Interoperability Of Tools Research Articles

The U.S. EPA Activities and Information Systems Used for Chemical Exposure Screening, Modelling and Prioritisation and Risk-Based Decision Making: Needs, Challenges and Opportunities for Data Sharing and Interoperability of Tools on Global Scale Including IPCHEM

Within the US EPA Office of Research and Development’s (ORD’s) Chemicals for Safety and Sustainability (CSS) research program, efforts are underway to provide information that is useful for the risk-based prioritization of thousands of chemicals, particularly those found in consumer products. The information has been made publicly available through ORD’s CompTox Chemistry Dashboard (https://comptox.epa.gov). In this presentation the research efforts that contribute to the collection and curation of consumer product formulations, article compositions and ingredient uses will be discussed. This information is obtained through both automated collection techniques from manufacturer-supplied documents and measurement of chemicals via suspect screening analysis. Finally, predictions from ORD-developed models for such values as physicochemical properties, functional use, product composition, and chemical exposure, which are provided via the Chemistry Dashboard, will be discussed. The views expressed in this abstract are those of the authors and do not necessarily reflect the views or policies of the US Environmental Agency.

Sharing a Library between Proof Assistants: Reaching out to the HOL Family

We observe today a large diversity of proof systems. This diversity has the negative consequence that a lot of theorems are proved many times. Unlike programming languages, it is difficult for these systems to co-operate because they do not implement the same logic. Logical frameworks are a class of theorem provers that overcome this issue by their capacity of implementing various logics. In this work, we study the STTforall logic, an extension of Simple Type Theory that has been encoded in the logical framework Dedukti. We present a translation from this logic to OpenTheory, a proof system and interoperability tool between provers of the HOL family. We have used this translation to export an arithmetic library containing Fermat's little theorem to OpenTheory and to two other proof systems that are Coq and Matita.

MIRACUM: Medical Informatics in Research and Care in University Medicine.

Summary Introduction: This article is part of the Focus Theme of Methods of Information in Medicine on the German Medical Informatics Initiative. Similar to other large international data sharing networks (e.g. OHDSI, PCORnet, eMerge, RD-Connect) MIRACUM is a consortium of academic and hospital partners as well as one industrial partner in eight German cities which have joined forces to create interoperable data integration centres (DIC) and make data within those DIC available for innovative new IT solutions in patient care and medical research. Objectives: Sharing data shall be supported by common interoperable tools and services, in order to leverage the power of such data for biomedical discovery and moving towards a learning health system. This paper aims at illustrating the major building blocks and concepts which MIRACUM will apply to achieve this goal. Governance and Policies: Besides establishing an efficient governance structure within the MIRACUM consortium (based on the steering board, a central administrative office, the general MIRACUM assembly, six working groups and the international scientific advisory board), defining DIC governance rules and data sharing policies, as well as establishing (at each MIRACUM DIC site, but also for MIRACUM in total) use and access committees are major building blocks for the success of such an endeavor. Architectural Framework and Methodology: The MIRACUM DIC architecture builds on a comprehensive ecosystem of reusable open source tools (MIRACOLIX), which are linkable and interoperable amongst each other, but also with the existing software environment of the MIRACUM hospitals. Efficient data protection measures, considering patient consent, data harmonization and a MIRACUM metadata repository as well as a common data model are major pillars of this framework. The methodological approach for shared data usage relies on a federated querying and analysis concept. Use Cases: MIRACUM aims at proving the value of their DIC with three use cases: IT support for patient recruitment into clinical trials, the development and routine care implementation of a clinico-molecular predictive knowledge tool, and molecular-guided therapy recommendations in molecular tumor boards. Results: Based on the MIRACUM DIC release in the nine months conceptual phase first large scale analysis for stroke and colorectal cancer cohorts have been pursued. Discussion: Beyond all technological challenges successfully applying the MIRACUM tools for the enrichment of our knowledge about diagnostic and therapeutic concepts, thus supporting the concept of a Learning Health System will be crucial for the acceptance and sustainability in the medical community and the MIRACUM university hospitals.

