Dataset Information

Electronic Medical Record-Based Case Phenotyping for the Charlson Conditions: Scoping Review.

ABSTRACT:

Background

Electronic medical records (EMRs) contain large amounts of rich clinical information. Developing EMR-based case definitions, also known as EMR phenotyping, is an active area of research that has implications for epidemiology, clinical care, and health services research.

Objective

This review aims to describe and assess the present landscape of EMR-based case phenotyping for the Charlson conditions.

Methods

A scoping review of EMR-based algorithms for defining the Charlson comorbidity index conditions was completed. This study covered articles published between January 2000 and April 2020, both inclusive. Embase (Excerpta Medica database) and MEDLINE (Medical Literature Analysis and Retrieval System Online) were searched using keywords developed in the following 3 domains: terms related to EMR, terms related to case finding, and disease-specific terms. The manuscript follows the Preferred Reporting Items for Systematic reviews and Meta-analyses extension for Scoping Reviews (PRISMA) guidelines.

Results

A total of 274 articles representing 299 algorithms were assessed and summarized. Most studies were undertaken in the United States (181/299, 60.5%), followed by the United Kingdom (42/299, 14.0%) and Canada (15/299, 5.0%). These algorithms were mostly developed either in primary care (103/299, 34.4%) or inpatient (168/299, 56.2%) settings. Diabetes, congestive heart failure, myocardial infarction, and rheumatology had the highest number of developed algorithms. Data-driven and clinical rule-based approaches have been identified. EMR-based phenotype and algorithm development reflect the data access allowed by respective health systems, and algorithms vary in their performance.

Conclusions

Recognizing similarities and differences in health systems, data collection strategies, extraction, data release protocols, and existing clinical pathways is critical to algorithm development strategies. Several strategies to assist with phenotype-based case definitions have been proposed.

SUBMITTER: Lee S

PROVIDER: S-EPMC7884219 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

Electronic Medical Record-Based Case Phenotyping for the Charlson Conditions: Scoping Review.

Lee Seungwon S Doktorchik Chelsea C Martin Elliot Asher EA D'Souza Adam Giles AG Eastwood Cathy C Shaheen Abdel Aziz AA Naugler Christopher C Lee Joon J Quan Hude H

JMIR medical informatics 20210201 2

<h4>Background</h4>Electronic medical records (EMRs) contain large amounts of rich clinical information. Developing EMR-based case definitions, also known as EMR phenotyping, is an active area of research that has implications for epidemiology, clinical care, and health services research.<h4>Objective</h4>This review aims to describe and assess the present landscape of EMR-based case phenotyping for the Charlson conditions.<h4>Methods</h4>A scoping review of EMR-based algorithms for defining the ...[more]

PMID: 33522976

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Project description:IntroductionElectronic health records (EHR) are linked together to examine disease history and to undertake research into the causes and outcomes of disease. However, the process of constructing algorithms for phenotyping (e.g., identifying disease characteristics) or health characteristics (e.g., smoker) is very time consuming and resource costly. In addition, results can vary greatly between researchers. Reusing or building on algorithms that others have created is a compelling solution to these problems. However, sharing algorithms is not a common practice and many published studies do not detail the clinical code lists used by the researchers in the disease/characteristic definition. To address these challenges, a number of centres across the world have developed health data portals which contain concept libraries (e.g., algorithms for defining concepts such as disease and characteristics) in order to facilitate disease phenotyping and health studies.ObjectivesThis study aims to review the literature of existing concept libraries, examine their utilities, identify the current gaps, and suggest future developments.MethodsThe five-stage framework of Arksey and O'Malley was used for the literature search. This approach included defining the research questions, identifying relevant studies through literature review, selecting eligible studies, charting and extracting data, and summarising and reporting the findings.ResultsThis review identified seven publicly accessible Electronic Health data concept libraries which were developed in different countries including UK, USA, and Canada. The concept libraries (n = 7) investigated were either general libraries that hold phenotypes of multiple specialties (n = 4) or specialized libraries that manage only certain specialities such as rare diseases (n = 3). There were some clear differences between the general libraries such as archiving data from different electronic sources, and using a range of different types of coding systems. However, they share some clear similarities such as enabling users to upload their own code lists, and allowing users to use/download the publicly accessible code. In addition, there were some differences between the specialized libraries such as difference in ability to search, and if it was possible to use different searching queries such as simple or complex searches. Conversely, there were some similarities between the specialized libraries such as enabling users to upload their own concepts into the libraries and to show where they were published, which facilitates assessing the validity of the concepts. All the specialized libraries aimed to encourage the reuse of research methods such as lists of clinical code and/or metadata.ConclusionThe seven libraries identified have been developed independently and appear to replicate similar concepts but in different ways. Collaboration between similar libraries would greatly facilitate the use of these libraries for the user. The process of building code lists takes time and effort. Access to existing code lists increases consistency and accuracy of definitions across studies. Concept library developers should collaborate with each other to raise awareness of their existence and of their various functions, which could increase users' contributions to those libraries and promote their wide-ranging adoption.

