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      Validation of chief complaints, medical history, medications, and physician diagnoses structured with an integrated emergency department information system in Japan: the Next Stage ER system

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          Abstract

          Aim

          Emergency department information systems (EDIS) facilitate free‐text data use for clinical research; however, no study has validated whether the Next Stage ER system (NSER), an EDIS used in Japan, accurately translates electronic medical records (EMRs) into structured data.

          Methods

          This is a retrospective cohort study using data from the emergency department (ED) of a tertiary care hospital from 2018 to 2019. We used EMRs of 500 random samples from 27,000 ED visits during the study period. Through the NSER system, chief complaints were translated into 231 chief complaint categories based on the Japan Triage and Acuity Scale. Medical history and physician’s diagnoses were encoded using the International Classification of Diseases, 10th Revision; medications were encoded as Anatomical Therapeutic Chemical Classification System codes. Two reviewers independently reviewed 20 items (e.g., presence of fever) for each study component (e.g., chief complaints). We calculated association measures of the structured data by the NSER system, using the chart review results as the gold standard.

          Results

          Sensitivities were very high (>90%) in 17 chief complaints. Positive predictive values were high for 14 chief complaints (≥80%). Negative predictive values were ≥96% for all chief complaints. For medical history and medications, most of the association measures were very high (>90%). For physicians’ ED diagnoses, sensitivities were very high (>93%) in 16 diagnoses; specificities and negative predictive values were very high (>97%).

          Conclusions

          Chief complaints, medical history, medications, and physician’s ED diagnoses in EMRs were well‐translated into existing categories or coding by the NSER system.

          Abstract

          Little is known about whether emergency department information systems accurately translate medical records into structured data. The Next Stage ER system, an emergency department information system in Japan, provided accurate transcriptions of medical records to categorical and coded data. The results indicate that the data from the system is reliable for use in emergency department‐based clinical research and informing resource‐allocation decisions.

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          Most cited references 23

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          Comorbidity measures for use with administrative data.

          This study attempts to develop a comprehensive set of comorbidity measures for use with large administrative inpatient datasets. The study involved clinical and empirical review of comorbidity measures, development of a framework that attempts to segregate comorbidities from other aspects of the patient's condition, development of a comorbidity algorithm, and testing on heterogeneous and homogeneous patient groups. Data were drawn from all adult, nonmaternal inpatients from 438 acute care hospitals in California in 1992 (n = 1,779,167). Outcome measures were those commonly available in administrative data: length of stay, hospital charges, and in-hospital death. A comprehensive set of 30 comorbidity measures was developed. The comorbidities were associated with substantial increases in length of stay, hospital charges, and mortality both for heterogeneous and homogeneous disease groups. Several comorbidities are described that are important predictors of outcomes, yet commonly are not measured. These include mental disorders, drug and alcohol abuse, obesity, coagulopathy, weight loss, and fluid and electrolyte disorders. The comorbidities had independent effects on outcomes and probably should not be simplified as an index because they affect outcomes differently among different patient groups. The present method addresses some of the limitations of previous measures. It is based on a comprehensive approach to identifying comorbidities and separates them from the primary reason for hospitalization, resulting in an expanded set of comorbidities that easily is applied without further refinement to administrative data for a wide range of diseases.
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            Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review

