D2.2: Research Data Exchange Solution
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Semantic FAIR Data Web Me
SNOMED CT Research Webinar Today’ Presenter WELCOME! *We will begin shortly* Dr. Ronald Cornet UPCOMING WEBINARS: RESEARCH WEB SERIES CLINICAL WEB SERIES Save the Date! August TBA soon! August 19, 2020 Time: TBA https://www.snomed.org/news-and-events/events/web-series Dr Hyeoun-Ae Park Emeritus Dean & Professor Seoul National University Past President International Medical Informatics Association Research Reference Group Join our SNOMED Research Reference Group! Be notified of upcoming Research Webinars and other SNOMED CT research-related news. Email Suzy ([email protected]) to Join. SNOMED CT Research Webinar: SNOMED CT – OWL in a FAIR web of data Dr. Ronald Cornet SNOMED CT – OWL in a FAIR web of data Ronald Cornet Me SNOMED Use case CT Semantic FAIR data web Me • Associate professor at Amsterdam UMC, Amsterdam Public Health Research Institute, department of Medical Informatics • Research on knowledge representation; ontology auditing; SNOMED CT; reusable healthcare data; FAIR data Conflicts of Interest • 10+ years involvement with SNOMED International (Quality Assurance Committee, Technical Committee, Implementation SIG, Modeling Advisory Group) • Chair of the GO-FAIR Executive board • Funding from European Union (Horizon 2020) Me SNOMED Use case CT Semantic FAIR data web FAIR Guiding Principles https://go-fair.org/ FAIR Principles – concise • Findable • Metadata and data should be easy to find for both humans and computers • Accessible • The user needs to know how data can be accessed, possibly including authentication and authorization -
1 Data Policies of Highly-Ranked Social Science
1 Data policies of highly-ranked social science journals1 Mercè Crosas2, Julian Gautier2, Sebastian Karcher3, Dessi Kirilova3, Gerard Otalora2, Abigail Schwartz2 Abstract By encouraging and requiring that authors share their data in order to publish articles, scholarly journals have become an important actor in the movement to improve the openness of data and the reproducibility of research. But how many social science journals encourage or mandate that authors share the data supporting their research findings? How does the share of journal data policies vary by discipline? What influences these journals’ decisions to adopt such policies and instructions? And what do those policies and instructions look like? We discuss the results of our analysis of the instructions and policies of 291 highly-ranked journals publishing social science research, where we studied the contents of journal data policies and instructions across 14 variables, such as when and how authors are asked to share their data, and what role journal ranking and age play in the existence and quality of data policies and instructions. We also compare our results to the results of other studies that have analyzed the policies of social science journals, although differences in the journals chosen and how each study defines what constitutes a data policy limit this comparison. We conclude that a little more than half of the journals in our study have data policies. A greater share of the economics journals have data policies and mandate sharing, followed by political science/international relations and psychology journals. Finally, we use our findings to make several recommendations: Policies should include the terms “data,” “dataset” or more specific terms that make it clear what to make available; policies should include the benefits of data sharing; journals, publishers, and associations need to collaborate more to clarify data policies; and policies should explicitly ask for qualitative data. -
SHACL Satisfiability and Containment
SHACL Satisfiability and Containment Paolo Pareti1 , George Konstantinidis1 , Fabio Mogavero2 , and Timothy J. Norman1 1 University of Southampton, Southampton, United Kingdom {pp1v17,g.konstantinidis,t.j.norman}@soton.ac.uk 2 Università degli Studi di Napoli Federico II, Napoli, Italy [email protected] Abstract. The Shapes Constraint Language (SHACL) is a recent W3C recom- mendation language for validating RDF data. Specifically, SHACL documents are collections of constraints that enforce particular shapes on an RDF graph. Previous work on the topic has provided theoretical and practical results for the validation problem, but did not consider the standard decision problems of satisfiability and containment, which are crucial for verifying the feasibility of the constraints and important for design and optimization purposes. In this paper, we undertake a thorough study of different features of non-recursive SHACL by providing a translation to a new first-order language, called SCL, that precisely captures the semantics of SHACL w.r.t. satisfiability and containment. We study the interaction of SHACL features in this logic and provide the detailed map of decidability and complexity results of the aforementioned decision problems for different SHACL sublanguages. Notably, we prove that both problems are undecidable for the full language, but we present decidable combinations of interesting features. 1 Introduction The Shapes Constraint Language (SHACL) has been recently introduced as a W3C recommendation language for the validation of RDF graphs, and it has already been adopted by mainstream tools and triplestores. A SHACL document is a collection of shapes which define particular constraints and specify which nodes in a graph should be validated against these constraints. -
