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Václav Papež, Roman Mouček
PURPOSE: The purpose of this study is to investigate the feasibility of applying openEHR (an archetype-based approach for electronic health records representation) to modeling data stored in EEGBase, a portal for experimental electroencephalography/event-related potential (EEG/ERP) data management. The study evaluates re-usage of existing openEHR archetypes and proposes a set of new archetypes together with the openEHR templates covering the domain. The main goals of the study are to (i) link existing EEGBase data/metadata and openEHR archetype structures and (ii) propose a new openEHR archetype set describing the EEG/ERP domain since this set of archetypes currently does not exist in public repositories...
2017: Frontiers in Neuroinformatics
Catalina Martinez-Costa, Stefan Schulz
"A solid ontology-based analysis with a rigorous formal mapping for correctness" is one of the ten reasons why the HL7 standard Fast Healthcare Interoperability Resources (FHIR) is advertised to be better than other standards for EHR interoperability. In this paper, we aim at contributing to this formal analysis by proposing an RDF representation of a subset of FHIR resources based on a highly constrained top-level ontology and guided by the use of a set of Content Ontology Design Patterns (Content ODPs) for representing clinical information...
2017: Studies in Health Technology and Informatics
María Del Carmen Legaz-García, Kathrin Dentler, Jesualdo Tomás Fernández-Breis, Ronald Cornet
ArchMS is a framework that represents clinical information and knowledge using ontologies in OWL, which facilitates semantic interoperability and thereby the exploitation and secondary use of clinical data. However, it does not yet support the automated assessment of quality of care. CLIF is a stepwise method to formalize quality indicators. The method has been implemented in the CLIF tool which supports its users in generating computable queries based on a patient data model which can be based on archetypes...
2017: Studies in Health Technology and Informatics
Bernd Blobel
Advanced health and social services paradigms are supported by a comprehensive set of domains managed by different scientific disciplines. Interoperability has to evolve beyond information and communication technology (ICT) concerns, including the real world business domains and their processes, but also the individual context of all actors involved. So, the system must properly reflect the environment in front and around the computer as essential and even defining part of the health system. This paper introduces an ICT-independent system-theoretical, ontology-driven reference architecture model allowing the representation and harmonization of all domains involved including the transformation into an appropriate ICT design and implementation...
2017: Studies in Health Technology and Informatics
Samhar Mahmoud, Andy Boyd, Vasa Curcin, Richard Bache, Asad Ali, Simon Miles, Adel Taweel, Brendan Delaney, John Macleod
Data about patients are available from diverse sources, including those routinely collected as individuals interact with service providers, and those provided directly by individuals through surveys. Linking these data can lead to a more complete picture about the individual, to inform either care decision making or research investigations. However, post-linkage, differences in data recording systems and formats present barriers to achieving these aims. This paper describes an approach to combine linked GP records with study observations, and reports initial challenges related to semantic and syntactic interoperability issues...
2017: Studies in Health Technology and Informatics
Cristina Suárez-Mejías, Alicia Martínez-García, María Ángeles Martínez-Maestre, José Manuel Silvan-Alfaro, Jesús Moreno Conde, Carlos Luis Parra-Calderón
Clinical evidence demonstrates that BRCA 1 and BRCA2 mutations can develop a gynecological cancer but genetic testing has a high cost to the healthcare system. Besides, several studies in the literature indicate that performing these genetic tests to the population is not cost-efficient. Currently, our physicians do not have a system to provide them the support for prescribing genetic tests. A Decision Support System for prescribing these genetic tests in BRCA1 and BRCA2 and preventing gynecological cancer risks has been designed, developed and deployed in the Virgen del Rocío University Hospital (VRUH)...
2017: Studies in Health Technology and Informatics
Adie Blanchard, Laura Gilbert, Tom Dawson
As a result of increasing demand in the face of reducing resources, technology has been implemented in many social and health care services to improve service efficiency. This paper outlines the experiences of deploying a 'Software as a Service' application in the UK social and health care sectors. The case studies demonstrate that every implementation is different, and unique to each organisation. Technology design and integration can be facilitated by ongoing engagement and collaboration with all stakeholders, flexible design, and attention to interoperability to suit services and their workflows...
