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Design and development of a disease-specific clinical database system to increase the availability of hospital data in China

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HEALTH INFORMATION SCIENCE AND SYSTEMS 2023年第1期11卷 11页

作者： Liu, Mimi Luo, Jinni Li, Lin Pan, Xuemei Tan, Shuyan Ji, Weidong Zhang, Hongzheng Tang, Shengsheng Liu, Jingjing Wu, Bin Chen, Zebin Wu, Xiaoying Zhou, Yi Sun Yat Sen Univ Zhongshan Sch Med Guangzhou Guangdong Peoples R China Sun Yat Sen Univ Affiliated Hosp 3 Gastroenterol Dept Guangzhou Guangdong Peoples R China Sun Yat Sen Univ Affiliated Hosp 1 Ctr Hepatopancreat Biliary Surg Guangzhou Guangdong Peoples R China

PurposeIn order to meet restrictions and difficulties in the development of hospital medical informatization and clinical databases in China, in this study, a disease-specific clinical database system (DSCDS) was designed and built. It provides support for the full utilization of real world medical big data in clinical research and medical services for specific *** development of DSCDS involved (1) requirements analysis on precision medicine, medical big data, and clinical research;(2) design schematics and basic architecture;(3) standard datasets of specific diseases consisting of common data elements (CDEs);(4) collection and aggregation of specific disease data scattered in various medical business systems of the hospital;(5) governance and quality improvement of specific disease data;(6) data storage and computing;and (7) design of data application *** DSCDS for liver cirrhosis was created in the gastrointestinal department of a 3A grade hospital in China and had more than nine data application modules. Based on this DSCDS, a series of clinical studies are being carried out, such as retrospective or prospective cohorts, prognostic studies using multimodal data, and follow-up *** development of the DSCDS for liver cirrhosis in this paper provides experience and reference for the design and development of DSCDSs for other specific diseases in China;it can even expand to the development of DSCDSs in other countries if they have the demand for DSCDS and the same or better medical informatization foundation. DSCDS has more accurate, standard, comprehensive, multimodal and usable data of specific diseases than the general clinical database system and clinical data repository (CDR) and provides a credible data foundation for medical research, clinical decision-making and improving the medical service quality of specific diseases.

关键词： Disease-specific clinical database system Medical big data clinical data repository clinical database Liver cirrhosis Disease dataset clinical data aggregation

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Imbalanced target prediction with pattern discovery on clinical data repositories

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BMC MEDICAL INFORMATICS AND DECISION MAKING 2017年第1期17卷 1-12页

作者： Chan, Tak-Ming Li, Yuxi Chiau, Choo-Chiap Zhu, Jane Jiang, Jie Huo, Yong Philips Res China Hlth Syst Philips Innovat Campus Shanghai1 Bldg10Lane 88 Shanghai 200233 Peoples R China Peking Univ Hosp 1 Beijing Peoples R China

Background: clinical data repositories (CDR) have great potential to improve outcome prediction and risk modeling. However, most clinical studies require careful study design, dedicated data collection efforts, and sophisticated modeling techniques before a hypothesis can be tested. We aim to bridge this gap, so that clinical domain users can perform first-hand prediction on existing repository data without complicated handling, and obtain insightful patterns of imbalanced targets for a formal study before it is conducted. We specifically target for interpretability for domain users where the model can be conveniently explained and applied in clinical practice. Methods: We propose an interpretable pattern model which is noise (missing) tolerant for practice data. To address the challenge of imbalanced targets of interest in clinical research, e. g., deaths less than a few percent, the geometric mean of sensitivity and specificity (G-mean) optimization criterion is employed, with which a simple but effective heuristic algorithm is developed. Results: We compared pattern discovery to clinically interpretable methods on two retrospective clinical datasets. They contain 14.9% deaths in 1 year in the thoracic dataset and 9.1% deaths in the cardiac dataset, respectively. In spite of the imbalance challenge shown on other methods, pattern discovery consistently shows competitive cross-validated prediction performance. Compared to logistic regression, Naive Bayes, and decision tree, pattern discovery achieves statistically significant (p-values < 0.01, Wilcoxon signed rank test) favorable averaged testing G-means and F1-scores (harmonic mean of precision and sensitivity). Without requiring sophisticated technical processing of data and tweaking, the prediction performance of pattern discovery is consistently comparable to the best achievable performance. Conclusions: Pattern discovery has demonstrated to be robust and valuable for target prediction on existing clinical data

