Context-based electronic health record: toward patient specific healthcare

Semantically oriented EHR navigation with a patient specific knowledge base and a clinical context ontology

Widespread adoption of electronic health records (EHR) in the U.S. has been followed by unintended consequences, overexposing clinicians to widely reported EHR limitations. As an attempt to fixing the EHR, we propose the use of a clinical context ontology (CCO), applied to turn implicit contextual statements into formally represented data in the form of concept-relationship-concept tuples. These tuples form what we call a patient specific knowledge base (PSKB), a collection of formally defined tuples containing facts about the patient's care context. We report the process to create a CCO, which guides annotation of structured and narrative patient data to produce a PSKB. We also present an application of our PSKB using real patient data displayed on a semantically oriented patient summary to improve EHR navigation. Our approach can potentially save precious time spent by clinicians using today's EHRs, by showing a chronological view of the patient's record along with contextual statements needed for care decisions with minimum effort. We propose several other applications of a PSKB to improve multiple EHR functions to guide future research.

Impact of the Lightwave Health Information Management Software on the Dimensions of Quality of Healthcare Data

OBJECTIVES

The use of technology in healthcare to manage patient records, guide diagnosis, and make referrals is termed electronic healthcare. An electronic health record system called Lightwave Health Information Management System (LHIMS) was implemented in 2018 at Cape Coast Teaching Hospital (CCTH). This study evaluated the impact of LHIMS on the quality of healthcare data at CCTH, focusing on the extent to which its use has enhanced the main dimensions of data quality.

METHODS

Structured questionnaires were administered to doctors at CCTH to enquire about their opinions about the present state of LHIMS as measured against the parameters of interest in this study, mainly the dimensions of quality healthcare data and the specific issues plaguing the system as reported by respondents.

RESULTS

Most doctors found LHIMS convenient to use, mainly because it made access to patient records easier and had to some extent improved the dimensions of quality healthcare data, except for comprehensiveness, at CCTH. Major challenges that impeded the smooth running of the system were erratic power supply, inadequate logistics and technological drive, and poor internet connectivity.

CONCLUSIONS

LHIMS must be upgraded to include more decision support systems and additional add-ons such as patients' radiological reports, and laboratory results must be readily available on LHIMS to make patient health data more comprehensive.

Toward an Interdisciplinary Approach to Constructing Care Delivery Pathways From Electronic Health Care Databases to Support Integrated Care in Chronic Conditions: Systematic Review of Quantification and Visualization Methods

BACKGROUND

Electronic health care databases are increasingly used for informing clinical decision-making. In long-term care, linking and accessing information on health care delivered by different providers could improve coordination and health outcomes. Several methods for quantifying and visualizing this information into data-driven care delivery pathways (CDPs) have been proposed. To be integrated effectively and sustainably into routine care, these methods need to meet a range of prerequisites covering 3 broad domains: clinical, technological, and behavioral. Although advances have been made, development to date lacks a comprehensive interdisciplinary approach. As the field expands, it would benefit from developing common standards of development and reporting that integrate clinical, technological, and behavioral aspects.

OBJECTIVE

We aimed to describe the content and development of long-term CDP quantification and visualization methods and to propose recommendations for future work.

METHODS

We conducted a systematic review following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) recommendations. We searched peer-reviewed publications in English and reported the CDP methods by using the following data in the included studies: long-term care data and extracted data on clinical information and aims, technological development and characteristics, and user behaviors. The data are summarized in tables and presented narratively.

RESULTS

Of the 2921 records identified, 14 studies were included, of which 13 (93%) were descriptive reports and 1 (7%) was a validation study. Clinical aims focused primarily on treatment decision-making (n=6, 43%) and care coordination (n=7, 50%). Technological development followed a similar process from scope definition to tool validation, with various levels of detail in reporting. User behaviors (n=3, 21%) referred to accessing CDPs, planning care, adjusting treatment, or supporting adherence.

CONCLUSIONS

The use of electronic health care databases for quantifying and visualizing CDPs in long-term care is an emerging field. Detailed and standardized reporting of clinical and technological aspects is needed. Early consideration of how CDPs would be used, validated, and implemented in clinical practice would likely facilitate further development and adoption.

TRIAL REGISTRATION

PROSPERO CRD42019140494; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=140494.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.1136/bmjopen-2019-033573.

Patient Information Summarization in Clinical Settings: Scoping Review

BACKGROUND

Information overflow, a common problem in the present clinical environment, can be mitigated by summarizing clinical data. Although there are several solutions for clinical summarization, there is a lack of a complete overview of the research relevant to this field.

OBJECTIVE

This study aims to identify state-of-the-art solutions for clinical summarization, to analyze their capabilities, and to identify their properties.

