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https://www.readbyqxmd.com/read/29777206/the-fair-guiding-principles-for-data-stewardship-fair-enough
#1
REVIEW
Martin Boeckhout, Gerhard A Zielhuis, Annelien L Bredenoord
The FAIR guiding principles for research data stewardship (findability, accessibility, interoperability, and reusability) look set to become a cornerstone of research in the life sciences. A critical appraisal of these principles in light of ongoing discussions and developments about data sharing is in order. The FAIR principles point the way forward for facilitating data sharing more systematically-provided that a number of ethical, methodological, and organisational challenges are addressed as well.
May 17, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29766512/structured-radiology-reporting-on-an-institutional-level-benefit-or-new-administrative-burden
#2
REVIEW
Daniel Pinto Dos Santos, Elmar Kotter
Significant technical advances have been made in radiology since the first discovery of X-rays. Diagnostic techniques have become more and more complex, workflows have been digitized, and data production has increased exponentially. However, the radiology report as the main method for communicating examination results has largely remained unchanged. Growing evidence supports that more structured radiology reports offer various benefits over conventional narrative reports. Various efforts have been made to further develop and promote structured reporting...
May 16, 2018: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/29756002/ermrest-a-collaborative-data-catalog-with-fine-grain-access-control
#3
Karl Czajkowski, Carl Kesselman, Robert Schuler
Creating and maintaining an accurate description of data assets and the relationships between assets is a critical aspect of making data findable, accessible, interoperable, and reusable (FAIR). Typically, such metadata are created and maintained in a data catalog by a curator as part of data publication. However, allowing metadata to be created and maintained by data producers as the data is generated rather then waiting for publication can have significant advantages in terms of productivity and repeatability...
October 2017: Proceedings ... IEEE International Conference on EScience
https://www.readbyqxmd.com/read/29753616/an-interoperable-clinical-decision-support-system-for-early-detection-of-sirs-in-pediatric-intensive-care-using-openehr
#4
Antje Wulff, Birger Haarbrandt, Erik Tute, Michael Marschollek, Philipp Beerbaum, Thomas Jack
BACKGROUND: Clinical decision-support systems (CDSS) are designed to solve knowledge-intensive tasks for supporting decision-making processes. Although many approaches for designing CDSS have been proposed, due to high implementation costs, as well as the lack of interoperability features, current solutions are not well-established across different institutions. Recently, the use of standardized formalisms for knowledge representation as terminologies as well as the integration of semantically enriched clinical information models, as openEHR Archetypes, and their reuse within CDSS are theoretically considered as key factors for reusable CDSS...
May 9, 2018: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/29748852/dicomweb%C3%A2-background-and-application-of-the-web-standard-for-medical-imaging
#5
Brad W Genereaux, Donald K Dennison, Kinson Ho, Robert Horn, Elliot Lewis Silver, Kevin O'Donnell, Charles E Kahn
This paper describes why and how DICOM, the standard that has been the basis for medical imaging interoperability around the world for several decades, has been extended into a full web technology-based standard, DICOMweb. At the turn of the century, healthcare embraced information technology, which created new problems and new opportunities for the medical imaging industry; at the same time, web technologies matured and began serving other domains well. This paper describes DICOMweb, how it extended the DICOM standard, and how DICOMweb can be applied to problems facing healthcare applications to address workflow and the changing healthcare climate...
May 10, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29743102/extending-the-dideo-ontology-to-include-entities-from-the-natural-product-drug-interaction-domain-of-discourse
#6
John Judkins, Jessica Tay-Sontheimer, Richard D Boyce, Mathias Brochhausen
BACKGROUND: Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), the United States National Center for Complementary and Integrative Health has established a center of excellence for PK-NPDI. The Center is creating a public database to help researchers (primarly pharmacologists and medicinal chemists) to share and access data, results, and methods from PK-NPDI studies...
May 9, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29736486/aggregate-exposure-pathways-in-support-of-risk-assessment
#7
Yu-Mei Tan, Jeremy A Leonard, Stephen Edwards, Justin Teeguarden, Alicia Paini, Peter Egeghy
Over time, risk assessment has shifted from establishing relationships between exposure to a single chemical and a resulting adverse health outcome, to evaluation of multiple chemicals and disease outcomes simultaneously. As a result, there is an increasing need to better understand the complex mechanisms that influence risk of chemical and non-chemical stressors, beginning at their source and ending at a biological endpoint relevant to human or ecosystem health risk assessment. Just as the Adverse Outcome Pathway (AOP) framework has emerged as a means of providing insight into mechanism-based toxicity, the exposure science community has seen the recent introduction of the Aggregate Exposure Pathway (AEP) framework...