2017: Studies in Health Technology and Informatics
Jorge Miguel Silva, Tiago Marques Godinho, David Silva, Carlos Costa
The DICOM Standard has been fundamental for ensuring the interoperability of Picture Archive and Communications Systems (PACS). By compiling rigorously to the standard, medical imaging equipment and applications from different vendors can share their data, and create integrated workflows which contributes to better quality healthcare services. However, DICOM is a complex, flexible and very extensive standard. Thus, it is difficult to attest the conformity of data structures produced by DICOM applications resulting in unexpected behaviors, errors and malfunctions...
2017: Studies in Health Technology and Informatics
Archana Tapuria, Matt Evans, Vasa Curcin, Tony Austin, Nathan Lea, Dipak Kalra
INTRODUCTION: The aim of the paper is to establish the requirements and methodology for the development process of GreyMatters, a memory clinic system, outlining the conceptual, practical, technical and ethical challenges, and the experiences of capturing clinical and research oriented data along with the implementation of the system. METHODS: The methodology for development of the information system involved phases of requirements gathering, modeling and prototype creation, and 'bench testing' the prototype with experts...
2017: Studies in Health Technology and Informatics
Mie Vestergaard Andersen, Ida Hvass Kristensen, Malene Møller Larsen, Claus Hougaard Pedersen, Kirstine Rosenbeck Gøeg, Louise B Pape-Haugaard
Achieving interoperability in health is a challenge and requires standardization. The newly developed HL7 standard: Fast Healthcare Interoperability Resources (FHIR) promises both flexibility and interoperability. This study investigates the feasibility of expressing a Danish microbiology message model content in FHIR to explore whether complex in-use legacy models can be migrated and what challenges this may pose. The Danish microbiology message model (the DMM) is used as a case to illustrate challenges and opportunities accosted with applying the FHIR standard...
2017: Studies in Health Technology and Informatics
Damien M O'Halloran
BACKGROUND: Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. RESULTS: To address this problem, I have developed, phylo-node, which was developed using Node...
2017: PloS One
Michael Halle, Valentin Demeusy, Ron Kikinis
The Open Anatomy Browser (OABrowser) is an open source, web-based, zero-installation anatomy atlas viewer based on current web browser technologies and evolving anatomy atlas interoperability standards. OABrowser displays three-dimensional anatomical models, image cross-sections of labeled structures and source radiological imaging, and a text-based hierarchy of structures. The viewer includes novel collaborative tools: users can save bookmarks of atlas views for later access and exchange those bookmarks with other users, and dynamic shared views allow groups of users can participate in a collaborative interactive atlas viewing session...
2017: Frontiers in Neuroinformatics
César Domínguez, Jónathan Heras, Vico Pascual
BACKGROUND AND OBJECTIVE: The effective processing of biomedical images usually requires the interoperability of diverse software tools that have different aims but are complementary. The goal of this work is to develop a bridge to connect two of those tools: ImageJ, a program for image analysis in life sciences, and OpenCV, a computer vision and machine learning library. METHODS: Based on a thorough analysis of ImageJ and OpenCV, we detected the features of these systems that could be enhanced, and developed a library to combine both tools, taking advantage of the strengths of each system...
April 1, 2017: Computers in Biology and Medicine
Ekaterina Brocke, Mikael Djurfeldt, Upinder S Bhalla, Jeanette Hellgren Kotaleski, Michael Hanke
Multiscale modeling by means of co-simulation is a powerful tool to address many vital questions in neuroscience. It can for example be applied in the study of the process of learning and memory formation in the brain. At the same time the co-simulation technique makes it possible to take advantage of interoperability between existing tools and multi-physics models as well as distributed computing. However, the theoretical basis for multiscale modeling is not sufficiently understood. There is, for example, a need of efficient and accurate numerical methods for time integration...