关键词： Pattern discovery data mining Prediction Imbalanced data clinical data repository

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Practical issues in and applications of clinical data mining

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DRUG INFORMATION JOURNAL 2001年第3期35卷 791-808页

作者： Olaleye, D Tardiff, BE IBiomat LLC Cary NC 27513 USA Duke Univ Med Ctr Durham NC USA Duke Clin Res Inst Durham NC USA

Pharmaceutical and biotechnology companies accumulate large volumes of data throughout the drug development life cycle-from discovery through marketing. Many organizations consolidate these data assets in central repositories to facilitate access and compilation for New Drug Application (NDA) submissions and other efforts. These clinical data repositories represent a potential gold mine of knowledge that may be further exploited for competitive business advantage. clinical data mining solutions empower companies to extract previously unrealized information about their molecular compounds, product portfolio, clinical studies, and customers from data repositories. These companies must determine how to apply clinical data mining tools to get to the most useful information and, once knowledge is extracted, how to apply it for best business advantage. This paper provides an overview of the clinical data mining process and a framework for implementing a clinical data mining solution. The process begins with the data mining goal or objective and a database to be mined, followed by the application of data mining strategies to generate one or more models, and concluding with deployment of model results to relevant business areas. The process is illustrated in this paper through a case study using pooled studies from Phase I and Phase II clinical trials. data mining should be a team effort of quantitative analysts (eg, statisticians), domain experts (eg, clinicians, scientists, drug discoverers), business users (eg, marketing and regulatory department), and information technologists, and must be thoroughly supported by upper levels of management and throughout the organization.

关键词： data mining decision tree clinical data repository enterprise miner clinical trials two-stage model

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Gridded Field Observations of Polybrominated Diphenyl Ethers in Soils of North China

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ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2014年第4期66卷 482-490页

作者： Liu, Di Ma, Jin Qiu, Xinghua Zhao, Yifan Lin, Yan Yang, Qiaoyun Gao, Zhenji Zhu, Tong Chinese Res Inst Environm Sci State Key Lab Environm Criteria & Risk Assessment Beijing 100012 Peoples R China Peking Univ Coll Environm Sci & Engn State Key Joint Lab Environm Simulat & Pollut Con Beijing 100871 Peoples R China

Polybrominated diphenyl ethers (PBDEs) were measured in 87 soil samples collected from North China. Eleven PBDE congeners (BDE28, 47, 49, 66, 99, 100, 119, 183, 196, 203, and 209) were identified with a high frequency of detection (84-100 %) in soil samples, and their frequencies were used for statistical analysis in the present study. PBDE concentrations ranged from 0.08 to 8260 ng/g with a mean of 202 ng/g, thus indicating severe pollution at these sample sites. BDE209 was the predominant congener with concentrations of 0.08-8140 ng/g (mean 188). Analysis of the spatial distribution of PBDEs in North China soils indicated that relatively high concentrations of both lower- and higher-brominated BDEs were present in Shandong Province, and a decreasing trend in PBDE concentrations from the east toward the west of North China was observed. Source identification analysis suggested that Jinghai County in Tianjin and the coastal area of Laizhou Bay, Shandong province, were the major sources in North China. The sources in Jinghai County were connected with the dismantling of electronic waste, whereas the sources in the coastal area of Laizhou Bay were connected with the production of PBDEs. Modeling results showed that the distance between the sampling sites and these point sources had a large influence on the transfer of PBDEs.