METHODS

A scoping review of articles published between 2005 and 2022 was conducted. With a clinical focus, PubMed and Web of Science were queried to find an initial set of reports, later extended by articles found through a chain of citations. The included reports were analyzed to answer the questions of where, what, and how medical information is summarized; whether summarization conserves temporality, uncertainty, and medical pertinence; and how the propositions are evaluated and deployed. To answer how information is summarized, methods were compared through a new framework "collect-synthesize-communicate" referring to information gathering from data, its synthesis, and communication to the end user.

RESULTS

Overall, 128 articles were included, representing various medical fields. Exclusively structured data were used as input in 46.1% (59/128) of papers, text in 41.4% (53/128) of articles, and both in 10.2% (13/128) of papers. Using the proposed framework, 42.2% (54/128) of the records contributed to information collection, 27.3% (35/128) contributed to information synthesis, and 46.1% (59/128) presented solutions for summary communication. Numerous summarization approaches have been presented, including extractive (n=13) and abstractive summarization (n=19); topic modeling (n=5); summary specification (n=11); concept and relation extraction (n=30); visual design considerations (n=59); and complete pipelines (n=7) using information extraction, synthesis, and communication. Graphical displays (n=53), short texts (n=41), static reports (n=7), and problem-oriented views (n=7) were the most common types in terms of summary communication. Although temporality and uncertainty information were usually not conserved in most studies (74/128, 57.8% and 113/128, 88.3%, respectively), some studies presented solutions to treat this information. Overall, 115 (89.8%) articles showed results of an evaluation, and methods included evaluations with human participants (median 15, IQR 24 participants): measurements in experiments with human participants (n=31), real situations (n=8), and usability studies (n=28). Methods without human involvement included intrinsic evaluation (n=24), performance on a proxy (n=10), or domain-specific tasks (n=11). Overall, 11 (8.6%) reports described a system deployed in clinical settings.

CONCLUSIONS

The scientific literature contains many propositions for summarizing patient information but reports very few comparisons of these proposals. This work proposes to compare these algorithms through how they conserve essential aspects of clinical information and through the "collect-synthesize-communicate" framework. We found that current propositions usually address these 3 steps only partially. Moreover, they conserve and use temporality, uncertainty, and pertinent medical aspects to varying extents, and solutions are often preliminary.

Clinical named entity recognition and relation extraction using natural language processing of medical free text: A systematic review

BACKGROUND

Natural Language Processing (NLP) applications have developed over the past years in various fields including its application to clinical free text for named entity recognition and relation extraction. However, there has been rapid developments the last few years that there's currently no overview of it. Moreover, it is unclear how these models and tools have been translated into clinical practice. We aim to synthesize and review these developments.

METHODS

We reviewed literature from 2010 to date, searching PubMed, Scopus, the Association of Computational Linguistics (ACL), and Association of Computer Machinery (ACM) libraries for studies of NLP systems performing general-purpose (i.e., not disease- or treatment-specific) information extraction and relation extraction tasks in unstructured clinical text (e.g., discharge summaries).

RESULTS

We included in the review 94 studies with 30 studies published in the last three years. Machine learning methods were used in 68 studies, rule-based in 5 studies, and both in 22 studies. 63 studies focused on Named Entity Recognition, 13 on Relation Extraction and 18 performed both. The most frequently extracted entities were "problem", "test" and "treatment". 72 studies used public datasets and 22 studies used proprietary datasets alone. Only 14 studies defined clearly a clinical or information task to be addressed by the system and just three studies reported its use outside the experimental setting. Only 7 studies shared a pre-trained model and only 8 an available software tool.

DISCUSSION

Machine learning-based methods have dominated the NLP field on information extraction tasks. More recently, Transformer-based language models are taking the lead and showing the strongest performance. However, these developments are mostly based on a few datasets and generic annotations, with very few real-world use cases. This may raise questions about the generalizability of findings, translation into practice and highlights the need for robust clinical evaluation.

ChartWalk: Navigating large collections of text notes in electronic health records for clinical chart review

Before seeing a patient for the first time, healthcare workers will typically conduct a comprehensive clinical chart review of the patient's electronic health record (EHR). Within the diverse documentation pieces included there, text notes are among the most important and thoroughly perused segments for this task; and yet they are among the least supported medium in terms of content navigation and overview. In this work, we delve deeper into the task of clinical chart review from a data visualization perspective and propose a hybrid graphics+text approach via ChartWalk, an interactive tool to support the review of text notes in EHRs. We report on our iterative design process grounded in input provided by a diverse range of healthcare professionals, with steps including: (a) initial requirements distilled from interviews and the literature, (b) an interim evaluation to validate design decisions, and (c) a task-based qualitative evaluation of our final design. We contribute lessons learned to better support the design of tools not only for clinical chart reviews but also other healthcare-related tasks around medical text analysis.

