Electronic Health Records Narratives Research Articles

Linking Electronic Health Records and In-Depth Interviews to Inform Efforts to Integrate Social Determinants of Health Into Health Care Delivery: Protocol for a Qualitative Research Study.

BackgroundHealth systems are attempting to capture social determinants of health (SDoH) in electronic health records (EHR) and use these data to adjust care plans. To date, however, methods for identifying social needs, which are the SDoH prioritized by patients, have been underexplored, and there is little guidance as to how clinicians should act on SDoH data when caring for patients. Moreover, the unintended consequences of collecting and responding to SDoH are poorly understood.ObjectiveThe objective of this study is to use two data sources, EHR data and patient interviews, to describe divergences between the EHR and patient experiences that could help identify gaps in the documentation of SDoH in the EHR; highlight potential missed opportunities for addressing social needs, and identify unintended consequences of efforts to integrate SDoH into clinical care.MethodsWe are conducting a qualitative study that merges discrete and free-text data from EHRs with in-depth interviews with women residing in rural, socioeconomically deprived communities in the Mid-Atlantic region of the United States. Participants had to confirm that they had at least one visit with the large health system that serves the region. Interviews with the women included questions regarding health, interaction with the health system, and social needs. Next, with consent, we extracted discrete data (eg, diagnoses and medication orders) for each participant and free-text clinician notes from this health system’s EHRs between 1996 and the year of the interview. We used a standardized protocol to create an EHR narrative, a free-text summary of the EHR data. We used NVivo to identify themes in the interviews and the EHR narratives.ResultsTo date, we have interviewed 88 women, including 51 White women, 19 Black women, 14 Latina women, 2 mixed Black and Latina women, and 2 Asian Pacific women. We have completed the EHR narratives on 66 women. The women range in age from 18 to 90 years. We found corresponding EHR data on all but 4 of the interview participants. Participants had contact with a wide range of clinical departments (eg, psychiatry, neurology, and infectious disease) and received care in various clinical settings (eg, primary care clinics, emergency departments, and inpatient hospitalizations). A preliminary review of the EHR narratives revealed that the clinician notes were a source of data on a range of SDoH but did not always reflect the social needs that participants described in the interviews.ConclusionsThis study will provide unique insight into the demands and consequences of integrating SDoH into clinical care. This work comes at a pivotal point in time, as health systems, payors, and policymakers accelerate attempts to deliver care within the context of social needs.International Registered Report Identifier (IRRID)DERR1-10.2196/36201

Rich Text Formatted EHR Narratives: A Hidden and Ignored Trove.

This study presents an approach for mining structured information from clinical narratives in Electronic Health Records (EHRs) by using Rich Text Formatted (RTF) records. RTF is adopted by many medical information management systems. There is rich structural information in these files which can be extracted and interpreted, yet such information is largely ignored. We investigate multiple types of EHR narratives in the Enterprise Data Warehouse from a multisite large healthcare chain consisting of both, an academic medical center and community hospitals. We focus on the RTF constructs related to tables and sections that are not available in plain text EHR narratives. We show how to parse these RTF constructs, analyze their prevalence and characteristics in the context of multiple types of EHR narratives. Our case study demonstrates the additional utility of the features derived from RTF constructs over plain text oriented NLP.

Current approaches to identify sections within clinical narratives from electronic health records: a systematic review