关键词： clinical data repository data analysis data filtering method data mining method data visualization Hierarchical terminology Threshold selection Threshold setting Point sources Soil pentabromodiphenyl ether soil sampling Brominated Diphenyl Ethers data visualisation data analysis Statistical analysis Demolition High frequency detection electronic waste coastal area

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Sample and data sharing: Observations from a central data repository

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clinical BIOCHEMISTRY 2014年第4-5期47卷 252-257页

作者： Ardini, Mary-Anne Pan, Huaqin Qin, Ying Cooley, Philip C. RTI Int Res Triangle Pk NC 27709 USA

Objectives: From 2003 to 2013, RTI International served as the data repository for the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK). RTI worked closely with two sample repository partners to build and maintain the Central repository (CR) that made data and samples available to approved requestors. In this paper, we recap aspects of establishing the mechanism;detail the challenges and limitations of data and sample sharing, and explore the future of resource sharing in light of the evolving environment of research funding. Design and methods: Effective maintenance required the system to be flexible and dynamic while at the same time compliant with established data standards. Results: Our years serving as the CR for NIDDK have yielded a number of observations about the difficulties of running a repository, an operation that is by definition dependent on many outside parties whose degree of expertise and efficiency have a direct impact on repository functioning. Conclusion: The bio-banking industry will likely continue to become more globally centralized for studying specific genetic diseases and monitoring the health of our environment. The dynamic relationship between emerging technologies and the infrastructure will be needed to support future research that requires the ability of organizations providing support to remain flexible even while following established standards. (C) 2013 The Canadian Society of clinical Chemists. Published by Elsevier Inc. All rights reserved.

关键词： clinical data repository Biobank NIDDK

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Putting the Value Framework to Work in Surgery

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JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS 2015年第4期220卷 596-604页

作者： Yount, Kenan W. Turrentine, Florence E. Lau, Christine L. Jones, R. Scott Univ Virginia Dept Surg Charlottesville VA 22908 USA

BACKGROUND: Health policy experts have proposed a framework defining value as outcomes achieved per dollar spent on health care. However, few institutions quantify their delivery of care along these dimensions. Our objective was to measure the value of our surgical services over time. STUDY DESIGN: We reviewed the data of patients undergoing general and vascular surgery from 2002 through 2012 at a tertiary care university hospital as abstracted by the American College of Surgeons NSQIP. Morbidity and mortality data from the American College of Surgeons NSQIP database were risk adjusted to calculate observed-to-expected ratios, which were then inverted into a numerator as a surrogate for quality. Costs, the denominator of the value equation, were determined for each patient's hospitalization. The ratio was then transformed by a constant and analyzed with linear regression to analyze and compare values from 2002 through 2012. RESULTS: A total of 25,453 patients met criteria for inclusion. Overall, the value of surgical services increased from 2002 through 2012. The observed increase in value was greater in general surgery than in vascular surgery, and value actually decreased in vascular procedures. Although there was a similar increase in outcomes in vascular surgery compared with general surgery, costs rose significantly higher ($474/year vs - $302/year;p < 0.001). These increased costs were mostly observed from 2006 through 2010 with the adoption of endovascular technology. CONCLUSIONS: Despite the challenges posed by current information systems, calculating risk-adjusted value in surgical services represents a critical first step for providers seeking to improve outcomes, avoid ill-advised cost containment, and determine the costs of innovation. (C) 2015 by the American College of Surgeons

关键词： Abbreviations and AcronymsACS American College of Surgeons CDR clinical data repository CMS Center for Medicare and Medicaid Services O/E observed to expected R2 coefficient of determination

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Analyzing data from a multi-hospital healthcare information system using graphical flowchart models

Analyzing data from a multi-hospital healthcare information ...

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11th World Multi-Conference on Systemics, Cybernetics and Informatics/13th International Conference on Information Systems Analysis and Synthesis

作者： Huser, Vojtech Rocha, Roberto A. Intermt Healthcare Salt Lake City UT 84111 USA Univ Utah Biomed Informat Salt Lake City UT USA RemedyMD Inc Sandy UT USA

ISBN: (纸本)9781934272183

Analyzing large volumes of healthcare data is a challenging task for most healthcare organizations. Current analytical tools do not support very well time-oriented analyses. We present two case studies where we applied a data retrieval and analysis tool called "RetroGuide". The main advantages of RetroGuide are a graphical user-friendly query modeling methodology and the ability to handle complex temporal problems.

关键词： temporal reasoning workflow technology clinical data repository data analysis quality improvement Hepatitis C adverse drug events SQL flowchart model

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Development and Implementation of an Integrated EHR for Homecare Service: A South American Experience 13

Development and Implementation of an Integrated EHR for Home...

