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Journal of the American Medical Informatics Association: JAMIA

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https://www.readbyqxmd.com/read/29346583/datamed-an-open-source-discovery-index-for-finding-biomedical-datasets
#1
Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu
Objective: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium...
January 13, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29329456/designing-and-evaluating-an-automated-system-for-real-time-medication-administration-error-detection-in-a-neonatal-intensive-care-unit
#2
Yizhao Ni, Todd Lingren, Eric S Hall, Matthew Leonard, Kristin Melton, Eric S Kirkendall
Background: Timely identification of medication administration errors (MAEs) promises great benefits for mitigating medication errors and associated harm. Despite previous efforts utilizing computerized methods to monitor medication errors, sustaining effective and accurate detection of MAEs remains challenging. In this study, we developed a real-time MAE detection system and evaluated its performance prior to system integration into institutional workflows. Methods: Our prospective observational study included automated MAE detection of 10 high-risk medications and fluids for patients admitted to the neonatal intensive care unit at Cincinnati Children's Hospital Medical Center during a 4-month period...
January 10, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29329435/expanding-a-radiology-lexicon-using-contextual-patterns-in-radiology-reports
#3
Bethany Percha, Yuhao Zhang, Selen Bozkurt, Daniel Rubin, Russ B Altman, Curtis P Langlotz
Objective: Distributional semantics algorithms, which learn vector space representations of words and phrases from large corpora, identify related terms based on contextual usage patterns. We hypothesize that distributional semantics can speed up lexicon expansion in a clinical domain, radiology, by unearthing synonyms from the corpus. Materials and Methods: We apply word2vec, a distributional semantics software package, to the text of radiology notes to identify synonyms for RadLex, a structured lexicon of radiology terms...
January 10, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29329402/discovering-foodborne-illness-in-online-restaurant-reviews
#4
Thomas Effland, Anna Lawson, Sharon Balter, Katelynn Devinney, Vasudha Reddy, HaeNa Waechter, Luis Gravano, Daniel Hsu
Objective: We developed a system for the discovery of foodborne illness mentioned in online Yelp restaurant reviews using text classification. The system is used by the New York City Department of Health and Mental Hygiene (DOHMH) to monitor Yelp for foodborne illness complaints. Materials and Methods: We built classifiers for 2 tasks: (1) determining if a review indicated a person experiencing foodborne illness and (2) determining if a review indicated multiple people experiencing foodborne illness...
January 10, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29315417/interactive-or-static-reports-to-guide-clinical-interpretation-of-cancer-genomics
#5
Stacy W Gray, Jeffrey Gagan, Ethan Cerami, Angel M Cronin, Hajime Uno, Nelly Oliver, Carol Lowenstein, Ruth Lederman, Anna Revette, Aaron Suarez, Charlotte Lee, Jordan Bryan, Lynette Sholl, Eliezer M Van Allen
Objective: Misinterpretation of complex genomic data presents a major challenge in the implementation of precision oncology. We sought to determine whether interactive genomic reports with embedded clinician education and optimized data visualization improved genomic data interpretation. Materials and Methods: We conducted a randomized, vignette-based survey study to determine whether exposure to interactive reports for a somatic gene panel, as compared to static reports, improves physicians' genomic comprehension and report-related satisfaction (overall scores calculated across 3 vignettes, range 0-18 and 1-4, respectively, higher score corresponding with improved endpoints)...
January 5, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29300961/patient-portal-use-and-hospital-outcomes
#6
Adrian G Dumitrascu, M Caroline Burton, Nancy L Dawson, Colleen S Thomas, Lisa M Nordan, Hope E Greig, Duaa I Aljabri, James M Naessens
Objectives: To determine whether use of a patient portal during hospitalization is associated with improvement in hospital outcomes, 30-day readmissions, inpatient mortality, and 30-day mortality. Materials and Methods: We performed a retrospective propensity score-matched study that included all adult patients admitted to Mayo Clinic Hospital in Jacksonville, Florida, from August 1, 2012, to July 31, 2014, who had signed up for a patient portal account prior to hospitalization (N = 7538)...