June 2018: Current Opinion in Toxicology
https://www.readbyqxmd.com/read/29733719/data-sharing-for-precision-medicine-policy-lessons-and-future-directions
#8
Alessandro Blasimme, Marta Fadda, Manuel Schneider, Effy Vayena
Data sharing is a precondition of precision medicine. Numerous organizations have produced abundant guidance on data sharing. Despite such efforts, data are not being shared to a degree that can trigger the expected data-driven revolution in precision medicine. We set out to explore why. Here we report the results of a comprehensive analysis of data-sharing guidelines issued over the past two decades by multiple organizations. We found that the guidelines overlap on a restricted set of policy themes. However, we observed substantial fragmentation in the policy landscape across specific organizations and data types...
May 2018: Health Affairs
https://www.readbyqxmd.com/read/29728251/a-future-proof-architecture-for-telemedicine-using-loose-coupled-modules-and-hl7-fhir
#9
Kirstine Rosenbeck Gøeg, Rune Kongsgaard Rasmussen, Lasse Jensen, Christian Møller Wollesen, Søren Larsen, Louise Bilenberg Pape-Haugaard
BACKGROUND AND OBJECTIVES: Most telemedicine solutions are proprietary and disease specific which cause a heterogeneous and silo-oriented system landscape with limited interoperability. Solving the interoperability problem would require a strong focus on data integration and standardization in telemedicine infrastructures. Our objective was to suggest a future-proof architecture, that consisted of small loose-coupled modules to allow flexible integration with new and existing services, and the use of international standards to allow high re-usability of modules, and interoperability in the health IT landscape...
July 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29726456/achieving-interoperability-between-arden-syntax-based-clinical-decision-support-and-openehr-based-data-systems
#10
Martin Spineth, Andrea Rappelsberger, Klaus-Peter Adlassnig
BACKGROUND: Arden Syntax is an international standard for medical knowledge representation and processing. The openEHR Foundation publishes specifications for the creation of electronic health records based on interoperable data models. OBJECTIVES: To perform a feasibility study showing how Arden Syntax medical logic modules (MLMs) can access openEHR data. METHODS: Medexter's ArdenSuite was applied as an implementation of an Arden-Syntax-based clinical decision support framework, and Marand's EhrScape as an implementation of an openEHR system, for the purpose of data exchange...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29726437/clinical-knowledge-governance-framework-for-nationwide-data-infrastructure-projects
#11
Antje Wulff, Birger Haarbrandt, Michael Marschollek
BACKGROUND: The availability of semantically-enriched and interoperable clinical information models is crucial for reusing once collected data across institutions like aspired in the German HiGHmed project. Funded by the Federal Ministry of Education and Research, this nationwide data infrastructure project adopts the openEHR approach for semantic modelling. Here, strong governance is required to define high-quality and reusable models. OBJECTIVES: Design of a clinical knowledge governance framework for openEHR modelling in cross-institutional settings like HiGHmed...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29726429/development-of-a-protocol-for-automated-glucose-measurement-transmission-used-in-clinical-decision-support-systems-based-on-the-continua-design-guidelines
#12
Markus Meyer, Klaus Donsa, Thomas Truskaller, Matthias Frohner, Birgit Pohn, Alexander Felfernig, Frank Sinner, Thomas Pieber
BACKGROUND: A fast and accurate data transmission from glucose meter to clinical decision support systems (CDSSs) is crucial for the management of type 2 diabetes mellitus since almost all therapeutic interventions are derived from glucose measurements. OBJECTIVES: Aim was to develop a prototype of an automated glucose measurement transmission protocol based on the Continua Design Guidelines and to embed the protocol into a CDSS used by healthcare professionals...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29726358/how-advances-in-imaging-will-affect-precision-radiation-oncology
#13
David A Jaffray, Shiva Das, Paula M Jacobs, Robert Jeraj, Philippe Lambin
Radiation oncology is 1 of the most structured disciplines in medicine. It is of a highly technical nature with reliance on robotic systems to deliver intervention, engagement of diverse expertise, and early adoption of digital approaches to optimize and execute the application of this highly effective cancer treatment. As a localized intervention, the dependence on sensitive, specific, and accurate imaging to define the extent of disease, its heterogeneity, and adjacency to normal tissues directly affects the therapeutic ratio...