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13th World Congress on Medical and Health Informatics of International-Medical-Informatics-Association (Medinfo)

作者： Aguilera Diaz, Jeronimo Eduardo Arias, Antonio Mabel Budalich, Cintia Elizabeth Benitez, Sonia Damian Borbolla, Gaston Lopez Plazzotta, Fernando Luna, Daniel Bernaldo de Quiros, Fernan Gonzalez Hosp Italiano Buenos Aires Dept Hlth Informat Buenos Aires DF Argentina

ISBN: (纸本)9781607505884

This paper describes the development and implementation of a web based electronic health record for the Homecare Service program in the Hospital Italiano de Buenos Aires. It reviews the process of the integration of the new electronic health record to the hospital information system, allowing physicians to access the clinical data repository from their Pc's at home and with the capability of consulting past and present history of the patient health care, order, tests, and referrals with others professionals trough the new Electronic Health Record. We also discuss how workflow processes were changed and improved for the physicians, nurses, and administrative personnel of the Homecare Services and the educational methods used to improve acceptance and adoption of these new technologies. We also briefly describe the validation of physicians and their field work with electronic signatures.

关键词： Hospital information systems Homecare services clinical data repository Electronic signatures

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Rule extraction for detection and prevention of Asthma attacks 3

Rule extraction for detection and prevention of Asthma attac...

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IEEE 3rd International Conference on MOOCs, Innovation and Technology in Education (MITE)

作者： Shikalgar, Sajeeda Rai, Parisa Marathe, Surabhi Nadar, Divya Maharashtra Inst Technol Dept Informat Technol Pune Maharashtra India

ISBN: (纸本)9781467367479

this paper solves the problem of prevention of asthma attacks, and also it can predict a future asthma attack based on prevalent asthma triggers. The system forms an opinion of the everyday condition of the user, for example, if the user is doing fine today but might not be fine tomorrow. With the help of neural networks, it is possible to predict precisely and correct the user habits. A user who is not an asthma patient but thinks he may have the disease can also use this system. Monthly reports are generated of every user stating whether the patient's condition has worsened or got better.

关键词： neural network clinical data repository asthma triggers ontology IoT sensors

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A survey of openEHR clinical data Repositories

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INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS 2024年 191卷 105591-105591页

作者： Delussu, Giovanni Frexia, Francesca Mascia, Cecilia Sulis, Alessandro Del Rio, Mauro Lianas, Luca CRS4 Ctr Adv Studies Res & Dev Sardinia Pula Italy

center dot Background: clinical data Repositories (CDRs) lie at the core of both primary and secondary utilisation of vast amounts of health information. These data are intricate, heterogeneous and constantly evolving alongside advancements in biomedical sciences. The separation between clinical content and its persistence renders the archetype-based paradigm naturally well-suited to manage this complexity. This approach is adopted by a number of open source and commercial CDR solutions, mostly implementing the openEHR specifications, which also encompass the Archetype Query Language (AQL) to define portable queries independently of the persistence scheme. center dot Aim: To provide a wide knowledge base and a set of customisable tools as a support in the selection of openEHR CDRs according to a broad ensemble of features relevant to different use cases. center dot Approach: After conducting an extensive search of the existing openEHR CDRs, a survey consisting of fiftyfour questions was administered to all the nineteen identified vendors/developers, covering an ample set of aspects such as licensing, implementation, interoperability and ecosystem. Subsequently, the answers from the eleven responders were processed and analysed, also applying statistical techniques. center dot Results: Two detailed tables depict the current landscape of openEHR CDRs, presenting a structured view of the most relevant survey answers. Unsupervised clustering led to the categorisation of CDRs into four groups, and a decision-making diagram has been designed to aid the CDR selection according to a restricted set of desired features. center dot Conclusions: Compared to a similar study conducted in 2013, the results indicate a worldwide rise in the number of openEHR CDRs, marked by a wider adoption of the dedicated query language, to leverage AQL universality across openEHR platforms. The evolution in the last ten years also included an increased attention to exchange data with non-openEHR

关键词： openEHR Archetype ISO 13606 clinical data repository CDR Survey

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