Automatic argument assessment of final project reports of computer engineering students

AbstractArguments in final course project reports written by engineering students are an essential feature of academic texts. Further revisions of instructors reveal to the students their mistakes, such as a lack of argumentation. However, the depth of revisions is often limited by the time availability of the instructor. In this paper, we present a system for argument assessment embedded in an Internet‐based Moodle course with Learning Tools Interoperability (LTI) standard, to help students improve argumentation in the problem statement, justification and conclusion sections of their final project report. The system identifies argumentative paragraphs along with argumentation level and provides recommendations to improve their writing. The analysis is achieved employing machine learning techniques with lexical features trained using an annotated collection of student writings. We performed a pilot test to compare control and experimental groups. Both groups consisted of undergraduate students of computer engineering programs from two different universities. We observed that using the argument assessment system increased the number of arguments in the experimental group. We discuss some further improvements for the system.

Traffic Planning for Time-Sensitive Communication

Many industries, including the automotive industry and industrial automation, have a need for reliable real-time communication. To satisfy this need, industry-specific, often proprietary, solutions have been developed in recent decades. Time-sensitive networking (TSN) is addressing a grand unification of these existing technologies to leverage cross-industry cost efficiency as well as to guarantee a stable growth path of communication capabilities. While the functionality of time-sensitive networking is exhaustively standardized in IEEE 802.1, configuration standards for TSN are largely missing. Thus, in this article we review the IEEE TSN standards, in particular 802.1Qbv, and continue to illustrate a reference model for traffic planning for time-sensitive communication. Furthermore, the article references a detailed technical report describing the complete model, which is ideally suited as a starting point for standardization and ensures the interoperability of future TSN traffic planning tools.

Semantic adaptation for FMI co-simulation with hierarchical simulators

Model-based design can shorten the development time of complex systems by the use of simulation techniques. However, it can be hard to simulate the system as a whole if it is developed in a concurrent fashion by multiple and specialized teams. Co-simulation, with the support of the Functional Mockup Interface (FMI) Standard, is proposed as a way to promote tool interoperability while protecting the intellectual property of subsystems. The standard allows uniform communication between subsystem simulators, but does not state how the inputs and outputs should be interpreted, nor how the subsystems should interact correctly. Semantic adaptations can be quickly made to correct the interactions with subsystem simulators that were produced with different assumptions, and avoid changing those subsystems, their simulators, or the orchestration algorithm that computes the co-simulation. In this work, we explore how to describe common adaptations and what their meaning is in the context of FMI co-simulation. The result is a sound language that enables the implementation of adaptations with minimal effort. A distinct feature is that it describes adaptations for groups of interconnected subsystem simulators in the same way as for a single simulator, and the implementation is itself a simulator, thanks to a sound definition of hierarchical co-simulation. This work paves the way for research into the correct combination and interfacing of different adaptations.

A standard‐based architecture to support learning interoperability: A practical experience in gamification

SummaryCreating quality online content requires a great deal of effort from teachers. In addition to issues specific to the design and creation of the elements of a course, teachers must face technical hurdles so as to perform common tasks, such as deploying the same content on different e‐learning platforms and integrating content into external tools, or acquiring the ability to analyze tracking data generated during learner interactions. These problems principally arise owing to the very limited level of interoperability provided by content creation tools. In order to facilitate the creation of interoperable contents, the Digital Content Production Center at the Polytechnic University of Cartagena (Spain) has developed the UPCTforma tool, whose main architectural driver has been interoperability. More specifically, the tool takes advantage of the Learning Tools Interoperability and Caliper interoperability specifications to provide several types of quality regarding three key aspects of content production: tool interoperability, learning analytics, and motivation. In this paper, we provide a detailed description of the component‐based architecture proposed and present a validation of the requirements elicited through the use of a UPCTforma gamification activity created for a real project involving approximately 4000 students. One of the novel aspects of this architecture is the transformation of tracking data into “learning analysis models” that represent the information in the tracked learning activities at a higher level of abstraction. These models are used to provide activity‐specific learning analytics and motivation. Platform independency with respect to data analytics technologies, messaging systems, and communication protocols is achieved by using adapters.