MediCoSpace : Visual Decision-Support for Doctor-Patient Consultations using Medical Concept Spaces from EHRs

Healthcare systems are under pressure from an aging population, rising costs, and increasingly complex conditions and treatments. Although data are determined to play a bigger role in how doctors diagnose and prescribe treatments, they struggle due to a lack of time and an abundance of structured and unstructured information. To address this challenge, we introduce MediCoSpace , a visual decision-support tool for more efficient doctor-patient consultations. The tool links patient reports to past and present diagnoses, diseases, drugs, and treatments, both for the current patient and other patients in comparable situations. MediCoSpace uses textual medical data, deep-learning supported text analysis and concept spaces to facilitate a visual discovery process. The tool is evaluated with five medical doctors. The results show that MediCoSpace facilitates a promising, yet complex way to discover unlikely relations and thus suggests a path toward the development of interactive visual tools to provide physicians with more holistic diagnoses and personalized, dynamic treatments for patients.

Formal representation of patients' care context data: the path to improving the electronic health record

Objective

To develop a collection of concept-relationship-concept tuples to formally represent patients’ care context data to inform electronic health record (EHR) development.

Materials and Methods

We reviewed semantic relationships reported in the literature and developed a manual annotation schema. We used the initial schema to annotate sentences extracted from narrative note sections of cardiology, urology, and ear, nose, and throat (ENT) notes. We audio recorded ENT visits and annotated their parsed transcripts. We combined the results of each annotation into a consolidated set of concept-relationship-concept tuples. We then compared the tuples used within and across the multiple data sources.

Results

We annotated a total of 626 sentences. Starting with 8 relationships from the literature, we annotated 182 sentences from 8 inpatient consult notes (initial set of tuples = 43). Next, we annotated 232 sentences from 10 outpatient visit notes (enhanced set of tuples = 75). Then, we annotated 212 sentences from transcripts of 5 outpatient visits (final set of tuples = 82). The tuples from the visit transcripts covered 103 (74%) concepts documented in the notes of their respective visits. There were 20 (24%) tuples used across all data sources, 10 (12%) used only in inpatient notes, 15 (18%) used only in visit notes, and 7 (9%) used only in the visit transcripts.

Conclusions

We produced a robust set of 82 tuples useful to represent patients’ care context data. We propose several applications of our tuples to improve EHR navigation, data entry, learning health systems, and decision support.

A Perioperative Care Display for Understanding High Acuity Patients

BACKGROUND

The data visualization literature asserts that the details of the optimal data display must be tailored to the specific task, the background of the user, and the characteristics of the data. The general organizing principle of a concept-oriented display is known to be useful for many tasks and data types.

OBJECTIVES

In this project, we used general principles of data visualization and a co-design process to produce a clinical display tailored to a specific cognitive task, chosen from the anesthesia domain, but with clear generalizability to other clinical tasks. To support the work of the anesthesia-in-charge (AIC) our task was, for a given day, to depict the acuity level and complexity of each patient in the collection of those that will be operated on the following day. The AIC uses this information to optimally allocate anesthesia staff and providers across operating rooms.

METHODS

We used a co-design process to collaborate with participants who work in the AIC role. We conducted two in-depth interviews with AICs and engaged them in subsequent input on iterative design solutions.

RESULTS

Through a co-design process, we found (1) the need to carefully match the level of detail in the display to the level required by the clinical task, (2) the impedance caused by irrelevant information on the screen such as icons relevant only to other tasks, and (3) the desire for a specific but optional trajectory of increasingly detailed textual summaries.

CONCLUSION

This study reports a real-world clinical informatics development project that engaged users as co-designers. Our process led to the user-preferred design of a single binary flag to identify the subset of patients needing further investigation, and then a trajectory of increasingly detailed, text-based abstractions for each patient that can be displayed when more information is needed.

User-Centered Clinical Display Design Issues for Inpatient Providers

BACKGROUND

Suboptimal information display in electronic health records (EHRs) is a notorious pain point for users. Designing an effective display is difficult, due in part to the complex and varied nature of clinical practice.

OBJECTIVE

This article aims to understand the goals, constraints, frustrations, and mental models of inpatient medical providers when accessing EHR data, to better inform the display of clinical information.

METHODS

A multidisciplinary ethnographic study of inpatient medical providers.