December 28, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29272408/patient-preferences-toward-an-interactive-e-consent-application-for-research-using-electronic-health-records
#7
Christopher A Harle, Elizabeth H Golembiewski, Kiarash P Rahmanian, Janice L Krieger, Dorothy Hagmajer, Arch G Mainous Iii, Ray E Moseley
Objective: The purpose of this study was to assess patient perceptions of using an interactive electronic consent (e-consent) application when deciding whether or not to grant broad consent for research use of their identifiable electronic health record (EHR) information. Materials and Methods: For this qualitative study, we conducted a series of 42 think-aloud interviews with 32 adults. Interview transcripts were coded and analyzed using a modified grounded theory approach...
December 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29267964/biomedical-informatics-and-data-science-evolving-fields-with-significant-overlap
#8
Patricia Flatley Brennan, Michael F Chiang, Lucila Ohno-Machado
No abstract text is available yet for this article.
December 18, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29253166/corrigendum
#9
(no author information available yet)
No abstract text is available yet for this article.
December 15, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29253169/a-value-set-for-documenting-adverse-reactions-in-electronic-health-records
#10
Foster R Goss, Kenneth H Lai, Maxim Topaz, Warren W Acker, Leigh Kowalski, Joseph M Plasek, Kimberly G Blumenthal, Diane L Seger, Sarah P Slight, Kin Wah Fung, Frank Y Chang, David W Bates, Li Zhou
Objective: To develop a comprehensive value set for documenting and encoding adverse reactions in the allergy module of an electronic health record. Materials and Methods: We analyzed 2 471 004 adverse reactions stored in Partners Healthcare's Enterprise-wide Allergy Repository (PEAR) of 2.7 million patients. Using the Medical Text Extraction, Reasoning, and Mapping System, we processed both structured and free-text reaction entries and mapped them to Systematized Nomenclature of Medicine - Clinical Terms...
December 14, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29240930/britain-breathing-using-the-experience-sampling-method-to-collect-the-seasonal-allergy-symptoms-of-a-country
#11
Markel Vigo, Lamiece Hassan, William Vance, Caroline Jay, Andrew Brass, Sheena Cruickshank
Objective: Allergies are increasing, but the reasons for this are unclear. Although environmental factors are thought to be important, there is a lack of data on how they contribute to symptom development. To understand this relationship better, we need accurate data about both symptoms and environmental factors. Our objective here is to ascertain whether experience sampling is a reliable approach for collecting allergy symptom data in the general population, allowing us to map symptoms and understand etiology...
December 12, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29240899/patient-perceptions-of-receiving-test-results-via-online-portals-a-mixed-methods-study
#12
Traber D Giardina, Jessica Baldwin, Daniel T Nystrom, Dean F Sittig, Hardeep Singh
Objective: Online portals provide patients with access to their test results, but it is unknown how patients use these tools to manage results and what information is available to promote understanding. We conducted a mixed-methods study to explore patients' experiences and preferences when accessing their test results via portals. Materials and Methods: We conducted 95 interviews (13 semistructured and 82 structured) with adults who viewed a test result in their portal between April 2015 and September 2016 at 4 large outpatient clinics in Houston, Texas...
December 12, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29237028/response-to-letter-to-the-editor-regarding-online-physician-ratings-fail-to-predict-actual-performance-on-measures-of-quality-value-and-peer-review
#13
Timothy J Daskivich, Brennan Spiegel
No abstract text is available yet for this article.
December 11, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29237006/letter-to-the-editor-in-response-to-online-physician-ratings-fail-to-predict-actual-performance-on-measures-of-quality-value-and-peer-review
#14
Naomi S Bardach
No abstract text is available yet for this article.
December 11, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29228196/data-discovery-with-dats-exemplar-adoptions-and-lessons-learned
#15
Alejandra N Gonzalez-Beltran, John Campbell, Patrick Dunn, Diana Guijarro, Sanda Ionescu, Hyeoneui Kim, Jared Lyle, Jeffrey Wiser, Susanna-Assunta Sansone, Philippe Rocca-Serra
The DAta Tag Suite (DATS) is a model supporting dataset description, indexing, and discovery. It is available as an annotated serialization with schema.org, a vocabulary used by major search engines, thus making the datasets discoverable on the web. DATS underlies DataMed, the National Institutes of Health Big Data to Knowledge Data Discovery Index prototype, which aims to provide a "PubMed for datasets." The experience gained while indexing a heterogeneous range of >60 repositories in DataMed helped in evaluating DATS's entities, attributes, and scope...