A Comprehensive Analysis of the Journal Evaluation System in China
A comprehensive analysis of the journal evaluation system in China Ying HUANG1,2, Ruinan LI1, Lin ZHANG1,2,*, Gunnar SIVERTSEN3 1School of Information Management, Wuhan University, China 2Centre for R&D Monitoring (ECOOM) and Department of MSI, KU Leuven, Belgium 3Nordic Institute for Studies in Innovation, Research and Education, Tøyen, Oslo, Norway Abstract Journal evaluation systems are important in science because they focus on the quality of how new results are critically reviewed and published. They are also important because the prestige and scientific impact of journals is given attention in research assessment and in career and funding systems. Journal evaluation has become increasingly important in China with the expansion of the country’s research and innovation system and its rise as a major contributor to global science. In this paper, we first describe the history and background for journal evaluation in China. Then, we systematically introduce and compare the most influential journal lists and indexing services in China. These are: the Chinese Science Citation Database (CSCD); the journal partition table (JPT); the AMI Comprehensive Evaluation Report (AMI); the Chinese STM Citation Report (CJCR); the “A Guide to the Core Journals of China” (GCJC); the Chinese Social Sciences Citation Index (CSSCI); and the World Academic Journal Clout Index (WAJCI). Some other lists published by government agencies, professional associations, and universities are briefly introduced as well. Thereby, the tradition and landscape of the journal evaluation system in China is comprehensively covered. Methods and practices are closely described and sometimes compared to how other countries assess and rank journals. Keywords: scientific journal; journal evaluation; peer review; bibliometrics 1 1. -
Letter, If Not the Spirit, of One Or the Other Definition
Producing Open Source Software How to Run a Successful Free Software Project Karl Fogel Producing Open Source Software: How to Run a Successful Free Software Project by Karl Fogel Copyright © 2005-2021 Karl Fogel, under the CreativeCommons Attribution-ShareAlike (4.0) license. Version: 2.3214 Home site: https://producingoss.com/ Dedication This book is dedicated to two dear friends without whom it would not have been possible: Karen Under- hill and Jim Blandy. i Table of Contents Preface ............................................................................................................................. vi Why Write This Book? ............................................................................................... vi Who Should Read This Book? ..................................................................................... vi Sources ................................................................................................................... vii Acknowledgements ................................................................................................... viii For the first edition (2005) ................................................................................ viii For the second edition (2021) .............................................................................. ix Disclaimer .............................................................................................................. xiii 1. Introduction ................................................................................................................... -
Definition of Data Exchange Standard for Railway Applications
PRACE NAUKOWE POLITECHNIKI WARSZAWSKIEJ z. 113 Transport 2016 6/*!1 Uniwersytet Technologiczno-:]! w Radomiu, (,? DEFINITION OF DATA EXCHANGE STANDARD FOR RAILWAY APPLICATIONS The manuscript delivered: March 2016 Abstract: Railway similar to the other branches of economy commonly uses information technologies in its business. This includes, inter alia, issues such as railway traffic management, rolling stock management, stacking timetables, information for passengers, booking and selling tickets. Variety aspects of railway operations as well as a large number of companies operating in the railway market causes that currently we use a lot of independent systems that often should work together. The lack of standards for data structures and protocols causes the need to design and maintain multiple interfaces. This approach is inefficient, time consuming and expensive. Therefore, the initiative to develop an open standard for the exchange of data for railway application was established. This new standard was named railML. The railML is based on Extensible Markup Language (XML) and uses XML Schema to define a new data exchange format and structures for data interoperability of railway applications. In this paper the current state of railML specification and the trend of development were discussed. Keywords: railway traffic control systems, railML, XML 1. INTRODUCTION It is hard to imagine the functioning of the modern world without information technologies. It is a result of numerous advantages of the modern IT solutions. One of the most important arguments for using IT systems is cost optimisation [1, 3, 6]. Variety aspects of railway operations as well as a large number of companies operating in the railway market causes that currently we use a lot of independent systems that often should cooperate. -
