Data Exchange Standards Research Articles

474 Innovative solutions to streamline data collection, exchange, and utilization in translational research

OBJECTIVES/GOALS: To determine the utility of any standard, one must first evaluate whether or not the standard meets the needs of the use case it is meant to support. We aim to quantify data availability of the HL7 FHIR standard to support data collection for three state-based registries in a rural state and measure the potential effects on data quality and collection time. METHODS/STUDY POPULATION: FHIR mapping will be performed to assess the level of HL7 FHIR standard completeness (or data element coverage) in supporting data collection for the three registries. A systematic approach, previously developed and used by Garza and Zozus, will be used to map registry data elements to corresponding HL7 FHIR standard resources. FHIR coverage will be calculated as a percentage (total data elements “Available in FHIR” vs. total data elements overall) and will be observed across different domain areas (i.e., demographics vs. medications vs. vital signs, etc.) in order to identify the domains with the least and most coverage. RESULTS/ANTICIPATED RESULTS: Although there have been informatics solutions that relied on data exchange standards to improve data collection, none have actually evaluated the coverage of the standard for supporting the needs of clinical data registries. To address this gap, we aim to evaluate the availability of the HL7 FHIR standard to support data collection for three state-based registries. These results will provide insight into the generalizability of a FHIR-based solution to support data acquisition and processing across multiple registries and demonstrate the potential for seamless exchange of that data for secondary use in clinical and translational research. Quantifying the coverage will also be used to further advance its development in order to meet the data collection needs of state and national clinical data registries. DISCUSSION/SIGNIFICANCE: Registries often rely on manual abstraction of EHR data. These manual approaches have had a negative impact on data quality and cost, often due to the complexities associated with collection and mapping of the data to fit the registry model. HL7 FHIR has the potential to address these issues by automating part or all of the data collection process.

Impact of NOTAM on security and efficiency performance of flights (overview)

The purpose of this work is to analyze and assess the impact of NOTAM on the flight safety and efficiency. The main problems associated with NOTAM were considered: number of NOTAMs, the practical use of NOTAM information, technical limitations of the current NOTAM system. Examples of the negative impact of NOTAM on the quality of air navigation support, safety and efficiency of flights are presented. Also, the best practice of solving problems, related to NOTAM in the world, is presented with using: Q-code and flight planning systems (on the example of Lido Flight 4D). The concept of the European AIS Database (EAD), developed on the basis of the Aeronautical Information Exchange Model (AIXM), is presented. The concept of Digital NOTAM, implemented on the basis of AIXM and intended for the exchange, automatic processing and interpretation of the dynamic aeronautical data, is considered. The research studies the new modernized NOTAM system – Federal NOTAM System (FNS – Federal NOTAM System), developed by the Federal Aviation Administration (FAA) of the United States, which allows encoding the Digital NOTAM. ICAO's plans for the transition from the concept of Aeronautical Information Service (AIS) to the Aeronautical Information Management (AIM), applying the principles of the System Wide Information Management (SWIM) concept, were analyzed. As a result of the analysis of the current NOTAM system and the modernized NOTAM system (FNS from FAA), conclusions were drawn that the implementation of Digital NOTAM should solve the technical part of the problems associated with NOTAM, brought about by the use of modern communications (internet) and new data exchange standards (AIXM), which, as a result, will lead to an increase in the level of safety and efficiency of flights. At the same time, problems with NOTAM caused by human factors remain unresolved, due to incorrect use of the NOTAM instrument.

EnzymeML-a data exchange format for biocatalysis and enzymology.

EnzymeML is an XML-based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modeling tools, and databases. EnzymeML supports the scientific community by introducing a standardized data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An application programming interface in Python supports the integration of software tools for data acquisition, data analysis, and publication. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modeling using the modeling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO-RK.