December 8, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29206922/pie-a-prior-knowledge-guided-integrated-likelihood-estimation-method-for-bias-reduction-in-association-studies-using-electronic-health-records-data
#16
Jing Huang, Rui Duan, Rebecca A Hubbard, Yonghui Wu, Jason H Moore, Hua Xu, Yong Chen
Objectives: This study proposes a novel Prior knowledge guided Integrated likelihood Estimation (PIE) method to correct bias in estimations of associations due to misclassification of electronic health record (EHR)-derived binary phenotypes, and evaluates the performance of the proposed method by comparing it to 2 methods in common practice. Methods: We conducted simulation studies and data analysis of real EHR-derived data on diabetes from Kaiser Permanente Washington to compare the estimation bias of associations using the proposed method, the method ignoring phenotyping errors, the maximum likelihood method with misspecified sensitivity and specificity, and the maximum likelihood method with correctly specified sensitivity and specificity (gold standard)...
December 1, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29202205/3d-mice-integration-of-cross-sectional-and-longitudinal-imputation-for-multi-analyte-longitudinal-clinical-data
#17
Yuan Luo, Peter Szolovits, Anand S Dighe, Jason M Baron
Objective: A key challenge in clinical data mining is that most clinical datasets contain missing data. Since many commonly used machine learning algorithms require complete datasets (no missing data), clinical analytic approaches often entail an imputation procedure to "fill in" missing data. However, although most clinical datasets contain a temporal component, most commonly used imputation methods do not adequately accommodate longitudinal time-based data. We sought to develop a new imputation algorithm, 3-dimensional multiple imputation with chained equations (3D-MICE), that can perform accurate imputation of missing clinical time series data...
November 30, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29202203/user-needs-analysis-and-usability-assessment-of-datamed-a-biomedical-data-discovery-index
#18
Ram Dixit, Deevakar Rogith, Vidya Narayana, Mandana Salimi, Anupama Gururaj, Lucila Ohno-Machado, Hua Xu, Todd R Johnson
Objective: To present user needs and usability evaluations of DataMed, a Data Discovery Index (DDI) that allows searching for biomedical data from multiple sources. Materials and Methods: We conducted 2 phases of user studies. Phase 1 was a user needs analysis conducted before the development of DataMed, consisting of interviews with researchers. Phase 2 involved iterative usability evaluations of DataMed prototypes. We analyzed data qualitatively to document researchers' information and user interface needs...
November 30, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29202188/estimating-the-causal-effects-of-chronic-disease-combinations-on-30-day-hospital-readmissions-based-on-observational-medicaid-data
#19
Sabrina Casucci, Li Lin, Sharon Hewner, Alexander Nikolaev
Objective: Demonstrate how observational causal inference methods can generate insights into the impact of chronic disease combinations on patients' 30-day hospital readmissions. Materials and Methods: Causal effect estimation was used to quantify the impact of each risk factor scenario (ie, chronic disease combination) associated with chronic kidney disease and heart failure (HF) for adult Medicaid beneficiaries with initial hospitalizations in 2 New York State counties...
November 30, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29202185/clinical-documentation-variations-and-nlp-system-portability-a-case-study-in-asthma-birth-cohorts-across-institutions
#20
Sunghwan Sohn, Yanshan Wang, Chung-Il Wi, Elizabeth A Krusemark, Euijung Ryu, Mir H Ali, Young J Juhn, Hongfang Liu
Objective: To assess clinical documentation variations across health care institutions using different electronic medical record systems and investigate how they affect natural language processing (NLP) system portability. Materials and Methods: Birth cohorts from Mayo Clinic and Sanford Children's Hospital (SCH) were used in this study (n = 298 for each). Documentation variations regarding asthma between the 2 cohorts were examined in various aspects: (1) overall corpus at the word level (ie, lexical variation), (2) topics and asthma-related concepts (ie, semantic variation), and (3) clinical note types (ie, process variation)...
November 30, 2017: Journal of the American Medical Informatics Association: JAMIA
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