RESULTS

Our participants' primary goal was usually to assemble a clinical picture around a given question, under the constraints of time pressure and incomplete information. To do so, they tend to use a mental model of multiple layers of abstraction when thinking of patients and disease; they prefer immediate pattern recognition strategies for answering clinical questions, with breadth-first or depth-first search strategies used subsequently if needed; and they are sensitive to data relevance, completeness, and reliability when reading a record.

CONCLUSION

These results conflict with the ubiquitous display design practice of separating data by type (test results, medications, notes, etc.), a mismatch that is known to encumber efficient mental processing by increasing both navigation burden and memory demands on users. A popular and obvious solution is to select or filter the data to display exactly what is presumed to be relevant to the clinical question, but this solution is both brittle and mistrusted by users. A less brittle approach that is more aligned with our users' mental model could use abstraction to summarize details instead of filtering to hide data. An abstraction-based approach could allow clinicians to more easily assemble a clinical picture, to use immediate pattern recognition strategies, and to adjust the level of displayed detail to their particular needs. It could also help the user notice unanticipated patterns and to fluidly shift attention as understanding evolves.

What You Need to Know Before Implementing a Clinical Research Data Warehouse: Comparative Review of Integrated Data Repositories in Health Care Institutions

Background

Integrated data repositories (IDRs), also referred to as clinical data warehouses, are platforms used for the integration of several data sources through specialized analytical tools that facilitate data processing and analysis. IDRs offer several opportunities for clinical data reuse, and the number of institutions implementing an IDR has grown steadily in the past decade.

Objective

The architectural choices of major IDRs are highly diverse and determining their differences can be overwhelming. This review aims to explore the underlying models and common features of IDRs, provide a high-level overview for those entering the field, and propose a set of guiding principles for small- to medium-sized health institutions embarking on IDR implementation.

Methods

We reviewed manuscripts published in peer-reviewed scientific literature between 2008 and 2020, and selected those that specifically describe IDR architectures. Of 255 shortlisted articles, we found 34 articles describing 29 different architectures. The different IDRs were analyzed for common features and classified according to their data processing and integration solution choices.

Results

Despite common trends in the selection of standard terminologies and data models, the IDRs examined showed heterogeneity in the underlying architecture design. We identified 4 common architecture models that use different approaches for data processing and integration. These different approaches were driven by a variety of features such as data sources, whether the IDR was for a single institution or a collaborative project, the intended primary data user, and purpose (research-only or including clinical or operational decision making).

Conclusions

IDR implementations are diverse and complex undertakings, which benefit from being preceded by an evaluation of requirements and definition of scope in the early planning stage. Factors such as data source diversity and intended users of the IDR influence data flow and synchronization, both of which are crucial factors in IDR architecture planning.

Data Tagging in Medical Images: A Survey of the State-of-Art

A huge amount of medical data is generated every second, and a significant percentage of the data are images that need to be analyzed and processed. One of the key challenges in this regard is the recovery of the data of medical images. The medical image recovery procedure should be done automatically by the computers that are the method of identifying object concepts and assigning homologous tags to them. To discover the hidden concepts in the medical images, the lowlevel characteristics should be used to achieve high-level concepts and that is a challenging task. In any specific case, it requires human involvement to determine the significance of the image. To allow machine-based reasoning on the medical evidence collected, the data must be accompanied by additional interpretive semantics; a change from a pure data-intensive methodology to a model of evidence rich in semantics. In this state-of-art, data tagging methods related to medical images are surveyed which is an important aspect for the recognition of a huge number of medical images. Different types of tags related to the medical image, prerequisites of medical data tagging, different techniques to develop medical image tags, different medical image tagging algorithms and different tools that are used to create the tags are discussed in this paper. The aim of this state-of-art paper is to produce a summary and a set of guidelines for using the tags for the identification of medical images and to identify the challenges and future research directions of tagging medical images.

Patient information organization in the intensive care setting: expert knowledge elicitation with card sorting methods

Introduction

Many electronic health records fail to support information uptake because they impose low-level information organization tasks on users. Clinical concept-oriented views have shown information processing improvements, but the specifics of this organization for critical care are unclear.

Objective

To determine high-level cognitive processes and patient information organization schema in critical care.

Methods

We conducted an open card sort of 29 patient data elements and a modified Delphi card sort of 65 patient data elements. Study participants were 39 clinicians with varied critical care training and experience. We analyzed the open sort with a hierarchical cluster analysis (HCA) and factor analysis (FA). The Delphi sort was split into three initiating groups that resulted in three unique solutions. We compared results between open sort analyses (HCA and FA), between card sorting exercises (open and Delphi), and across the Delphi solutions.