Examining the Landscape of Prognostic Factors and Clinical Outcomes for Cancer Control

Prognostic factors have important utility in various aspects of cancer surveillance, including research, patient care, and cancer control programmes. Nevertheless, there is heterogeneity in the collection of prognostic factors and outcomes data globally. This study aimed to investigate perspectives on the utility and application of prognostic factors and clinical outcomes in cancer control programmes. A qualitative phenomenology approach using expert interviews was taken to derive a rich description of the current state and future outlook of cancer prognostic factors and clinical outcomes. Individuals with expertise in this work and from various regions and institutions were invited to take part in one-on-one semi-structured interviews. Four areas related to infrastructure and funding challenges were identified by participants, including (1) data collection and access; (2) variability in data reporting, coding, and definitions; (3) limited coordination among databases; and (4) conceptualization and prioritization of meaningful prognostic factors and outcomes. Two areas were identified regarding important future priorities for cancer control: (1) global investment and intention in cancer surveillance and (2) data governance and exchange globally. Participants emphasized the need for better global collection of prognostic factors and clinical outcomes data and support for standardized data collection and data exchange practices by cancer registries.

Pipeline for ontology-based modeling and automated deployment of digital twins for planning and control of manufacturing systems

The demand for individualized products drives modern manufacturing systems towards greater adaptability and flexibility. This increases the focus on data-driven digital twins enabling swift adaptations. Within the framework of cyber-physical systems, the digital twin is a digital model that is fully connected to the physical and digital assets. A digital model must follow a standardization for interoperable data exchange. Established ontologies and meta-models offer a basis in the definition of a schema, which is the first phase of creating a digital twin. The next phase is the standardized and structured modeling with static use-case specific data. The final phase is the deployment of digital twins into operation with a full connection of the digital model with the remaining cyber-physical system. In this deployment phase communication standards and protocols provide a standardized data exchange. A survey on the state-of-the-art of these three digital twin phases reveals the lack of a consistent workflow from ontology-driven definition to standardized modeling. Therefore, one goal of this paper is the design of an end-to-end digital twin pipeline to lower the threshold of creating and deploying digital twins. As the task of establishing a communication connection is highly repetitive, an automation concept by providing structured protocol data is the second goal. The planning and control of a line-less assembly system with manual stations and a mobile robot as resources and an industrial dog as the product serve as exemplary digital twin applications. Along this use-case the digital twin pipeline is transparently explained.

PDBe-KB: collaboratively defining the biological context of structural data.

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

A pathway map of signaling events triggered upon SARS-CoV infection.

Severe acute respiratory syndrome coronaviruses (SARS-CoVs) caused worldwide epidemics over the past few decades. Extensive studies on various strains of coronaviruses provided a basic understanding of the pathogenesis of the disease. Presently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is leading a global pandemic with unprecedented challenges. This is the third coronavirus outbreak of this century. A signaling pathway map of signaling events induced by SARS-CoV infection is not yet available. In this study, we present a literature-annotated signaling pathway map of reactions induced by SARS-CoV infected cells. Multiple signaling modules were found to be orchestrated including PI3K-AKT, Ras-MAPK, JAK-STAT, Type 1 IFN and NFκB. The signaling pathway map of SARS-CoV consists of 110 molecules and 101 reactions mediated by SARS-CoV proteins. The pathway reaction data are available in various community standard data exchange formats including Systems Biology Graphical Notation (SBGN). The pathway map is publicly available through the GitHub repository and data in various formats can be freely downloadable.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12079-021-00642-2.

SPART: A versatile and standardized data exchange format for species partition information.

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.

Interaction concept and system architecture for the sterile information system OR-Pad in the perioperative area

Abstract Access to clinical information during interventions is an important aspect to support the surgeon and his team in the OR. The OR-Pad research project aims at displaying clinically relevant information close to the patient during surgery. With the OR-Pad system, the surgeon shall be able to access case-specific information, displayed on a sterilepackaged, portable display device. Therefore, information shall be prepared before surgery and also be available afterwards. The project follows an user-centered design process. Within the third iteration, the interaction concept was finalized, resulting in an application that can be used in two modes, mobile and intraoperative, to support the surgeon before/after and during surgery, respectively. By supporting the surgeon perioperatively, it is expected to improve the information situation in the OR and thereby the quality of surgical results. Based on this concept, the system architecture was designed in detail, using a client-server architecture. Components, communication interfaces, exchanged data, and intended standards for data exchange of the OR-Pad system including connecting systems were conceived. Expert interviews by using a clickable prototype were conducted to evaluate the concepts.