A Service-Oriented Tool-Chain for Model-Based Systems Engineering of Aero-Engines

This paper proposes a service-oriented tool-chain with an emphasis on domain-specific views, simulation automation, and process management to support model-based system engineering of aero-engines. In the tool-chain, a domain-specific modeling approach is adopted to facilitate the descriptions of co-design workflows and the related development information. The relevant domain-specific models are the basis for automated creation of a Web-based process management system consolidating and controlling service-oriented technical resources (models, data, and tools). In particular, the system also provides support for automated orchestration of tool operations, model, and simulation configurations. In order to promote the model and tool interoperability, the tool-chain adopts open standards for integrations, including open services for lifecycle collaboration and functional mock-up interface. Finally, through a case study of simulation-based aero-engine performance analysis, we evaluate the flexibility and efficiency of this tool chain by comparing it with a traditional simulation process both qualitatively and quantitatively.

A Design and Implementation of a DCAT-based Metadata Transformation Tool for Interoperability in Open Data Platforms

A Design and Implementation of a DCAT-based Metadata Transformation Tool for Interoperability in Open Data Platforms

Semantic interoperability of GIS and MCDA tools for environmental assessment and decision making

A promising approach to environmental assessment and decision making analyses is based on integrating Multicriteria Decision Analysis (MCDA) and GIS tools. Integration of GIS and MCDA tools can be potentially achieved through interoperability, where these tools can exchange relevant information to tackle a particular environmental problem. However, the problem of semantic heterogeneity caused by different meanings of data, terminologies, and models used in GIS and MCDA has been recognized as an obstacle in the interoperability of these tools. Conventionally, exchange of data between GIS and MCDA systems for environmental applications relies on prior knowledge to mediate meanings between the two components. This paper proposes an ontology-enabled framework for semantic interoperability of GIS and MCDA web services. In particular, this study has made significant contribution to environmental decision making by providing an interoperable framework to exchange environmental data with intended and unambiguous meanings between GIS and MCDA services.

HIRMEOS – High Integration of Research Monographs in the European Open Science infrastructure

Open Access has matured for journals, but open access uptake in the book market is still delayed, despite the fact that books continue to be the leading publishing format for qualitative social sciences and humanities. HIRMEOS, High Integration of Research Monographs in the European Open Science infrastructure, is a 30-month EU-funded project and tackles the main obstacles of the full integration of important platforms supporting open access monographs and their contents.HIRMEOS will work on innovative services on identification, entities recognition, annotation, and altmetrics, using when possible common standards. These standards are well established in journal publishing, however not common enough yet in book publishing to pave the way for deeper linking of book and journal content or crosslinking of references, entities or usage. HIRMEOS is based upon 5 Open Access book-publishing platforms, OpenEdition Books, OAPEN Library, EKT Open Book Press, Ubiquity Press and Göttingen University Press. During the run of the project these platforms integrate tools for identification, authentication and interoperability (DOI, ORCID, Fundref), for additional information and entity extraction (INRIA (N)ERD), the ability to annotate monographs (Hypothes.is), and gather usage and alternative metric data. HIRMEOS will also enrich the technical capacities of the Directory of Open Access Books (DOAB), a most significant indexing service for open access monographs globally, to receive automated information for ingestion, while it will also develop a structured certification system to document monograph peer-review. The project consortium will develop shared minimum standards for their monograph publications, such that allow the full embedding of technologies and content in the European Science Cloud. Finally, the project will have a catalyst effect in including more disciplines into the Open Science paradigm, widening its boundaries towards the SSH.The poster will give facts and figures aboutthe involved platforms and their catalogues,the types of services to be implemented and the used standards,the expected benefit for the Social Sciences and Humanities playersthe global benefits for the Open Science environment

A usability case study of algorithmic differentiation tools on the ISSM ice sheet model