Project description:ObjectiveHealthcare provider (HCP) burnout is on the rise with electronic medical record (EMR) use being cited as a factor, particularly with the rise of the COVID-19 pandemic. Burnout in HCPs is associated with negative patient outcomes, and, therefore, it is crucial to understand and address each factor that affects HCP burnout. This study aims to (a) assess the relationship between EMR use and burnout and (b) explore interventions to reduce EMR-related burnout.MethodsWe searched MEDLINE (Ovid), CINAHL and SCOPUS on 29 July 2021. We selected all studies in English from any publication year and country that discussed burnout in HCPs (physicians, nurse practitioners and registered nurses) related to EMR use. Studies must have reported a quantitative relationship to be included. Studies that implemented an intervention to address this burnout were also included. All titles and abstracts were screened by two reviewers, and all full-text articles were reviewed by two reviewers. Any conflicts were addressed with a third reviewer and resolved through discussion. Quality of evidence of all included articles was assessed using the Quality Rating Scheme for Studies and Other Evidence.FindingsThe search identified 563 citations with 416 citations remaining after duplicate removal. A review of abstracts led to 59 studies available for full-text assessment, resulting in 25 studies included in the scoping review. Commonly identified associations between EMR-related burnout in HCPs included: message and alert load, time spent on EMRs, organisational support, EMR functionality and usability and general use of EMRs. Two articles employed team-based interventions to improve burnout symptoms without significant improvement in burnout scores.Conclusions and relevanceCurrent literature supports an association between EMR use and provider burnout. Very limited evidence exists for burnout-reducing interventions that address factors such as time spent on EMRs, organisational support or EMR design.

Project description:BackgroundElectronic medical record (EMR) systems and electronic messages are an increasingly common conduit between physicians and patients. Clear benefits of this type of communication have been established, especially among cancer patients. Studies suggest that patient portals and electronic messaging platforms can help with care coordination between oncology providers and facilitate asynchronous patient-provider communication. Despite the many benefits, there is little research regarding EMR and secure messaging use, particularly among patients with breast cancer.ObjectivesThe objective of this systematic review was to examine the evidence supporting the use of EMR-based messaging systems in patients with breast cancer.MethodsA systematic literature search of Ovid MEDLINE, PubMed, Scopus, Web of Science CINAHL, and Cochrane Library was conducted. Studies were required to be published between 2005 and 2022 and report data on demographic information and electronic messaging between patients and providers. Studies were excluded if they reported insufficient data, did not include breast cancer patients, or were not published in English.ResultsThis study identified 10 articles that met inclusion criteria. The resulting studies investigated topics such as: patterns of messaging and medication adherence, cancer screening, messaging as a predictor of behavior or outcomes, and symptom management. The literature indicates that electronic messaging with providers was associated with clinical benefits for breast cancer patients and improved screening behaviors.ConclusionThis review uncovered multiple areas to focus future research on, including ideal volume of electronic messages sent and their relation to prescription adherence, studies focusing solely on the breast cancer population, racial disparities in electronic messaging, and provider perceptions of electronic messaging. It is vital that more work be done to understand barriers and gaps in EMR usage to ensure that all individuals can access this increasingly essential medical service while minimizing physician workload and burnout.

Project description:To develop and evaluate a novel strategy that automates the retrospective identification of sepsis using electronic health record data.DesignRetrospective cohort study of emergency department and in-hospital patient encounters from 2014 to 2018.SettingOne community and two academic hospitals in Maryland.PatientsAll patients 18 years old or older presenting to the emergency department or admitted to any acute inpatient medical or surgical unit including patients discharged from the emergency department.InterventionsNone.Measurements and main resultsFrom the electronic health record, 233,252 emergency department and inpatient encounters were identified. Patient data were used to develop and validate electronic health record-based sepsis phenotyping, an adaptation of "the Centers for Disease Control Adult Sepsis Event toolkit" that accounts for comorbid conditions when identifying sepsis patients. The performance of this novel system was then compared with 1) physician case review and 2) three other commonly used strategies using metrics of sensitivity and precision relative to sepsis billing codes, termed "billing code sensitivity" and "billing code predictive value." Physician review of electronic health record-based sepsis phenotyping identified cases confirmed 79% as having sepsis; 88% were confirmed or had a billing code for sepsis; and 99% were confirmed, had a billing code, or received at least 4 days of antibiotics. At comparable billing code sensitivity (0.91; 95% CI, 0.88-0.93), electronic health record-based sepsis phenotyping had a higher billing code predictive value (0.32; 95% CI, 0.30-0.34) than either the Centers for Medicare and Medicaid Services Sepsis Core Measure (SEP-1) definition or the Sepsis-3 consensus definition (0.12; 95% CI, 0.11-0.13; and 0.07; 95% CI, 0.07-0.08, respectively). When compared with electronic health record-based sepsis phenotyping, Adult Sepsis Event had a lower billing code sensitivity (0.75; 95% CI, 0.72-0.78) and similar billing code predictive value (0.29; 95% CI, 0.26-0.31). Electronic health record-based sepsis phenotyping identified patients with higher in-hospital mortality and nearly one-half as many false-positive cases when compared with SEP-1 and Sepsis-3.ConclusionsBy accounting for comorbid conditions, electronic health record-based sepsis phenotyping exhibited better performance when compared with other automated definitions of sepsis.