Standard health data exchange model enables the use and reuse of data to improve maternal health programs and services: a case study from India

Background The evidence on development of a health data exchange (HDX) in India is lacking, both in terms of the use of data for patient care (use) and aggregate data use (reuse) to improve maternal health services and programs. This study describes the requirements and proposes an HDX model development, focused on the adoption and use of design standardization. Methods A landscape analysis was conducted through a literature review to understand the existing HDX models. A qualitative case study focusing on a tertiary care state government hospital in India was performed. Twenty key informants were selected through purposive sampling and virtual interviews were undertaken. A mix of deductive and primarily inductive data analysis was conducted using the NVIVO 12.0 software. Findings Following an iterative design process and based on the essential requirements suggested by the key informants, an inter-organizational HDX scheme was developed. The HDX model leverages the electronic health records to enable the use of data for patient care, and use of aggregate patient data to support management and administrative decisions at the institutional, state-wide and national levels. The model describes how to balance the inter-organizational and intra-organizational data exchange needs. Integrating systems at the local level with those at the state and the national level was identified as one of the key components of this process. Conclusions The patient-level data is critical for the delivery of best attainable health care. At the same time, the aggregate data is critical, especially in the domain of decision-making and global health. The development of a versatile HDX model is a pre-requisite for a successful use and reuse of data, by ensuring that no functionality is lost and that the data is used in the best way possible.

Maturity assessment of Kenya’s health information system interoperability readiness

BackgroundThe use of digital technology in healthcare promises to improve quality of care and reduce costs over time. This promise will be difficult to attain without interoperability: facilitating seamless health...

Can FHIR Support Standardization in Post-Market Safety Surveillance?

The Fast Healthcare Interoperability Resources (FHIR) contain multiple data-exchange standards that aim at optimizing healthcare information exchange. One of them, the FHIR AdverseEvent, may support post-market safety surveillance. We examined its readiness using the Food and Drug Administration's (FDA) Adverse Event Reporting System (FAERS). Our methodology focused on mapping the public FAERS data fields to the FHIR AdverseEvent Resource elements and developing a software tool to automate this process. We mapped directly nine and indirectly two of the twenty-six FAERS elements, while six elements were assigned default values. This exploration further revealed opportunities for adding extra elements to the FHIR standard, based on critical FAERS pieces of information reviewed at the FDA. The existing version of the FHIR AdverseEvent Resource may standardize some of the FAERS information but has to be modified and extended to maximize its value in post-market safety surveillance.

Digital Home-Monitoring of Patients after Kidney Transplantation: The MACCS Platform.

The MACCS (Medical Assistant for Chronic Care Service) platform enables secure sharing of key medical information between patients after kidney transplantation and physicians. Patients provide information such as vital signs, well-being, and medication intake via smartphone apps. The information is transferred directly into a database and electronic health record at the kidney transplant center, which is used for routine patient care and research. Physicians can send an updated medication plan and laboratory data directly to the patient app via this secure platform. Other features of the app are medical messages and video consultations. Consequently, the patient is better-informed, and self-management is facilitated. In addition, the transplant center and the patient's local nephrologist automatically exchange notes, medical reports, laboratory values, and medication data via the platform. A telemedicine team reviews all incoming data on a dashboard and takes action, if necessary. Tools to identify patients at risk for complications are under development. The platform exchanges data via a standardized secure interface (Health Level 7 (HL7), Fast Healthcare Interoperability Resources (FHIR)). The standardized data exchange based on HL7 FHIR guarantees interoperability with other eHealth solutions and allows rapid scalability to other chronic diseases. The underlying data protection concept is in concordance with the latest European General Data Protection Regulation. Enrollment started in February 2020, and 131 kidney transplant recipients are actively participating as of July 2020. Two large German health insurance companies are currently funding the telemedicine services of the project. The deployment for other chronic kidney diseases and solid organ transplant recipients is planned. In conclusion, the platform is designed to enable home monitoring and automatic data exchange, empower patients, reduce hospitalizations, and improve adherence, and outcomes after kidney transplantation.

