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Mengyi Zhao, Songmao Zhang, Weizhuo Li, Guowei Chen
BACKGROUND: The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i...
March 19, 2018: Journal of Biomedical Semantics
Christiaan Vis, Mayke Mol, Annet Kleiboer, Leah Bührmann, Tracy Finch, Jan Smit, Heleen Riper
BACKGROUND: Electronic mental health interventions (eMental health or eMH) can be used to increase accessibility of mental health services for mood disorders, with indications of comparable clinical outcomes as face-to-face psychotherapy. However, the actual use of eMH in routine mental health care lags behind expectations. Identifying the factors that might promote or inhibit implementation of eMH in routine care may help to overcome this gap between effectiveness studies and routine care...
March 16, 2018: JMIR Mental Health
Manuel Corpas, Nadezda V Kovalevskaya, Amanda McMurray, Fiona G G Nielsen
It is generally acknowledged that, for reproducibility and progress of human genomic research, data sharing is critical. For every sharing transaction, a successful data exchange is produced between a data consumer and a data provider. Providers of human genomic data (e.g., publicly or privately funded repositories and data archives) fulfil their social contract with data donors when their shareable data conforms to FAIR (findable, accessible, interoperable, reusable) principles. Based on our experiences via Repositive (https://repositive...
March 2018: PLoS Computational Biology
Zaiyang Long, Donald J Tradup, Pengfei Song, Scott F Stekel, Shigao Chen, Katrina N Glazebrook, Nicholas J Hangiandreou
Because of the rapidly growing use of ultrasound shear wave elastography (SWE) in clinical practices, there is a significant need for development of clinical physics performance assessment methods for this technology. This study aims to report two clinical medical physicists' tasks: (a) acceptance testing (AT) of SWE function on ten commercial ultrasound systems for clinical liver application and (b) comparison of SWE measurements of targets across vendors for clinical musculoskeletal application. For AT, ten GE LOGIQ E9 XDclear 2...
March 15, 2018: Journal of Applied Clinical Medical Physics
Bonnie L Westra, Steven G Johnson, Samira Ali, Karen M Bavuso, Christopher A Cruz, Sarah Collins, Meg Furukawa, Mary L Hook, Anne LaFlamme, Kay Lytle, Lisiane Pruinelli, Tari Rajchel, Theresa Tess Settergren, Kathryn F Westman, Luann Whittenburg
BACKGROUND:  Secondary use of electronic health record (EHR) data can reduce costs of research and quality reporting. However, EHR data must be consistent within and across organizations. Flowsheet data provide a rich source of interprofessional data and represents a high volume of documentation; however, content is not standardized. Health care organizations design and implement customized content for different care areas creating duplicative data that is noncomparable. In a prior study, 10 information models (IMs) were derived from an EHR that included 2...
January 2018: Applied Clinical Informatics
Liz Potterton, Jon Agirre, Charles Ballard, Kevin Cowtan, Eleanor Dodson, Phil R Evans, Huw T Jenkins, Ronan Keegan, Eugene Krissinel, Kyle Stevenson, Andrey Lebedev, Stuart J McNicholas, Robert A Nicholls, Martin Noble, Navraj S Pannu, Christian Roth, George Sheldrick, Pavol Skubak, Johan Turkenburg, Ville Uski, Frank von Delft, David Waterman, Keith Wilson, Martyn Winn, Marcin Wojdyr
The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results...
February 1, 2018: Acta Crystallographica. Section D, Structural Biology
Louis Raymond, Guy Paré, Éric Maillet, Ana Ortiz de Guinea, Marie-Claude Trudel, Josianne Marsan
BACKGROUND: The accessibility of laboratory test results is crucial to the performance of emergency departments and to the safety of patients. This study aims to develop a better understanding of which laboratory information exchange (LIE) systems emergency care physicians (ECPs) are using to consult their patients' laboratory test results and which benefits they derive from such use. METHODS: A survey of 163 (36%) ECPs in Quebec was conducted in collaboration with the Quebec's Department of Health and Social Services...
March 12, 2018: International Journal of Emergency Medicine
Driss Berdaï, Florence Thomas-Delecourt, Karine Szwarcensztein
Early market access of health products is associated with a larger number of requests for information by the health authorities. Compared with these expectations, the growing expansion of health databases represents an opportunity for responding to questions raised by the authorities. The computerised nature of the health system provides numerous sources of data, and first and foremost medical/administrative databases such as the French National Inter-Scheme Health Insurance Information System (SNIIRAM) database...
December 30, 2017: Thérapie
Justin Wagner, Florin Chelaru, Jayaram Kancherla, Joseph N Paulson, Alexander Zhang, Victor Felix, Anup Mahurkar, Niklas Elmqvist, Héctor Corrada Bravo
Large studies profiling microbial communities and their association with healthy or disease phenotypes are now commonplace. Processed data from many of these studies are publicly available but significant effort is required for users to effectively organize, explore and integrate it, limiting the utility of these rich data resources. Effective integrative and interactive visual and statistical tools to analyze many metagenomic samples can greatly increase the value of these data for researchers. We present Metaviz, a tool for interactive exploratory data analysis of annotated microbiome taxonomic community profiles derived from marker gene or whole metagenome shotgun sequencing...
