Transitioning from XML to RDF: Considerations for an Effective
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Including Co-Referent Uris in a SPARQL Query
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Heriot Watt Pure Including Co-referent URIs in a SPARQL Query Christian Y A Brenninkmeijer1, Carole Goble1, Alasdair J G Gray1, Paul Groth2, Antonis Loizou2, and Steve Pettifer1 1 School of Computer Science, University of Manchester, UK. 2 Department of Computer Science, VU University of Amsterdam, The Netherlands. Abstract. Linked data relies on instance level links between potentially differing representations of concepts in multiple datasets. However, in large complex domains, such as pharmacology, the inter-relationship of data instances needs to consider the context (e.g. task, role) of the user and the assumptions they want to apply to the data. Such context is not taken into account in most linked data integration procedures. In this paper we argue that dataset links should be stored in a stand-off fashion, thus enabling different assumptions to be applied to the data links during query execution. We present the infrastructure developed for the Open PHACTS Discovery Platform to enable this and show through evaluation that the incurred performance cost is below the threshold of user perception. 1 Introduction A key mechanism of linked data is the use of equality links between resources across different datasets. However, the semantics of such links are often not triv- ial: as Halpin et al. have shown sameAs, is not always sameAs [12]; and equality is often context- and even task-specific, especially in complex domains. For ex- ample, consider the drug \Gleevec". A search over different chemical databases return records about two different chemical compounds { \Imatinib" and \Ima- tinib Mesylate" { which differ in chemical weight and other characteristics. -
Mapping Spatiotemporal Data to RDF: a SPARQL Endpoint for Brussels
International Journal of Geo-Information Article Mapping Spatiotemporal Data to RDF: A SPARQL Endpoint for Brussels Alejandro Vaisman 1, * and Kevin Chentout 2 1 Instituto Tecnológico de Buenos Aires, Buenos Aires 1424, Argentina 2 Sopra Banking Software, Avenue de Tevuren 226, B-1150 Brussels, Belgium * Correspondence: [email protected]; Tel.: +54-11-3457-4864 Received: 20 June 2019; Accepted: 7 August 2019; Published: 10 August 2019 Abstract: This paper describes how a platform for publishing and querying linked open data for the Brussels Capital region in Belgium is built. Data are provided as relational tables or XML documents and are mapped into the RDF data model using R2RML, a standard language that allows defining customized mappings from relational databases to RDF datasets. In this work, data are spatiotemporal in nature; therefore, R2RML must be adapted to allow producing spatiotemporal Linked Open Data.Data generated in this way are used to populate a SPARQL endpoint, where queries are submitted and the result can be displayed on a map. This endpoint is implemented using Strabon, a spatiotemporal RDF triple store built by extending the RDF store Sesame. The first part of the paper describes how R2RML is adapted to allow producing spatial RDF data and to support XML data sources. These techniques are then used to map data about cultural events and public transport in Brussels into RDF. Spatial data are stored in the form of stRDF triples, the format required by Strabon. In addition, the endpoint is enriched with external data obtained from the Linked Open Data Cloud, from sites like DBpedia, Geonames, and LinkedGeoData, to provide context for analysis. -
Versioning Linked Datasets
Master’s Thesis Versioning Linked Datasets Towards Preserving History on the Semantic Web Author Paul Meinhardt 744393 July 13, 2015 Supervisors Magnus Knuth and Dr. Harald Sack Semantic Technologies Research Group Internet Technologies and Systems Chair Abstract Linked data provides methods for publishing and connecting structured data on the web using standard protocols and formats, namely HTTP, URIs, and RDF. Much like on the web of documents, linked data resources continuously evolve over time, but for the most part only their most recent state is accessible. In or- der to investigate the evolution of linked datasets and understand the impact of changes on the web of data it is necessary to make prior versions of such re- sources available. The lack of a common “self-service” versioning platform in the linked data community makes it