Results

Between the HCA and FA, we observed common constructs including cardiovascular and hemodynamics, infectious disease, medications, neurology, patient overview, respiratory, and vital signs. The more comprehensive Delphi sort solutions also included gastrointestinal, renal, and imaging constructs.

Conclusions

We identified primarily system-based groupings (e.g., cardiovascular, respiratory). Source-based (e.g., medications, laboratory) groups became apparent when participants were asked to sort a longer list of concepts. These results suggest a hybrid approach to information organization, which may combine systems, source, or problem-based groupings, best supports clinicians' mental models. These results can contribute to the design of information displays to better support clinicians' access and interpretation of information for critical care decisions.

TRANSLATOR Database-A Vision for a Multi-Institutional Research Network

The formation of the CTSI One Health Alliance (COHA) network has generated the infrastructure necessary to support "Big Data" collaborative comparative and translational research in veterinary medicine. We describe the first step in the design, implementation, and dissemination of a collaborative information technology infrastructure that will serve the public and clinicians (COHA public/member based web site at https://ctsaonehealthalliance.org/) and its research focused COHA Research Workbench application. The core research infrastructure, TRANSLATOR (TRanslational ANimal Shared ColLAboraTive Observational Research), represents the foundation of a federated research-capable network to enable pooling large datasets from both electronic health records and publications. The public facing COHA website is a mechanism for both the dissemination of knowledge to the public and to foster collaborations amongst veterinary clinician scientists and the greater medical research community.

Machine Learning in Neurooncology Imaging: From Study Request to Diagnosis and Treatment

OBJECTIVE

Machine learning has potential to play a key role across a variety of medical imaging applications. This review seeks to elucidate the ways in which machine learning can aid and enhance diagnosis, treatment, and follow-up in neurooncology.

CONCLUSION

Given the rapid pace of development in machine learning over the past several years, a basic proficiency of the key tenets and use cases in the field is critical to assessing potential opportunities and challenges of this exciting new technology.

Doccurate: A Curation-Based Approach for Clinical Text Visualization

Before seeing a patient, physicians seek to obtain an overview of the patient's medical history. Text plays a major role in this activity since it represents the bulk of the clinical documentation, but reviewing it quickly becomes onerous when patient charts grow too large. Text visualization methods have been widely explored to manage this large scale through visual summaries that rely on information retrieval algorithms to structure text and make it amenable to visualization. However, the integration with such automated approaches comes with a number of limitations, including significant error rates and the need for healthcare providers to fine-tune algorithms without expert knowledge of their inner mechanics. In addition, several of these approaches obscure or substitute the original clinical text and therefore fail to leverage qualitative and rhetorical flavours of the clinical notes. These drawbacks have limited the adoption of text visualization and other summarization technologies in clinical practice. In this work we present Doccurate, a novel system embodying a curation-based approach for the visualization of large clinical text datasets. Our approach offers automation auditing and customizability to physicians while also preserving and extensively linking to the original text. We discuss findings of a formal qualitative evaluation conducted with 6 domain experts, shedding light onto physicians' information needs, perceived strengths and limitations of automated tools, and the importance of customization while balancing efficiency. We also present use case scenarios to showcase Doccurate's envisioned usage in practice.

How Do Experienced Physicians Access and Evaluate Laboratory Test Results for the Chronic Patient? A Qualitative Analysis

BACKGROUND

Electronic health records may present laboratory test results in a variety of ways. Little is known about how the usefulness of different visualizations of laboratory test results is influenced by the complex and varied process of clinical decision making.

OBJECTIVE

The purpose of this study was to investigate how clinicians access and utilize laboratory test results when caring for patients with chronic illness.

METHODS

We interviewed 10 attending physicians about how they access and assess laboratory tests when following up patients with chronic illness. The interviews were audio-recorded, transcribed verbatim, and analyzed qualitatively.

RESULTS

Informants preferred different visualizations of laboratory test results, depending on what aspects of the data they were interested in. As chronic patients may have laboratory test results that are permanently outside standardized reference ranges, informants would often look for significant change, rather than exact values. What constituted significant change depended on contextual information (e.g., the results of other investigations, intercurrent diseases, and medical interventions) spread across multiple locations in the electronic health record. For chronic patients, the temporal relations between data could often be of special interest. Informants struggled with finding and synthesizing fragmented information into meaningful overviews.

CONCLUSION

The presentation of laboratory test results should account for the large variety of associated contextual information needed for clinical comprehension. Future research is needed to improve the integration of the different parts of the electronic health record.