April 7, 2017: Journal of Computational Neuroscience
Ahmed Abdelaziz, Ang Tan Fong, Abdullah Gani, Usman Garba, Suleman Khan, Adnan Akhunzada, Hamid Talebian, Kim-Kwang Raymond Choo
Software Defined Networking (SDN) is an emerging promising paradigm for network management because of its centralized network intelligence. However, the centralized control architecture of the software-defined networks (SDNs) brings novel challenges of reliability, scalability, fault tolerance and interoperability. In this paper, we proposed a novel clustered distributed controller architecture in the real setting of SDNs. The distributed cluster implementation comprises of multiple popular SDN controllers...
2017: PloS One
Dov Greenbaum, Joel Rozowsky, Victoria Stodden, Mark Gerstein
Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable, and reusable (i.e., "FAIR"). Moreover, properly off-loading to them the data and detail in a paper could make the main text more readable. We propose a hierarchical organization for supplements, with some parts paralleling and "shadowing" the main text and other elements branching off from it, and we suggest a specific formatting to make this structure explicit...
April 5, 2017: Genome Biology
Adam Culbertson, Satyender Goel, Margaret B Madden, Niloufar Safaeinili, Kathryn L Jackson, Thomas Carton, Russ Waitman, Mei Liu, Ashok Krishnamurthy, Lauren Hall, Nickie Cappella, Shyam Visweswaran, Michael J Becich, Reuben Applegate, Elmer Bernstam, Russell Rothman, Michael Matheny, Gloria Lipori, Jiang Bian, William Hogan, Douglas Bell, Andrew Martin, Shaun Grannis, Jeff Klann, Rebecca Sutphen, Amy B O'Hara, Abel Kho
BACKGROUND: Patient matching is a key barrier to achieving interoperability. Patient demographic elements must be consistently collected over time and region to be valuable elements for patient matching. OBJECTIVES: We sought to determine what patient demographic attributes are collected at multiple institutions in the United States and see how their availability changes over time and across clinical sites. METHODS: We compiled a list of 36 demographic elements that stakeholders previously identified as essential patient demographic attributes that should be collected for the purpose of linking patient records...
April 5, 2017: Applied Clinical Informatics
Jerry D VanVactor
This paper discusses the role of healthcare supply chain management in disaster mitigation and management. While there is an abundance of literature examining emergency management and disaster preparedness efforts across an array of industries, little information has been directed specifically toward the emergency interface, interoperability and unconventional relationships among civilian institutions and the US Department of Defense (US DoD) or supply chain operations involved therein. To address this imbalance, this paper provides US DoD healthcare supply chain managers with concepts related to communicating and planning more effectively...
December 1, 2017: Journal of Business Continuity & Emergency Planning
Georgios M Milis, Christos G Panayiotou, Marios M Polycarpou
Recent progress toward the realization of the ``Internet of Things'' has improved the ability of physical and soft/cyber entities to operate effectively within large-scale, heterogeneous systems. It is important that such capacity be accompanied by feedback control capabilities sufficient to ensure that the overall systems behave according to their specifications and meet their functional objectives. To achieve this, such systems require new architectures that facilitate the online deployment, composition, interoperability, and scalability of control system components...
March 31, 2017: IEEE Transactions on Cybernetics
Petra Ten Hoopen, Ramona L Walls, Ethalinda Ks Cannon, Guy Cochrane, James Cole, Anjanette Johnston, Ilene Karsch-Mizrachi, Pelin Yilmaz
The Compliance and Interoperability Working Group of the Genomic Standards Consortium facilitates the establishment of a community of experts and the development of recommendations to describe genomic data and associated information. Here we present our ongoing conation to harmonise the reporting of contextual plant specimen data associated with genomics and functional genomics. This commentary summarises the current state of our plant sample contextual data harmonisation efforts to engage a broad plant science community...
December 1, 2016: GigaScience
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