BackgroundThe identification of sections in narrative content of Electronic Health Records (EHR) has demonstrated to improve the performance of clinical extraction tasks; however, there is not yet a shared understanding of the concept and its existing methods. The objective is to report the results of a systematic review concerning approaches aimed at identifying sections in narrative content of EHR, using both automatic or semi-automatic methods.MethodsThis review includes articles from the databases: SCOPUS, Web of Science and PubMed (from January 1994 to September 2018). The selection of studies was done using predefined eligibility criteria and applying the PRISMA recommendations. Search criteria were elaborated by using an iterative and collaborative keyword enrichment.ResultsFollowing the eligibility criteria, 39 studies were selected for analysis. The section identification approaches proposed by these studies vary greatly depending on the kind of narrative, the type of section, and the application. We observed that 57% of them proposed formal methods for identifying sections and 43% adapted a previously created method. Seventy-eight percent were intended for English texts and 41% for discharge summaries. Studies that are able to identify explicit (with headings) and implicit sections correspond to 46%. Regarding the level of granularity, 54% of the studies are able to identify sections, but not subsections. From the technical point of view, the methods can be classified into rule-based methods (59%), machine learning methods (22%) and a combination of both (19%). Hybrid methods showed better results than those relying on pure machine learning approaches, but lower than rule-based methods; however, their scope was more ambitious than the latter ones. Despite all the promising performance results, very few studies reported tests under a formal setup. Almost all the studies relied on custom dictionaries; however, they used them in conjunction with a controlled terminology, most commonly the UMLSⓇ metathesaurus.ConclusionsIdentification of sections in EHR narratives is gaining popularity for improving clinical extraction projects. This study enabled the community working on clinical NLP to gain a formal analysis of this task, including the most successful ways to perform it.

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.

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes

Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2× 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.

Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning.

BackgroundMedication and adverse drug event (ADE) information extracted from electronic health record (EHR) notes can be a rich resource for drug safety surveillance. Existing observational studies have mainly relied on structured EHR data to obtain ADE information; however, ADEs are often buried in the EHR narratives and not recorded in structured data.ObjectiveTo unlock ADE-related information from EHR narratives, there is a need to extract relevant entities and identify relations among them. In this study, we focus on relation identification. This study aimed to evaluate natural language processing and machine learning approaches using the expert-annotated medical entities and relations in the context of drug safety surveillance, and investigate how different learning approaches perform under different configurations.MethodsWe have manually annotated 791 EHR notes with 9 named entities (eg, medication, indication, severity, and ADEs) and 7 different types of relations (eg, medication-dosage, medication-ADE, and severity-ADE). Then, we explored 3 supervised machine learning systems for relation identification: (1) a support vector machines (SVM) system, (2) an end-to-end deep neural network system, and (3) a supervised descriptive rule induction baseline system. For the neural network system, we exploited the state-of-the-art recurrent neural network (RNN) and attention models. We report the performance by macro-averaged precision, recall, and F1-score across the relation types.ResultsOur results show that the SVM model achieved the best average F1-score of 89.1% on test data, outperforming the long short-term memory (LSTM) model with attention (F1-score of 65.72%) as well as the rule induction baseline system (F1-score of 7.47%) by a large margin. The bidirectional LSTM model with attention achieved the best performance among different RNN models. With the inclusion of additional features in the LSTM model, its performance can be boosted to an average F1-score of 77.35%.ConclusionsIt shows that classical learning models (SVM) remains advantageous over deep learning models (RNN variants) for clinical relation identification, especially for long-distance intersentential relations. However, RNNs demonstrate a great potential of significant improvement if more training data become available. Our work is an important step toward mining EHRs to improve the efficacy of drug safety surveillance. Most importantly, the annotated data used in this study will be made publicly available, which will further promote drug safety research in the community.

Assessing the Readability of Medical Documents: A Ranking Approach.

BackgroundThe use of electronic health record (EHR) systems with patient engagement capabilities, including viewing, downloading, and transmitting health information, has recently grown tremendously. However, using these resources to engage patients in managing their own health remains challenging due to the complex and technical nature of the EHR narratives.ObjectiveOur objective was to develop a machine learning–based system to assess readability levels of complex documents such as EHR notes.MethodsWe collected difficulty ratings of EHR notes and Wikipedia articles using crowdsourcing from 90 readers. We built a supervised model to assess readability based on relative orders of text difficulty using both surface text features and word embeddings. We evaluated system performance using the Kendall coefficient of concordance against human ratings.ResultsOur system achieved significantly higher concordance (.734) with human annotators than did a baseline using the Flesch-Kincaid Grade Level, a widely adopted readability formula (.531). The improvement was also consistent across different disease topics. This method’s concordance with an individual human user’s ratings was also higher than the concordance between different human annotators (.658).ConclusionsWe explored methods to automatically assess the readability levels of clinical narratives. Our ranking-based system using simple textual features and easy-to-learn word embeddings outperformed a widely used readability formula. Our ranking-based method can predict relative difficulties of medical documents. It is not constrained to a predefined set of readability levels, a common design in many machine learning–based systems. Furthermore, the feature set does not rely on complex processing of the documents. One potential application of our readability ranking is personalization, allowing patients to better accommodate their own background knowledge.