JSON Application Programming Interface for Discrete Event Simulation Data Exchange
JSON Application Programming Interface for Discrete Event Simulation data exchange Ioannis Papagiannopoulos Enterprise Research Centre Faculty of Science and Engineering Design and Manufacturing Technology University of Limerick Submitted to the University of Limerick for the degree of Master of Engineering 2015 1. Supervisor: Prof. Cathal Heavey Enterprise Research Centre University of Limerick Ireland ii Abstract This research is conducted as part of a project that has the overall aim to develop an open source discrete event simulation (DES) platform that is expandable, and modular aiming to support the use of DES at multi-levels of manufacturing com- panies. The current work focuses on DES data exchange within this platform. The goal of this thesis is to develop a DES exchange interface between three different modules: (i) ManPy an open source discrete event simulation engine developed in Python on the SimPy library; (ii) A Knowledge Extraction (KE) tool used to populate the ManPy simulation engine from shop-floor data stored within an Enterprise Requirements Planning (ERP) or a Manufacturing Execution System (MES) to allow the potential for real-time simulation. The development of the tool is based on R scripting language, and different Python libraries; (iii) A Graphical User Interface (GUI) developed in JavaScript used to provide an interface in a similar manner to Commercial off-the-shelf (COTS) DES tools. In the literature review the main standards that could be used are reviewed. Based on this review and the requirements above, the data exchange format standard JavaScript Object Notation (JSON) was selected. The proposed solution accom- plishes interoperability between different modules using an open source, expand- able, and easy to adopt and maintain, in an all inclusive JSON file. -
Downloaded Manually1
The Journal Coverage of Web of Science and Scopus: a Comparative Analysis Philippe Mongeon and Adèle Paul-Hus [email protected]; [email protected] Université de Montréal, École de bibliothéconomie et des sciences de l'information, C.P. 6128, Succ. Centre-Ville, H3C 3J7 Montréal, Qc, Canada Abstract Bibliometric methods are used in multiple fields for a variety of purposes, namely for research evaluation. Most bibliometric analyses have in common their data sources: Thomson Reuters’ Web of Science (WoS) and Elsevier’s Scopus. This research compares the journal coverage of both databases in terms of fields, countries and languages, using Ulrich’s extensive periodical directory as a base for comparison. Results indicate that the use of either WoS or Scopus for research evaluation may introduce biases that favor Natural Sciences and Engineering as well as Biomedical Research to the detriment of Social Sciences and Arts and Humanities. Similarly, English-language journals are overrepresented to the detriment of other languages. While both databases share these biases, their coverage differs substantially. As a consequence, the results of bibliometric analyses may vary depending on the database used. Keywords Bibliometrics, citations indexes, Scopus, Web of Science, research evaluation Introduction Bibliometric and scientometric methods have multiple and varied application realms, that goes from information science, sociology and history of science to research evaluation and scientific policy (Gingras, 2014). Large scale bibliometric research was made possible by the creation and development of the Science Citation Index (SCI) in 1963, which is now part of Web of Science (WoS) alongside two other indexes: the Social Science Citation Index (SSCI) and the Arts and Humanities Citation Index (A&HCI) (Wouters, 2006). -
Strategic Directions for Sakai and Data Interoperability Charles Severance ([email protected]), Joseph Hardin ([email protected])
Strategic Directions for Sakai and Data Interoperability Charles Severance ([email protected]), Joseph Hardin ([email protected]) Sakai is emerging as the leading open source enterprise-class collaboration and learning environment. Sakai's initial purpose was to produce a single application but increasingly, Sakai will need to operate with other applications both within and across enterprises. This document is intended to propose a roadmap as to where Sakai should go in terms of data interoperability both amongst applications running within Sakai and with applications interacting with Sakai. There will be other aspects of future Sakai development that are not covered here. This document takes a long-term view on the evolution of Sakai - it is complementary to the Sakai Requirements process, which captures short to medium term priorities. The tasks discussed in this document should not be seen as the "most important" tasks for Sakai. The document only covers data exchange aspects of Sakai. Nothing in this document is set in stone - since Sakai is a community effort, everyone is a volunteer. However, by publishing this overview we hope to facilitate consensus and alignment of goals within the community over the longer- term future of Sakai. Sakai is currently a Service-Oriented-Architecture. This work maintains and enhances the Service-Oriented aspects of Sakai and adds the ability to use Sakai as an set of objects. This work move be both Service Oriented and Object- Oriented. Making Sakai Web 2.0 While "Web 2.0" is a vastly overused term, in some ways, this effort can be likened to building the Web 2.0 version of Sakai. -