A metamodeling approach for the simulation of energy and media demand for the brewing industry

AbstractDue to economic, social and technical trends, as well as rising energy costs, the food and beverage industry is challenged to work energy‐efficiently. Small and medium‐sized enterprises in particular lack of both time and knowledge to identify and implement suitable energy efficiency measures. With the help of simulation, decision‐makers can pursue numerous approaches and make well‐founded decisions. A metamodel based on four modeling pillars (physical‐, process‐, article/recipe‐, and production plan model) for an entire production system concerning the forecast of energy and media consumption is presented. The metamodel is implemented in a user‐friendly modeling tool, which enables a simple hybrid modeling without prequalification of the user. Subsequently, a standardized data exchange file, as basis for a simulation model, is generated. For validation, various use cases were modeled and the tool was validated using a systematic test. In addition, two simulation studies were performed to show that the presented approach provides the opportunity to create a holistic model in terms of forecasting energy and media consumption.

Human-centered development of an electronic health record-embedded, interactive information visualization in the emergency department using fast healthcare interoperability resources.

Develop and evaluate an interactive information visualization embedded within the electronic health record (EHR) by following human-centered design (HCD) processes and leveraging modern health information exchange standards. We applied an HCD process to develop a Fast Healthcare Interoperability Resources (FHIR) application that displays a patient's asthma history to clinicians in a pediatric emergency department. We performed a preimplementation comparative system evaluation to measure time on task, number of screens, information retrieval accuracy, cognitive load, user satisfaction, and perceived utility and usefulness. Application usage and system functionality were assessed using application logs and a postimplementation survey of end users. Usability testing of the Asthma Timeline Application demonstrated a statistically significant reduction in time on task (P < .001), number of screens (P < .001), and cognitive load (P < .001) for clinicians when compared to base EHR functionality. Postimplementation evaluation demonstrated reliable functionality and high user satisfaction. Following HCD processes to develop an application in the context of clinical operations/quality improvement is feasible. Our work also highlights the potential benefits and challenges associated with using internationally recognized data exchange standards as currently implemented. Compared to standard EHR functionality, our visualization increased clinician efficiency when reviewing the charts of pediatric asthma patients. Application development efforts in an operational context should leverage existing health information exchange standards, such as FHIR, and evidence-based mixed methods approaches.

Structured Data Capture for Oncology.

Lack of interoperability is one of the greatest challenges facing healthcare informatics. Recent interoperability efforts have focused primarily on data transmission and generally ignore data capture standardization. Structured Data Capture (SDC) is an open-source technical framework that enables the capture and exchange of standardized and structured data in interoperable data entry forms (DEFs) at the point of care. Some of SDC’s primary use cases concern complex oncology data such as anatomic pathology, biomarkers, and clinical oncology data collection and reporting. Its interoperability goals are the preservation of semantic, contextual, and structural integrity of the captured data throughout the data’s lifespan. SDC documents are written in eXtensible Markup Language (XML) and are therefore computer readable, yet technology agnostic—SDC can be implemented by any EHR vendor or registry. Any SDC-capable system can render an SDC XML file into a DEF, receive and parse an SDC transmission, and regenerate the original SDC form as a DEF or synoptic report with the response data intact. SDC is therefore able to facilitate interoperable data capture and exchange for patient care, clinical trials, cancer surveillance and public health needs, clinical research, and computable care guidelines. The usability of SDC-captured oncology data is enhanced when the SDC data elements are mapped to standard terminologies. For example, an SDC map to Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) enables aggregation of SDC data with other related data sets and permits advanced queries and groupings on the basis of SNOMED CT concept attributes and description logic. SDC supports terminology maps using separate map files or as terminology codes embedded in an SDC document.