Direct estimation of patient attributes from anatomical MRI based on multi-atlas voting

MRI brain atlases are widely used for automated image segmentation, and in particular, recent developments in multi-atlas techniques have shown highly accurate segmentation results. In this study, we extended the role of the atlas library from mere anatomical reference to a comprehensive knowledge database with various patient attributes, such as demographic, functional, and diagnostic information. In addition to using the selected (heavily-weighted) atlases to achieve high segmentation accuracy, we tested whether the non-anatomical attributes of the selected atlases could be used to estimate patient attributes. This can be considered a context-based image retrieval (CBIR) approach, embedded in the multi-atlas framework. We first developed an image similarity measurement to weigh the atlases on a structure-by-structure basis, and then, the attributes of the multiple atlases were weighted to estimate the patient attributes. We tested this concept first by estimating age in a normal population; we then performed functional and diagnostic estimations in Alzheimer's disease patients. The accuracy of the estimated patient attributes was measured against the actual clinical data, and the performance was compared to conventional volumetric analysis. The proposed CBIR framework by multi-atlas voting would be the first step toward a knowledge-based support system for quantitative radiological image reading and diagnosis.

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Patient attributes are estimated directly by retrieving information from multi-atlas.

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Non-imaging attributes of the atlases are weighted to estimate patient attributes.

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The method achieved high accuracy in estimating age in the normal population.

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The method can estimate functional and diagnostic attributes in dementia patients.

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The estimation accuracy was higher than volumetric analysis in subcortical areas.

Electronic Health Records: Then, Now, and in the Future

OBJECTIVES

Describe the state of Electronic Health Records (EHRs) in 1992 and their evolution by 2015 and where EHRs are expected to be in 25 years. Further to discuss the expectations for EHRs in 1992 and explore which of them were realized and what events accelerated or disrupted/derailed how EHRs evolved.

METHODS

Literature search based on "Electronic Health Record", "Medical Record", and "Medical Chart" using Medline, Google, Wikipedia Medical, and Cochrane Libraries resulted in an initial review of 2,356 abstracts and other information in papers and books. Additional papers and books were identified through the review of references cited in the initial review.

RESULTS

By 1992, hardware had become more affordable, powerful, and compact and the use of personal computers, local area networks, and the Internet provided faster and easier access to medical information. EHRs were initially developed and used at academic medical facilities but since most have been replaced by large vendor EHRs. While EHR use has increased and clinicians are being prepared to practice in an EHR-mediated world, technical issues have been overshadowed by procedural, professional, social, political, and especially ethical issues as well as the need for compliance with standards and information security. There have been enormous advancements that have taken place, but many of the early expectations for EHRs have not been realized and current EHRs still do not meet the needs of today's rapidly changing healthcare environment.

CONCLUSION

The current use of EHRs initiated by new technology would have been hard to foresee. Current and new EHR technology will help to provide international standards for interoperable applications that use health, social, economic, behavioral, and environmental data to communicate, interpret, and act intelligently upon complex healthcare information to foster precision medicine and a learning health system.

Evaluating topic model interpretability from a primary care physician perspective

BACKGROUND AND OBJECTIVE

Probabilistic topic models provide an unsupervised method for analyzing unstructured text. These models discover semantically coherent combinations of words (topics) that could be integrated in a clinical automatic summarization system for primary care physicians performing chart review. However, the human interpretability of topics discovered from clinical reports is unknown. Our objective is to assess the coherence of topics and their ability to represent the contents of clinical reports from a primary care physician's point of view.

METHODS

Three latent Dirichlet allocation models (50 topics, 100 topics, and 150 topics) were fit to a large collection of clinical reports. Topics were manually evaluated by primary care physicians and graduate students. Wilcoxon Signed-Rank Tests for Paired Samples were used to evaluate differences between different topic models, while differences in performance between students and primary care physicians (PCPs) were tested using Mann-Whitney U tests for each of the tasks.

RESULTS

While the 150-topic model produced the best log likelihood, participants were most accurate at identifying words that did not belong in topics learned by the 100-topic model, suggesting that 100 topics provides better relative granularity of discovered semantic themes for the data set used in this study. Models were comparable in their ability to represent the contents of documents. Primary care physicians significantly outperformed students in both tasks.

CONCLUSION

This work establishes a baseline of interpretability for topic models trained with clinical reports, and provides insights on the appropriateness of using topic models for informatics applications. Our results indicate that PCPs find discovered topics more coherent and representative of clinical reports relative to students, warranting further research into their use for automatic summarization.

Development and Preliminary Evaluation of a Prototype of a Learning Electronic Medical Record System

Electronic medical records (EMRs) are capturing increasing amounts of data per patient. For clinicians to efficiently and accurately understand a patient's clinical state, better ways are needed to determine when and how to display EMR data. We built a prototype system that records how physicians view EMR data, which we used to train models that predict which EMR data will be relevant in a given patient. We call this approach a Learning EMR (LEMR). A physician used the prototype to review 59 intensive care unit (ICU) patient cases. We used the data-access patterns from these cases to train logistic regression models that, when evaluated, had AUROC values as high as 0.92 and that averaged 0.73, supporting that the approach is promising. A preliminary usability study identified advantages of the system and a few concerns about implementation. Overall, 3 of 4 ICU physicians were enthusiastic about features of the prototype.