more difficult for dataset maintainers to preserve past states of their data themselves. By implementing such a platform which also provides a consistent interface to historic information, dataset main- tainers can more easily start versioning their datasets while application develop- ers and researchers instantly have the possibility of working with the additional temporal data without laboriously collecting it on their own. This thesis, researches the possibility of creating a linked data versioning plat- form. It describes a basic model view for linked datasets, their evolution and presents a service approach to preserving the history of arbitrary linked datasets over time. Zusammenfassung Linked Data beschreibt Methoden für die Veröffentlichung und Verknüpfung strukturierter Daten im Web mithilfe standardisierter Protokolle und Formate, nämlich HTTP, URIs und RDF. Ähnlich wie andere Dokumente im World Wide Web, verändern sich auch Linked-Data-Resourcen stetig mit der Zeit. -
Semantics Developer's Guide
MarkLogic Server Semantic Graph Developer’s Guide 2 MarkLogic 10 May, 2019 Last Revised: 10.0-8, October, 2021 Copyright © 2021 MarkLogic Corporation. All rights reserved. MarkLogic Server MarkLogic 10—May, 2019 Semantic Graph Developer’s Guide—Page 2 MarkLogic Server Table of Contents Table of Contents Semantic Graph Developer’s Guide 1.0 Introduction to Semantic Graphs in MarkLogic ..........................................11 1.1 Terminology ..........................................................................................................12 1.2 Linked Open Data .................................................................................................13 1.3 RDF Implementation in MarkLogic .....................................................................14 1.3.1 Using RDF in MarkLogic .........................................................................15 1.3.1.1 Storing RDF Triples in MarkLogic ...........................................17 1.3.1.2 Querying Triples .......................................................................18 1.3.2 RDF Data Model .......................................................................................20 1.3.3 Blank Node Identifiers ..............................................................................21 1.3.4 RDF Datatypes ..........................................................................................21 1.3.5 IRIs and Prefixes .......................................................................................22 1.3.5.1 IRIs ............................................................................................22 -
OWL 2 Web Ontology Language Quick Reference Guide
OWL 2 Web Ontology Language Quick Reference W3C Proposed Recommendation 22 September Guide 2009 OWL 2 Web Ontology Language Quick Reference Guide W3C Proposed Recommendation 22 September 2009 This version: http://www.w3.org/TR/2009/PR-owl2-quick-reference-20090922/ Latest version: http://www.w3.org/TR/owl2-quick-reference/ Previous version: http://www.w3.org/TR/2009/WD-owl2-quick-reference-20090611/ (color-coded diff) Editors: Jie Bao, Rensselaer Polytechnic Institute Elisa F. Kendall, Sandpiper Software, Inc. Deborah L. McGuinness, Rensselaer Polytechnic Institute Peter F. Patel-Schneider, Bell Labs Research, Alcatel-Lucent Contributors: Li Ding, Rensselaer Polytechnic Institute Ankesh Khandelwal, Rensselaer Polytechnic Institute This document is also available in these non-normative formats: PDF version, Reference Card. Copyright © 2009 W3C® (MIT, ERCIM, Keio), All Rights Reserved. W3C liability, trademark and document use rules apply. Abstract The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information written in RDF, and OWL 2 ontologies themselves are primarily exchanged as RDF documents. The OWL 2 Document Overview describes the overall state of OWL 2, and should be read before other OWL 2 documents. Page 1 of 15 http://www.w3.org/TR/2009/PR-owl2-quick-reference-20090922/ OWL 2 Web Ontology Language Quick Reference W3C Proposed Recommendation 22 September Guide 2009 This document provides a non-normative quick reference guide to the OWL 2 language. -
Property Graph Vs RDF Triple Store: a Comparison on Glycan Substructure Search