Assessing Provider-Generated Free-Text Quality in EHR-Integrated Handoff Notes.

Handoff notes are increasingly integrated within electronic health record (EHR) systems and often contain data automatically generated from the EHR and free-text narratives. We examined the quality of data entered by providers in the free-text portion of our institutional EHR handoff tool. Overall, 65% of handoff notes contained at least one error (average 1.7 errors per note). Most errors were omissions in information around patient plan/management or assessment/diagnosis rather than entry of false data. Factors associated with increased error rate were increasing hospital day number; weekend note; medical (vs. surgical) service team; and authorship by a medical student, first or fourth year resident physician, or attending physician. Our findings suggest that errors are common in handoff notes, and while these errors are not completely false data, they may provide individuals caring for patients an inaccurate understanding of patient status.

Design of an extensive information representation scheme for clinical narratives

BackgroundKnowledge representation frameworks are essential to the understanding of complex biomedical processes, and to the analysis of biomedical texts that describe them. Combined with natural language processing (NLP), they have the potential to contribute to retrospective studies by unlocking important phenotyping information contained in the narrative content of electronic health records (EHRs). This work aims to develop an extensive information representation scheme for clinical information contained in EHR narratives, and to support secondary use of EHR narrative data to answer clinical questions.MethodsWe review recent work that proposed information representation schemes and applied them to the analysis of clinical narratives. We then propose a unifying scheme that supports the extraction of information to address a large variety of clinical questions.ResultsWe devised a new information representation scheme for clinical narratives that comprises 13 entities, 11 attributes and 37 relations. The associated annotation guidelines can be used to consistently apply the scheme to clinical narratives and are https://cabernet.limsi.fr/annotation_guide_for_the_merlot_french_clinical_corpus-Sept2016.pdf.ConclusionThe information scheme includes many elements of the major schemes described in the clinical natural language processing literature, as well as a uniquely detailed set of relations.

Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review.

The goal of pharmacovigilance is to detect, monitor, characterize and prevent adverse drug events (ADEs) with pharmaceutical products. This article is a comprehensive structured review of recent advances in applying natural language processing (NLP) to electronic health record (EHR) narratives for pharmacovigilance. We review methods of varying complexity and problem focus, summarize the current state-of-the-art in methodology advancement, discuss limitations and point out several promising future directions. The ability to accurately capture both semantic and syntactic structures in clinical narratives becomes increasingly critical to enable efficient and accurate ADE detection. Significant progress has been made in algorithm development and resource construction since 2000. Since 2012, statistical analysis and machine learning methods have gained traction in automation of ADE mining from EHR narratives. Current state-of-the-art methods for NLP-based ADE detection from EHRs show promise regarding their integration into production pharmacovigilance systems. In addition, integrating multifaceted, heterogeneous data sources has shown promise in improving ADE detection and has become increasingly adopted. On the other hand, challenges and opportunities remain across the frontier of NLP application to EHR-based pharmacovigilance, including proper characterization of ADE context, differentiation between off- and on-label drug-use ADEs, recognition of the importance of polypharmacy-induced ADEs, better integration of heterogeneous data sources, creation of shared corpora, and organization of shared-task challenges to advance the state-of-the-art.

Structured prediction models for RNN based sequence labeling in clinical text.

Sequence labeling is a widely used method for named entity recognition and information extraction from unstructured natural language data. In clinical domain one major application of sequence labeling involves extraction of medical entities such as medication, indication, and side-effects from Electronic Health Record narratives. Sequence labeling in this domain, presents its own set of challenges and objectives. In this work we experimented with various CRF based structured learning models with Recurrent Neural Networks. We extend the previously studied LSTM-CRF models with explicit modeling of pairwise potentials. We also propose an approximate version of skip-chain CRF inference with RNN potentials. We use these methodologies for structured prediction in order to improve the exact phrase detection of various medical entities.