Automated methods for the summarization of electronic health records

Objectives This review examines work on automated summarization of electronic health record (EHR) data and in particular, individual patient record summarization. We organize the published research and highlight methodological challenges in the area of EHR summarization implementation.

Target audience The target audience for this review includes researchers, designers, and informaticians who are concerned about the problem of information overload in the clinical setting as well as both users and developers of clinical summarization systems.

Scope Automated summarization has been a long-studied subject in the fields of natural language processing and human–computer interaction, but the translation of summarization and visualization methods to the complexity of the clinical workflow is slow moving. We assess work in aggregating and visualizing patient information with a particular focus on methods for detecting and removing redundancy, describing temporality, determining salience, accounting for missing data, and taking advantage of encoded clinical knowledge. We identify and discuss open challenges critical to the implementation and use of robust EHR summarization systems.

Clinical information modeling processes for semantic interoperability of electronic health records: systematic review and inductive analysis

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.

Content-based image retrieval for brain MRI: an image-searching engine and population-based analysis to utilize past clinical data for future diagnosis

Radiological diagnosis is based on subjective judgment by radiologists. The reasoning behind this process is difficult to document and share, which is a major obstacle in adopting evidence-based medicine in radiology. We report our attempt to use a comprehensive brain parcellation tool to systematically capture image features and use them to record, search, and evaluate anatomical phenotypes. Anatomical images (T1-weighted MRI) were converted to a standardized index by using a high-dimensional image transformation method followed by atlas-based parcellation of the entire brain. We investigated how the indexed anatomical data captured the anatomical features of healthy controls and a population with Primary Progressive Aphasia (PPA). PPA was chosen because patients have apparent atrophy at different degrees and locations, thus the automated quantitative results can be compared with trained clinicians' qualitative evaluations. We explored and tested the power of individual classifications and of performing a search for images with similar anatomical features in a database using partial least squares-discriminant analysis (PLS-DA) and principal component analysis (PCA). The agreement between the automated z-score and the averaged visual scores for atrophy (r = 0.8) was virtually the same as the inter-evaluator agreement. The PCA plot distribution correlated with the anatomical phenotypes and the PLS-DA resulted in a model with an accuracy of 88% for distinguishing PPA variants. The quantitative indices captured the main anatomical features. The indexing of image data has a potential to be an effective, comprehensive, and easily translatable tool for clinical practice, providing new opportunities to mine clinical databases for medical decision support.

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Brain parcellation tools define structures automatically and convert images into standardized and quantitative matrices.

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We tested if an automated tool and the resultant vector of structural volumes can accurately capture anatomical phenotypes.

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The agreement between visual and automated atrophy detection was virtually the same as the inter-evaluator agreement.

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The quantitative indices captured the main anatomical features in brains with atrophy in different degrees and location.

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The image quantification has potential to be an effective, comprehensive, and easily translatable tool for clinical practice.

A natural language processing pipeline for pairing measurements uniquely across free-text CT reports

OBJECTIVE

To standardize and objectivize treatment response assessment in oncology, guidelines have been proposed that are driven by radiological measurements, which are typically communicated in free-text reports defying automated processing. We study through inter-annotator agreement and natural language processing (NLP) algorithm development the task of pairing measurements that quantify the same finding across consecutive radiology reports, such that each measurement is paired with at most one other ("partial uniqueness").

METHODS AND MATERIALS

Ground truth is created based on 283 abdomen and 311 chest CT reports of 50 patients each. A pre-processing engine segments reports and extracts measurements. Thirteen features are developed based on volumetric similarity between measurements, semantic similarity between their respective narrative contexts and structural properties of their report positions. A Random Forest classifier (RF) integrates all features. A "mutual best match" (MBM) post-processor ensures partial uniqueness.

RESULTS

In an end-to-end evaluation, RF has precision 0.841, recall 0.807, F-measure 0.824 and AUC 0.971; with MBM, which performs above chance level (P<0.001), it has precision 0.899, recall 0.776, F-measure 0.833 and AUC 0.935. RF (RF+MBM) has error-free performance on 52.7% (57.4%) of report pairs.

DISCUSSION

Inter-annotator agreement of three domain specialists with the ground truth (κ>0.960) indicates that the task is well defined. Domain properties and inter-section differences are discussed to explain superior performance in abdomen. Enforcing partial uniqueness has mixed but minor effects on performance.