Information Retrieval and Mining in Distributed Environments Studies in Computational Intelligence,Volume 324 Editor-In-Chief Prof
Alessandro Soro, Eloisa Vargiu, Giuliano Armano, and Gavino Paddeu (Eds.) Information Retrieval and Mining in Distributed Environments Studies in Computational Intelligence,Volume 324 Editor-in-Chief Prof. Janusz Kacprzyk Systems Research Institute Polish Academy of Sciences ul. Newelska 6 01-447 Warsaw Poland E-mail: [email protected] Further volumes of this series can be found on our homepage: springer.com Vol. 313. Imre J. Rudas, J´anos Fodor, and Janusz Kacprzyk (Eds.) Vol. 301. Giuliano Armano, Marco de Gemmis, Computational Intelligence in Engineering, 2010 Giovanni Semeraro, and Eloisa Vargiu (Eds.) ISBN 978-3-642-15219-1 Intelligent Information Access, 2010 Vol. 314. Lorenzo Magnani,Walter Carnielli, and ISBN 978-3-642-13999-4 Claudio Pizzi (Eds.) Vol. 302. Bijaya Ketan Panigrahi,Ajith Abraham, Model-Based Reasoning in Science and Technology, 2010 and Swagatam Das (Eds.) ISBN 978-3-642-15222-1 Computational Intelligence in Power Engineering, 2010 Vol. 315. Mohammad Essaaidi, Michele Malgeri, and ISBN 978-3-642-14012-9 Costin Badica (Eds.) Vol. 303. Joachim Diederich, Cengiz Gunay, and Intelligent Distributed Computing IV, 2010 James M. Hogan ISBN 978-3-642-15210-8 Recruitment Learning, 2010 Vol. 316. Philipp Wolfrum ISBN 978-3-642-14027-3 Information Routing, Correspondence Finding, and Object Vol. 304.Anthony Finn and Lakhmi C. Jain (Eds.) Recognition in the Brain, 2010 Innovations in Defence Support Systems, 2010 ISBN 978-3-642-15253-5 ISBN 978-3-642-14083-9 Vol. 317. Roger Lee (Ed.) Vol. 305. Stefania Montani and Lakhmi C. Jain (Eds.) Computer and Information Science 2010 Successful Case-Based Reasoning Applications-1, 2010 ISBN 978-3-642-15404-1 ISBN 978-3-642-14077-8 Vol. -
Web Architecture: Structured Formats (DOM, JSON/YAML)
INFO/CS 4302 Web Informaon Systems FT 2012 Week 5: Web Architecture: StructureD Formats – Part 4 (DOM, JSON/YAML) (Lecture 9) Theresa Velden Haslhofer & Velden COURSE PROJECTS Q&A Example Web Informaon System Architecture User Interface REST / Linked Data API Web Application Raw combine, (Relational) Database / Dataset(s), clean, In-memory store / refine Web API(s) File-based store RECAP XML & RelateD Technologies overview Purpose Structured Define Document Access Transform content Structure Document Document Items XML XML Schema XPath XSLT JSON RELAX NG DOM YAML DTD XSLT • A transformaon in the XSLT language is expresseD in the form of an XSL stylesheet – root element: <xsl:stylesheet> – an xml Document using the XSLT namespace, i.e. tags are in the namespace h_p://www.w3.org/1999/XSL/Transform • The body is a set of templates or rules – The ‘match’ aribute specifies an XPath of elements in source tree – BoDy of template specifies contribu6on of source elements to result tree • You neeD an XSLT processor to apply the style sheet to a source XML Document XSLT – In-class Exercise Recap • Example 1 (empty stylesheet – Default behavior) • Example 2 (output format text, local_name()) • Example 3 (pulll moDel, one template only) • Example 4 (push moDel, moDular Design) XSLT: ConDi6onal Instruc6ons • Programming languages typically proviDe ‘if- then, else’ constructs • XSLT proviDes – If-then: <xsl:If> – If-then-(elif-then)*-else: <xsl:choose> XML Source Document xsl:if xsl:if ? xsl:if <html> <boDy> <h2>Movies</h2> <h4>The Others (English 6tle)</h4> -
2014 URCA Abstracts for Oral and Poster Presentations
Oral & Poster Presentation Abstracts Katheryn Adam, Chemistry Faculty Mentor: Marco Bonizzoni, Chemistry An off-the-shelf sensing system for physiologically relevant phosphates We have developed a chemical sensing system that can differentiate biologically relevant phosphates (nucleoside diphosphates, pyrophosphate) in neutral water solution using only commercially available components. Our approach uses a common fluorescent indicator and a poly(amidoamine) (PAMAM) polycationic receptor to construct an indicator displacement assay (IDA). The system crucially relies on multivariate data collection and analysis. In fact, using different phosphates in the dye-displacement assay results in subtle differences in the optical signals; however, it is not possible to capture this information using classical univariate data presentation techniques. Instead, we rely on principal component analysis, a multivariate data analysis technique, to evaluate these differences and thus distinguish between the biologically relevant phosphates. We will also present supporting data reporting on the anion binding capabilities of the PAMAM system acquired using optical spectroscopy methods. Alison Adams, Biological Sciences Faculty Mentor: Laura Reed, Biological Sciences QTL affecting genotype-by-diet interactions of larval triglyceride levels Metabolic Syndrome (MetS) is a complex disease that is becoming increasingly prevalent in the world today. It is identified by an assortment of symptoms such as obesity, insulin resistance, and elevated blood lipids. This disease and its various phenotypes can be modeled in Drosophila melanogaster. In a previous study of MetS, our lab implemented a round-robin crossing scheme on approximately 800 isogenic lines from a recombinant inbred line population, and a linear regression was used to determine genotype, diet, and genotype-by-diet interactions.