Algorithmic differentiation (AD) based on operator overloading is often the only feasible approach for applying AD in complex C++ software environments. Challenges pertaining to the introduction of an AD tool based on operator overloading have been studied in the past. However, in order to assess possible performance gains or to verify derivative values, it is advantageous to be able to apply more than one AD tool to a given code. Hence, in this work, we investigate usability issues when exchanging AD tools. Our study is based on the NASA/JPL/UCI Ice Sheet System Model (ISSM) which currently employs the AD tool ADOL-C. We introduce CoDiPack to ISSM, a more recent AD tool offering a similar set of features while promising performance improvements. In addition to the obvious type change for the AD-augmented float type, this transition requires the change to a different adjoint MPI library, adaptation of the MUMPS solver wrapper, and changes to the derivative seeding and extraction routines. We believe that these issues are fairly generic for numerical simulation software, and the issues we report on provide a blueprint for similar undertakings. We also believe that our experiences provide guidance towards the development of AD interfaces that support AD tool interoperability. In addition, we improve upon the memory management of the existing ADOL-C instrumentation, which exhibited considerable runtime problems for higher mesh resolutions. We conduct serial and parallel ISSM model runs on a 2D mass transport benchmark as well as a model of the Pine Island Glacier to verify the derivatives computed by both tools and report on runtime performance and memory usage. In comparison, the CoDiPack AD variant of ISSM runs faster with less memory overhead than the ADOL-C variant and, thus, enables future model runs with an increased number of mesh elements. But the existence of two different AD implementations provides added confidence in the correctness of derivatives, in particular for future AD tool versions.

Improving Interoperability of Engineering Tools – Data Exchange in Plant Design

AbstractSoftware interoperability plays a key role regarding digitalization in process industries. In this contribution, an overview of current developments in the field of data exchange and standardization is given. A prototypical framework for the heterogeneous data exchange between the piping and instrumentation diagram (P&ID) software X‐Visual PlantEngineer, the integrated engineering tool MOSAIC PlantDesign, and the 3D CAD software AVEVA® PDMS is presented for distillation columns. Data exchange between P&ID tools of different vendors, developed by the DEXPI initiative, is considered as an instance of homogeneous data transfer.

Design and development of a Web based GIS platform for zero energy settlements monitoring

To support the next generation of multi-process big data and service-oriented computing, a Web-GIS platform is considered a viable solution for gathering and sharing of collected data from various case studies ΝΖΕ settlements, so that the information flows are easily managed and interpreted, by means of spatial thematic maps related to specific levels of information, within the various case studies. Smart interoperable sensor networks installed in the various case studies’ buildings, districts, and energy subsystems are prerequisites for the formulation of the physical layer of the monitoring platform. The aim of the present paper is to analyze the characteristics and architecture of a Web GIS Platform for Zero energy settlements monitoring.The platform development is based on open software tools, targeting to be a flexible and interoperable tool for zero energy buildings and communities.

Advancing coordinated cyber-investigations and tool interoperability using a community developed specification language

Any investigation can have a digital dimension, often involving information from multiple data sources, organizations and jurisdictions. Existing approaches to representing and exchanging cyber-investigation information are inadequate, particularly when combining data sources from numerous organizations or dealing with large amounts of data from various tools. To conduct investigations effectively, there is a pressing need to harmonize how this information is represented and exchanged. This paper addresses this need for information exchange and tool interoperability with an open community-developed specification language called Cyber-investigation Analysis Standard Expression (CASE). To further promote a common structure, CASE aligns with and extends the Unified Cyber Ontology (UCO) construct, which provides a format for representing information in all cyber domains. This ontology abstracts objects and concepts that are not CASE-specific, so that they can be used across other cyber disciplines that may extend UCO. This work is a rational evolution of the Digital Forensic Analysis eXpression (DFAX) for representing digital forensic information and provenance. CASE is more flexible than DFAX and can be utilized in any context, including criminal, corporate and intelligence. CASE also builds on the Hansken data model developed and implemented by the Netherlands Forensic Institute (NFI). CASE enables the fusion of information from different organizations, data sources, and forensic tools to foster more comprehensive and cohesive analysis. This paper includes illustrative examples of how CASE can be implemented and used to capture information in a structured form to advance sharing, interoperability and analysis in cyber-investigations. In addition to capturing technical details and relationships between objects, CASE provides structure for representing and sharing details about how cyber-information was handled, transferred, processed, analyzed, and interpreted. CASE also supports data marking for sharing information at different levels of trust and classification, and for protecting sensitive and private information. Furthermore, CASE supports the sharing of knowledge related to cyber-investigations, including distinctive patterns of activity/behavior that are common across cases. This paper features a proof-of-concept Application Program Interface (API) to facilitate implementation of CASE in tools. Community members are encouraged to participate in the development and implementation of CASE and UCO.