            Background Novel approaches that complement and go beyond evidence-based medicine are required in the domain of chronic diseases, given the growing incidence of such conditions on the worldwide population. A promising avenue is the secondary use of electronic health records (EHRs), where patient data are analyzed to conduct clinical and translational research. Methods based on machine learning to process EHRs are resulting in improved understanding of patient clinical trajectories and chronic disease risk prediction, creating a unique opportunity to derive previously unknown clinical insights. However, a wealth of clinical histories remains locked behind clinical narratives in free-form text. Consequently, unlocking the full potential of EHR data is contingent on the development of natural language processing (NLP) methods to automatically transform clinical text into structured clinical data that can guide clinical decisions and potentially delay or prevent disease onset. Objective The goal of the research was to provide a comprehensive overview of the development and uptake of NLP methods applied to free-text clinical notes related to chronic diseases, including the investigation of challenges faced by NLP methodologies in understanding clinical narratives. Methods Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed and searches were conducted in 5 databases using “clinical notes,” “natural language processing,” and “chronic disease” and their variations as keywords to maximize coverage of the articles. Results Of the 2652 articles considered, 106 met the inclusion criteria. Review of the included papers resulted in identification of 43 chronic diseases, which were then further classified into 10 disease categories using the International Classification of Diseases, 10th Revision. The majority of studies focused on diseases of the circulatory system (n=38) while endocrine and metabolic diseases were fewest (n=14). This was due to the structure of clinical records related to metabolic diseases, which typically contain much more structured data, compared with medical records for diseases of the circulatory system, which focus more on unstructured data and consequently have seen a stronger focus of NLP. The review has shown that there is a significant increase in the use of machine learning methods compared to rule-based approaches; however, deep learning methods remain emergent (n=3). Consequently, the majority of works focus on classification of disease phenotype with only a handful of papers addressing extraction of comorbidities from the free text or integration of clinical notes with structured data. There is a notable use of relatively simple methods, such as shallow classifiers (or combination with rule-based methods), due to the interpretability of predictions, which still represents a significant issue for more complex methods. Finally, scarcity of publicly available data may also have contributed to insufficient development of more advanced methods, such as extraction of word embeddings from clinical notes. Conclusions Efforts are still required to improve (1) progression of clinical NLP methods from extraction toward understanding; (2) recognition of relations among entities rather than entities in isolation; (3) temporal extraction to understand past, current, and future clinical events; (4) exploitation of alternative sources of clinical knowledge; and (5) availability of large-scale, de-identified clinical corpora.
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              Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review

              Natural language processing (NLP) of symptoms from electronic health records (EHRs) could contribute to the advancement of symptom science. We aim to synthesize the literature on the use of NLP to process or analyze symptom information documented in EHR free-text narratives. Our search of 1964 records from PubMed and EMBASE was narrowed to 27 eligible articles. Data related to the purpose, free-text corpus, patients, symptoms, NLP methodology, evaluation metrics, and quality indicators were extracted for each study. Symptom-related information was presented as a primary outcome in 14 studies. EHR narratives represented various inpatient and outpatient clinical specialties, with general, cardiology, and mental health occurring most frequently. Studies encompassed a wide variety of symptoms, including shortness of breath, pain, nausea, dizziness, disturbed sleep, constipation, and depressed mood. NLP approaches included previously developed NLP tools, classification methods, and manually curated rule-based processing. Only one-third (n = 9) of studies reported patient demographic characteristics. NLP is used to extract information from EHR free-text narratives written by a variety of healthcare providers on an expansive range of symptoms across diverse clinical specialties. The current focus of this field is on the development of methods to extract symptom information and the use of symptom information for disease classification tasks rather than the examination of symptoms themselves. Future NLP studies should concentrate on the investigation of symptoms and symptom documentation in EHR free-text narratives. Efforts should be undertaken to examine patient characteristics and make symptom-related NLP algorithms or pipelines and vocabularies openly available.
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                Author and article information

                Contributors
                tag695@mail.harvard.edu
                Journal
                Acute Med Surg
                Acute Med Surg
                10.1002/(ISSN)2052-8817
                AMS2
                Acute Medicine & Surgery
                John Wiley and Sons Inc. (Hoboken )
                2052-8817
                27 August 2020
                Jan-Dec 2020
                : 7
                : 1 ( doiID: 10.1002/ams2.v7.1 )
                Affiliations
                [ 1 ] Department of Clinical Epidemiology and Health Economics School of Public Health The University of Tokyo Tokyo Japan
                [ 2 ] TXP Medical Co. Ltd Tokyo Japan
                [ 3 ] Department of Public Health Graduate School of Medicine The University of Tokyo Tokyo Japan
                [ 4 ] Department of Emergency Medicine Southern Tohoku General Hospital Koriyama Japan
                [ 5 ] Department of Social Medicine Osaka University Graduate School of Medicine Osaka Japan
                [ 6 ] Department of Emergency Medicine Hitachi General Hospital Hitachi Japan
                Author notes
                [* ] Corresponding: Tadahiro Goto, MD, MPH, Department of Clinical Epidemiology and Health Economics, School of Public Health, The University of Tokyo, Tokyo 113‐0033, Japan. E‐mail: tag695@ 123456mail.harvard.edu .

                Article
                AMS2554
                10.1002/ams2.554
                7453131
                © 2020 The Authors. Acute Medicine & Surgery published by John Wiley & Sons Australia, Ltd on behalf of Japanese Association for Acute Medicine.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                Page count
                Figures: 0, Tables: 4, Pages: 8, Words: 5691
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                Original Article
                Original Articles
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                2.0
                January/December 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.8 mode:remove_FC converted:28.08.2020

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