Project description:BackgroundElectronic health record (EHR) system users devise workarounds to cope with mismatches between workflows designed in the EHR and preferred workflows in practice. Although workarounds appear beneficial at first sight, they frequently jeopardize patient safety, the quality of care, and the efficiency of care.ObjectiveThis review aims to aid in identifying, analyzing, and resolving EHR workarounds; the Sociotechnical EHR Workaround Analysis (SEWA) framework was published in 2019. Although the framework was based on a large case study, the framework still required theoretical validation, refinement, and enrichment.MethodsA scoping literature review was performed on studies related to EHR workarounds published between 2010 and 2021 in the MEDLINE, Embase, CINAHL, Cochrane, or IEEE databases. A total of 737 studies were retrieved, of which 62 (8.4%) were included in the final analysis. Using an analytic framework, the included studies were investigated to uncover the rationales that EHR users have for workarounds, attributes characterizing workarounds, possible scopes, and types of perceived impacts of workarounds.ResultsThe SEWA framework was theoretically validated and extended based on the scoping review. Extensive support for the pre-existing rationales, attributes, possible scopes, and types of impact was found in the included studies. Moreover, 7 new rationales, 4 new attributes, and 3 new types of impact were incorporated. Similarly, the descriptions of multiple pre-existing rationales for workarounds were refined to describe each rationale more accurately.ConclusionsSEWA is now grounded in the existing body of peer-reviewed empirical evidence on EHR workarounds and, as such, provides a theoretically validated and more complete synthesis of EHR workaround rationales, attributes, possible scopes, and types of impact. The revised SEWA framework can aid researchers and practitioners in a wider range of health care settings to identify, analyze, and resolve workarounds. This will improve user-centered EHR design and redesign, ultimately leading to improved patient safety, quality of care, and efficiency of care.

Project description:ObjectiveElectronic health records (EHR) offer medical and pharmacogenomics research unprecedented opportunities to identify and classify patients at risk. EHRs are collections of highly inter-dependent records that include biological, anatomical, physiological, and behavioral observations. They comprise a patient's clinical phenome, where each patient has thousands of date-stamped records distributed across many relational tables. Development of EHR computer-based phenotyping algorithms require time and medical insight from clinical experts, who most often can only review a small patient subset representative of the total EHR records, to identify phenotype features. In this research we evaluate whether relational machine learning (ML) using inductive logic programming (ILP) can contribute to addressing these issues as a viable approach for EHR-based phenotyping.MethodsTwo relational learning ILP approaches and three well-known WEKA (Waikato Environment for Knowledge Analysis) implementations of non-relational approaches (PART, J48, and JRIP) were used to develop models for nine phenotypes. International Classification of Diseases, Ninth Revision (ICD-9) coded EHR data were used to select training cohorts for the development of each phenotypic model. Accuracy, precision, recall, F-Measure, and Area Under the Receiver Operating Characteristic (AUROC) curve statistics were measured for each phenotypic model based on independent manually verified test cohorts. A two-sided binomial distribution test (sign test) compared the five ML approaches across phenotypes for statistical significance.ResultsWe developed an approach to automatically label training examples using ICD-9 diagnosis codes for the ML approaches being evaluated. Nine phenotypic models for each ML approach were evaluated, resulting in better overall model performance in AUROC using ILP when compared to PART (p=0.039), J48 (p=0.003) and JRIP (p=0.003).DiscussionILP has the potential to improve phenotyping by independently delivering clinically expert interpretable rules for phenotype definitions, or intuitive phenotypes to assist experts.ConclusionRelational learning using ILP offers a viable approach to EHR-driven phenotyping.

Dataset Information

Electronic Medical Record-Based Case Phenotyping for the Charlson Conditions: Scoping Review.

Background

Objective

Methods

Results

Conclusions

Publications

Electronic Medical Record-Based Case Phenotyping for the Charlson Conditions: Scoping Review.

Similar Datasets

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