Msktuple: An integrated R library for alignment-free multiple sequence k-tuple analysis

Recently alignment-free sequence comparison methods based on promoter-frequency distance measures have gained popularity. This paper reports on the implementation and validation of several alignment-free sequence analysis methods for representing and quantifying between-sequence distances and sequence variability. The msktuple library includes the following sequence comparison techniques: locational k-tuple, naive k-tuple, CV-Tree, and their ensemble variants. These metrics are used to determine the dissimilarity between sequences using k-letter words. In support of open-science, we provide open-source software, R-scripts, and protocols implementing the new techniques. These tools will support collaboration, enable independent validation, promote result reproducibility and enable tool interoperability.

Visual subsetting, conversion and complex query exploitation in large spatio-temporal databases

In recent years, large amounts of multidimensional data are being generated at a rapid pace, creating the need to: develop appropriate tools for visual data analytics and for enhancing accessibility and discoverability of the data; and new algorithms and methods for seamless integration, manipulation and interactive visualization of data. We describe an interactive tool and technique for data mining and visualization, called SubVizCon that integrates advanced concepts for spatio-temporal databases with interactive visualization capabilities of the geographic information system software. More specifically, we illustrate the development and implementation of the SubVizCon framework, which integrates geospatial data analysis, feature extraction, and visualization functions in ArcGIS with the advanced subsetting and querying functions of the Parametric Database Model. The seamless integration and interoperability of these software tools within SubVizCon framework enables users to not only visualize large amounts of data but also discover spatio-temporal patterns that might otherwise remain hidden.

Semantic interoperability for big-data in heterogeneous IoT infrastructure for healthcare

Interoperability remains a major burden to the developers of Internet of Things systems. It is due to IoT devices are extremely heterogeneous regarding basic communication protocols, data formats, and technologies. Furthermore, due to the absence of worldwide satisfactory standards, Interoperability tools remains imperfect. In this paper, we have proposed Semantic Interoperability Model for Big-data in IoT (SIMB-IoT) to deliver semantic interoperability among heterogeneous IoT devices in health care domain. This model is used to recommend medicine with side effects for different symptoms collected from heterogeneous IoT sensors. Two datasets are taken for the analysis of big-data. One dataset contains diseases with drug details and the second dataset contains medicines with side effects. Information between physician and patient are semantically annotated and transferred in a meaningful way. A Lightweight Model for Semantic annotation of Big-data using heterogeneous devices in IoT is proposed to provide annotations for big data. Resource Description Framework (RDF) is a semantic web framework that is recycled to communicate things using Triples to make it semantically significant. RDF annotated patients’ data and made it semantically interoperable. SPARQL query is used to extract records from RDF graph. Tableau, Gruff-6.2.0, and Mysql tools are used in simulation in this article.

The Argument Web: an Online Ecosystem of Tools, Systems and Services for Argumentation

The Argument Web is maturing as both a platform built upon a synthesis of many contemporary theories of argumentation in philosophy and also as an ecosystem in which various applications and application components are contributed by different research groups around the world. It already hosts the largest publicly accessible corpora of argumentation and has the largest number of interoperable and cross compatible tools for the analysis, navigation and evaluation of arguments across a broad range of domains, languages and activity types. Such interoperability is key in allowing innovative combinations of tool and data reuse that can further catalyse the development of the field of computational argumentation. The aim of this paper is to summarise the key foundations, the recent advances and the goals of the Argument Web, with a particular focus on demonstrating the relevance to, and roots in, philosophical argumentation theory.

IJ-OpenCV: Combining ImageJ and OpenCV for processing images in biomedicine

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. The library was implemented on top of the SciJava converter framework. We also provide a methodology to use this library.Results. We have developed the publicly available library IJ-OpenCV that can be employed to create applications combining features from both ImageJ and OpenCV. From the perspective of ImageJ developers, they can use IJ-OpenCV to easily create plugins that use any functionality provided by the OpenCV library and explore different alternatives. From the perspective of OpenCV developers, this library provides a link to the ImageJ graphical user interface and all its features to handle regions of interest.Conclusions. The IJ-OpenCV library bridges the gap between ImageJ and OpenCV, allowing the connection and the cooperation of these two systems.