June 1, 2018: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29725963/patient-centered-radiology-with-fhir-an-introduction-to-the-use-of-fhir-to-offer-radiology-a-clinically-integrated-platform
#14
Peter I Kamel, Paul G Nagy
Fast Healthcare Interoperability Resources (FHIR) is an open interoperability standard that allows external software to quickly search for and access clinical information from the electronic medical record (EMR) in a method that is developer-friendly, using current internet technology standards. In this article, we highlight the new FHIR standard and illustrate how FHIR can be used to offer the field of radiology a more clinically integrated and patient-centered system, opening the EMR to external radiology software in ways unfeasible with traditional standards...
May 3, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29725962/standard-lexicons-coding-systems-and-ontologies-for-interoperability-and-semantic-computation-in-imaging
#15
REVIEW
Kenneth C Wang
Standard clinical terms, codes, and ontologies promote clarity and interoperability. Within radiology, there is a variety of relevant content resources, tools and technologies. These provide the basis for fundamental imaging workflows such as reporting and billing, and also facilitate a range of applications in quality improvement and research. This article reviews the key characteristics of lexicons, coding systems, and ontologies. A number of standards are described, including International Classification of Diseases-10-Clinical Modification (ICD-10-CM), Current Procedural Terminology (CPT), Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT), Logical Observation Identifiers Names and Codes (LOINC), and RadLex...
May 3, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29725959/learning-hl7-fhir-using-the-hapi-fhir-server-and-its-use-in-medical-imaging-with-the-siim-dataset
#16
Mohannad A Hussain, Steve G Langer, Marc Kohli
Health Level 7's (HL7's) new standard, FHIR (Fast Health Interoperability Resources), is setting healthcare information technology and medical imaging specifically ablaze with excitement. This paper aims to describe the protocol's advantages in some detail and explore an easy path for those unfamiliar with FHIR to begin learning the standard using free, open-source tools, namely the HL7 application programming interface (HAPI) FHIR server and the SIIM Hackathon Dataset.
May 3, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29723188/beachmat-a-bioconductor-c-api-for-accessing-high-throughput-biological-data-from-a-variety-of-r-matrix-types
#17
Aaron T L Lun, Hervé Pagès, Mike L Smith
Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine experiments, which poses a challenge to the existing computational infrastructure for statistical data analysis. For example, single-cell RNA sequencing (scRNA-seq) experiments frequently generate large matrices containing expression values for each gene in each cell, requiring sparse or file-backed representations for memory-efficient manipulation in R...
May 3, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29719309/capabilities-and-advantages-of-cloud-computing-in-the-implementation-of-electronic-health-record
#18
Maryam Ahmadi, Nasim Aslani
Background: With regard to the high cost of the Electronic Health Record (EHR), in recent years the use of new technologies, in particular cloud computing, has increased. The purpose of this study was to review systematically the studies conducted in the field of cloud computing. Methods: The present study was a systematic review conducted in 2017. Search was performed in the Scopus, Web of Sciences, IEEE, Pub Med and Google Scholar databases by combination keywords...
2018: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/29718336/a-clinical-decision-support-system-algorithm-for-intravenous-to-oral-antibiotic-switch-therapy-validity-clinical-relevance-and-usefulness-in-a-three-step-evaluation-study
#19
H Akhloufi, M Hulscher, C P van der Hoeven, J M Prins, H van der Sijs, D C Melles, A Verbon
Objectives: To evaluate a clinical decision support system (CDSS) based on consensus-based intravenous to oral switch criteria, which identifies intravenous to oral switch candidates. Methods: A three-step evaluation study of a stand-alone CDSS with electronic health record interoperability was performed at the Erasmus University Medical Centre in the Netherlands. During the first step, we performed a technical validation. During the second step, we determined the sensitivity, specificity, negative predictive value and positive predictive value in a retrospective cohort of all hospitalized adult patients starting at least one therapeutic antibacterial drug between 1 and 16 May 2013...
April 26, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29718132/imagepy-an-open-source-python-based-and-platform-independent-software-package-for-boimage-analysis
#20
Anliang Wang, Xiaolong Yan, Zhijun Wei
Summary: This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. Availability: ImagePy is free and open source software, with documentation and code available at https://github...
April 27, 2018: Bioinformatics
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