models is crucial to guarantee standardised semantic representation in order to improve interoperability. The validation process is a practical way to better harmonise models that diverge due to necessary flexibility left open by the underlying formal reference model definitions.This case study provides evidence that both community- and tool-enabled review processes, structured in the Clinical Knowledge Manager, ensure archetype quality. It offers a pragmatic but feasible way to reduce variation in the representation of clinical information models towards a more unified and interoperable model.
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Affiliation(s)
- Michael Braun
- Center for Medical Biometry and Medical Informatics, Medical Center – University of Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany
| | - Alexander Ulrich Brandt
- NeuroCure Clinical Research Center, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Motognosis UG, Debenzer Str. 73, 12683 Berlin, Germany
| | - Stefan Schulz
- Center for Medical Biometry and Medical Informatics, Medical Center – University of Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany
- Institute for Medical Informatics, Statistics and Documentation; Medical University of Graz, Auenbruggerplatz 2, 8036 Graz, Austria
| | - Martin Boeker
- Center for Medical Biometry and Medical Informatics, Medical Center – University of Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany
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Linkage of Data from Diverse Data Sources (LDS): A Data Combination Model Provides Clinical Data of Corresponding Specimens in Biobanking Information System. J Med Syst 2013; 37:9975. [DOI: 10.1007/s10916-013-9975-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/29/2013] [Indexed: 11/26/2022]
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SNOMED CT module-driven clinical archetype management. J Biomed Inform 2013; 46:388-400. [PMID: 23402961 DOI: 10.1016/j.jbi.2013.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To explore semantic search to improve management and user navigation in clinical archetype repositories. METHODS In order to support semantic searches across archetypes, an automated method based on SNOMED CT modularization is implemented to transform clinical archetypes into SNOMED CT extracts. Concurrently, query terms are converted into SNOMED CT concepts using the search engine Lucene. Retrieval is then carried out by matching query concepts with the corresponding SNOMED CT segments. RESULTS A test collection of the 16 clinical archetypes, including over 250 terms, and a subset of 55 clinical terms from two medical dictionaries, MediLexicon and MedlinePlus, were used to test our method. The keyword-based service supported by the OpenEHR repository offered us a benchmark to evaluate the enhancement of performance. In total, our approach reached 97.4% precision and 69.1% recall, providing a substantial improvement of recall (more than 70%) compared to the benchmark. CONCLUSIONS Exploiting medical domain knowledge from ontologies such as SNOMED CT may overcome some limitations of the keyword-based systems and thus improve the search experience of repository users. An automated approach based on ontology segmentation is an efficient and feasible way for supporting modeling, management and user navigation in clinical archetype repositories.
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Meizoso García M, Iglesias Allones JL, Martínez Hernández D, Taboada Iglesias MJ. Semantic similarity-based alignment between clinical archetypes and SNOMED CT: An application to observations. Int J Med Inform 2012; 81:566-78. [DOI: 10.1016/j.ijmedinf.2012.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 02/13/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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