CONCLUSION

A combined machine learning-filtering approach is proposed for pairing measurements, which can support prospective (supporting treatment response assessment) and retrospective purposes (data mining).

Use of expert relevancy ratings to validate task-specific search strategies for electronic medical records

As electronic medical records (EMRs) grow in size and complexity, there is increasing need for automated EMR tools that highlight the medical record items most germane to a practitioner's task-specific needs. The development of such tools would be aided by gold standards of information relevance for a series of different clinical scenarios. We have previously proposed a process in which exemplar medical record data are extracted from actual patients' EMRs, anonymized, and presented to clinical experts, who then score each medical record item for its relevance to a specific clinical scenario. In this paper, we present how that body of expert relevancy data can be used to create a test framework to validate new EMR search strategies.

A software system to collect expert relevance ratings of medical record items for specific clinical tasks

Development of task-specific electronic medical record (EMR) searches and user interfaces has the potential to improve the efficiency and safety of health care while curbing rising costs. The development of such tools must be data-driven and guided by a strong understanding of practitioner information requirements with respect to specific clinical tasks or scenarios. To acquire this important data, this paper describes a model by which expert practitioners are leveraged to identify which components of the medical record are most relevant to a specific clinical task. We also describe the computer system that was created to efficiently implement this model of data gathering. The system extracts medical record data from the EMR of patients matching a given clinical scenario, de-identifies the data, breaks the data up into separate medical record items (eg, radiology reports, operative notes, laboratory results, etc), presents each individual medical record item to experts under the hypothetical of the given clinical scenario, and records the experts’ ratings regarding the relevance of each medical record item to that specific clinical scenario or task. After an iterative process of data collection, these expert relevance ratings can then be pooled and used to design point-of-care EMR searches and user interfaces tailored to the task-specific needs of practitioners.

Data processing and presentation for a personalised, image-driven medical graphical avatar

With the continuing digital revolution in the healthcare industry, patients are being confronted with the difficult task of managing their digital medical data. Current personal health record (PHR) systems are able to store and consolidate this data, but they are limited in providing tools to facilitate patients' understanding and management of the data. One reason for this stems from the limited use of contextual information, especially in presenting spatial details such as in volumetric images and videos, as well as time-based temporal data. Further, lack of meaningful visualisation techniques exist to represent the data stored in PHRs. In this paper we propose a medical graphical avatar (MGA) constructed from whole-body patient images, and a navigable timeline of the patient's medical records. A data mapping framework is presented that extracts information from medical multimedia data such as images, video and text, to populate our PHR timeline, while also embedding spatial and textual annotations such as regions of interest (ROIs) that are automatically derived from image processing algorithms. We developed a prototype to process the various forms of PHR data and present the data in a graphical avatar. We analysed the usefulness of our system under various scenarios of patient data use and present preliminary results that indicate that our system performs well on standard consumer hardware.

Automated before-procedure electronic health record screening to assess appropriateness for GI endoscopy and sedation

BACKGROUND

Endoscopists are performing greater numbers of procedures, often on patients with complex conditions, in ambulatory settings because of changing patient demographics and referral patterns. To assist with the pre-procedure assessment of such patients, we deployed an advanced electronic health record tool, the Queriable Patient Inference Dossier (QPID), to review clinical histories and generate e-mail alerts to providers, based on clinical guidelines.

OBJECTIVE

Study the feasibility of an automated pre-procedure alert system for outpatient endoscopy.

DESIGN

We retrospectively reviewed 5 physicians' use of the application and their responses to the alerts.

SETTING

A hospital-based endoscopy unit and its two satellite outpatient clinics, Boston area, Massachusetts.

PATIENTS

Adult outpatients referred for endoscopy with moderate sedation.

INTERVENTION

Pre-procedure alerts automatically sent 7 days before the procedure, highlighting any conditions/clinical history that may affect management of the patient.

MAIN OUTCOME MEASUREMENTS

Physician use of the pre-procedure alert system and its effect on patient management.

RESULTS

We studied 1682 procedures that met inclusion criteria for review by QPID and 364 alerts (1.6% of the eligible procedures). Nearly 80% of the alerts were reviewed and responded to by the physicians, and 70 total alerts resulted in a change in patient management (4.2% of eligible procedures).

LIMITATIONS

The small size of the study group and the low rate of adverse events during the study period limit our findings. We thus plan to conduct a larger follow-up study to demonstrate changes in safety and efficiency.

CONCLUSION

Use of advanced electronic health record technologies, such as QPID, may improve provider efficiency and patient outcomes in endoscopy units.