February 26, 2018: Nucleic Acids Research
David W Bates, Lipika Samal
No abstract text is available yet for this article.
March 11, 2018: Health Services Research
Brett G Olivier, Frank T Bergmann
Constraint-based modeling is a well established modeling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size and complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, flux balance analysis (FBA). The Flux balance constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modeling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing...
March 9, 2018: Journal of Integrative Bioinformatics
Wendelin Schramm
The way diabetes patients cope with their disease in day-to-day routines is decisive for the development or the prevention of medical complications. Smartphones have created the ubiquitous environment to support health care with mobile applications (mHealth). This article comments on the publication by Offringa et al in JDST, which is one of few studies that tries to isolate the effects of a diabetes app. At the same time, it is a good example to discuss general aspects of mHealth in diabetes care. Treatment context, eHealth literacy, interoperability, and efficiency will determine the success of diabetes apps...
March 1, 2018: Journal of Diabetes Science and Technology
Sungkee Lee, Hyoungho Do
Objectives: Increasing use of medical devices outside of healthcare facilities inevitably requires connectivity and interoperability between medical devices and healthcare information systems. To this end, standards have been developed and used to provide interoperability between personal health devices (PHDs) and external systems. ISO/IEEE 11073 standards and IHE PCD-01 standard messages have been used the most in the exchange of observation data of health devices. Recently, transmitting observation data using the HL7 FHIR standard has been devised in the name of DoF (Devices on FHIR) and adopted very fast...
January 2018: Healthcare Informatics Research
Farkhondeh Asadi, Somayeh Paydar
OBJECTIVE: Trauma is a major cause of 10% death in the worldwide and is considered as a global concern. This problem has made healthcare policy makers and managers to adopt a basic strategy in this context. Trauma registry has an important and basic role in decreasing the mortality and the disabilities due to injuries resulted from trauma. Today, different software are designed for trauma registry. Evaluation of this software improves management, increases efficiency and effectiveness of these systems...
April 2018: International Journal of Medical Informatics
Agustín Zaballos, Joan Navarro, Ramon Martín De Pozuelo
Information and communication technologies (ICTs) have enabled the evolution of traditional electric power distribution networks towards a new paradigm referred to as the smart grid. However, the different elements that compose the ICT plane of a smart grid are usually conceived as isolated systems that typically result in rigid hardware architectures, which are hard to interoperate, manage and adapt to new situations. In the recent years, software-defined systems that take advantage of software and high-speed data network infrastructures have emerged as a promising alternative to classic ad hoc approaches in terms of integration, automation, real-time reconfiguration and resource reusability...
February 28, 2018: Sensors
Cristina Soguero-Ruiz, Inmaculada Mora-Jiménez, Javier Ramos-López, Teresa Quintanilla Fernández, Antonio García-García, Daniel Díez-Mazuela, Arcadi García-Alberola, José Luis Rojo-Álvarez
Many indices have been proposed for cardiovascular risk stratification from electrocardiogram signal processing, still with limited use in clinical practice. We created a system integrating the clinical definition of cardiac risk subdomains from ECGs and the use of diverse signal processing techniques. Three subdomains were defined from the joint analysis of the technical and clinical viewpoints. One subdomain was devoted to demographic and clinical data. The other two subdomains were intended to obtain widely defined risk indices from ECG monitoring: a simple-domain (heart rate turbulence (HRT)), and a complex-domain (heart rate variability (HRV))...
March 1, 2018: International Journal of Environmental Research and Public Health
Denis Torre, Patrycja Krawczuk, Kathleen M Jagodnik, Alexander Lachmann, Zichen Wang, Lily Wang, Maxim V Kuleshov, Avi Ma'ayan
Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated 'canned' analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets...
February 27, 2018: Scientific Data
Susanna-Assunta Sansone, Patricia Cruse, Mark Thorley
Resources for data management, discovery and (re)use are numerous and diverse, and more specifically we need data resources that enable the FAIR principles1 of Findability, Accessibility, Interoperability and Reusability of data.
February 27, 2018: Scientific Data
Tracy A Kugler, Catherine A Fitch
The first version of the Integrated Public Use Microdata Series (IPUMS) was released to users in 1993, and since that time IPUMS has come to stand for interoperable and accessible census and survey data. Initially created to harmonize U.S. census microdata over time, IPUMS now includes microdata from the U.S. and international censuses and from surveys on health, employment, and other topics. IPUMS also provides geo-spatial data, aggregate population data, and environmental data. IPUMS supports ten data products, each disseminating an integrated data collection with a set of tools that make complex data easy to find, access, and use...
February 27, 2018: Scientific Data
Michael W Lawlor, Susan T Iannaccone, Katherine Mathews, Francesco Muntoni, Sherita Alai-Hansen, Joanne C Odenkirchen, Robin S Feldman
BACKGROUND: A Congenital Muscular Dystrophy (CMD) Working Group (WG) consisting of international experts reviewed common data elements (CDEs) previously developed for other neuromuscular diseases (NMDs) and made recommendations for all types of studies on CMD. OBJECTIVES: To develop a comprehensive set of CDEs, data definitions, case report forms and guidelines for use in CMD clinical research to facilitate interoperability of data collection, as part of the CDE project at the National Institute of Neurological Disorders and Stroke (NINDS)...
2018: Journal of Neuromuscular Diseases
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