Creation of special technical means on the basis of SDR devices

The article is devoted to the review of possibilities of creation of special technical means on the basis of SDR devices and principles of construction of transceiver devices which have a possibility of use at performance of various tasks and the purposes. The principles of construction of SDR devices and their features are considered in the article. When creating special hardware, the basic principle is a flexible architecture that can be changed with the help of software. This allows to organize communication between two or more different types of devices, for example, to switch between communication channels and change the type of modulation. When using SDR devices, it is possible to significantly simplify the technical part. The hardware platform can be quickly reprogrammed to support new communication and data exchange standards. Digital signal processing provides greater speed and it is easier to maintain than other analog systems. It is noted that the SDR receiver is a universal device that can combine the functions of various radio devices. Following the concept of SDR, the author concludes that the ideal SDR receiver should contain as few elements as possible, while an important factor in the use of SDR devices is the replacement of most analog components. It is emphasized that devices that are built on an analog element base have a much higher complexity of design than SDR devices and do not have the flexibility required in today’s conditions of rapid change in communication standards.

ГЕОИНФОРМАЦИОННОЕ ОБЕСПЕЧЕНИЕ ПРОГНОЗИРОВАНИЯ ЗОН ЗАТОПЛЕНИЙ НА ЮГЕ САХАЛИНА

Modern systems of hydrometeorological monitoring, for the most part, widely use WEB and GIS technology tools. Territorial fragmentation divisions of the World Meteorological Organization (WMO), Roshydromet, Russian Academy of Sciences and other services and departments interested in obtaining data requires creation of unified information environment for exchange of heterogeneous information. Formation field for geospatial data has become possible with the availability of industrial design platforms with high performance, supporting standard data exchange formats suitable of system for building projectoin. The purpose of the study is to develop requirements for geoinformation sup-port of the system necessary for flood forecasting. Methods: GIS mapping, interpretation and analysis of remote sensing data of the Earth. When developing system for hydrological monitoring of rivers in the Southern Sakhalin, we used the experience of operating similar observational network in services of several European countries, as well as the geographically distributed GIS created by Roshydromet. Considering the vast experience of predecessors and requirements for geoinformation support neces-sary for predicting flood zones in the rivers of Southern Sakhalin have been developed. The initial da-ta for creating the correct flood model are satellite images, large-scale topographic maps, digital terrain models, data from long-term hydrometeorological observations, and engineering surveys.

Telemedicine System Based on Medical Consultation Assistance Integration

With the aging of the global population, how to provide effective telemedicine for the aging population has become a very important issue, especially for the elderly with limited mobility. If there is a complete telemedicine system, it will not only greatly improve medical efficiency. It can reduce the chance of contact between people and avoid the medical risks caused by severe special infectious pneumonia. This paper focuses on the development of a high-efficiency telemedicine system platform that conforms to international standard data exchange formats. This system platform can not only solve the problem of shortage of medical staff but also allow patients to be free from medical outpatient time constraints. Achieve the effect of telemedicine at any time, and digitize the medical process rules to establish a complete online telemedicine system platform.

Advanced and Rapid Tool in Control Room to Determine the Cause and Location of Events in Transmission Network

Operating personnel in control room act on SCADA alarm generated on data from station computer. Using new technologies and advanced technical solutions assistance tool can be designed. This tool provides quick help in busy situations for operator. For this new tool with three types of case studies insight will be given in this paper. Introduction part has short information about numbers of alarms and events in Control centre, and their distribution during one month period. Basic principles for alarm handling in SCADA system is given with all limitations. New tool, Intelligent Alarm Processing system is designed and implemented in control room. It has connection to SCADA system with standard data exchange format CIM/XML and run in real time, with only few seconds delay. This system based on Multilevel Flow Model has root cause analyses implemented for power system. Detail fault location algorithm description with block scheme for this Intelligent Alarm Processing system is part of third chapter. Special attention must be paid for modelling protection data in SCADA system which are sent to this new tool. Demonstration of Intelligent Alarm Processing system operation is reported in fourth chapter. Three characteristic disturbances in transmission network were elaborated. Most complex and challenging disturbances for operator in control room is cascading event. This case study is presented in detail in four sequences through graphical user interface. Second case study is also challenging for operators, heavy winter storm with numerous isolated events. In this case study very effective graphical presentation and alarm list with three types, primary event, consequences and detail list for this events were demonstrated. This list pointed out exactly and clearly what happened in the network. Last case study presents common disturbances which appears on daily basis, where this tool is of great assistance because it points on transmission elements very fast.