RESEARCH ARTICLE Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search Davide Alocci1,2, Julien Mariethoz1, Oliver Horlacher1,2, Jerven T. Bolleman3, Matthew P. Campbell4, Frederique Lisacek1,2* 1 Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland, 2 Computer Science Department, University of Geneva, Geneva, 1227, Switzerland, 3 Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland, 4 Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia * [email protected] Abstract Resource description framework (RDF) and Property Graph databases are emerging tech- nologies that are used for storing graph-structured data. We compare these technologies OPEN ACCESS through a molecular biology use case: glycan substructure search. Glycans are branched Citation: Alocci D, Mariethoz J, Horlacher O, tree-like molecules composed of building blocks linked together by chemical bonds. The Bolleman JT, Campbell MP, Lisacek F (2015) molecular structure of a glycan can be encoded into a direct acyclic graph where each node Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search. PLoS ONE 10(12): represents a building block and each edge serves as a chemical linkage between two build- e0144578. doi:10.1371/journal.pone.0144578 ing blocks. In this context, Graph databases are possible software solutions for storing gly- Editor: Manuela Helmer-Citterich, University of can structures and Graph query languages, such as SPARQL and Cypher, can be used to Rome Tor Vergata, ITALY perform a substructure search. Glycan substructure searching is an important feature for Received: July 16, 2015 querying structure and experimental glycan databases and retrieving biologically meaning- ful data. -
SLA Information Technology Division Metadata for Video: Too Much
3/1/2019 Metadata for Video: Too Much Content, Not Enough Information | SLA Information Technology Division Home About Us » Events » Sections » Enter search keyword SLA Information Technology Division Awards » Making Edgier Easier. We're IT! Current b/ITe (v31n5) » b/ITe Archives Virtual Events What’s New Categorized | Uncategorized Metadata for Video: Too Much Content, Not Enough Information Posted on 31 August 2012. by Wayne Pender, McGill University, 2012 Joe Ann Clifton Student Award Winner (Published September 1, 2012) Abstract Television news libraries have struggled with cataloguing, organizing and storing visual materials for efficient search and retrieval for years. This task has been complicated by the emergence of digital video and the exponential growth in the holdings of television news libraries. In parallel, the ability for non-professionals to shoot, edit and publish videos of increasing production value and complexity on the web has flooded the Internet with videos that appeal to a wide audience and subject interest. The present survey looks at the metadata protocols and practices in place for an internal audience in professional operations and on display for the general public on the Internet. The study finds that the lack of a common metadata schema can make much of the material inaccessible. Literature pertaining to this area is reviewed and future direction is discussed. http://it.sla1.org/2012/08/metadata/ 1/10 3/1/2019 Metadata for Video: Too Much Content, Not Enough Information | SLA Information Technology Division Keywords: metadata, video, XML, RDF, MXF, television, news, YouTube Paper Searching and retrieving visual content is problematic. The search for specific moving images on film and video has long been a task for television news professionals, but now with wide spread availability of video resources on the Internet it has become a task for anyone. -
Schematron Overview Excerpted from Leigh Dodds’ 2001 XSLT UK Paper, “Schematron: Validating XML Using XSLT”
Schematron: validating XML using XSLT Schematron Overview excerpted from Leigh Dodds’ 2001 XSLT UK paper, “Schematron: validating XML using XSLT” Leigh Dodds, ingenta ltd, xmlhack.com April 2001 Abstract Schematron [Schematron] is a structural based validation language, defined by Rick Jelliffe, as an alternative to existing grammar based approaches. Tree patterns, defined as XPath expressions, are used to make assertions, and provide user-centred reports about XML documents. Expressing validation rules using patterns is often easier than defining the same rule using a content model. Tree patterns are collected together to form a Schematron schema. Schematron is a useful and accessible supplement to other schema languages. The open-source XSLT implementation is based around a core framework which is open for extension and customisation. Overview This paper provides an introduction to Schematron; an innovative XML validation language developed by Rick Jelliffe. This innovation stems from selecting an alternative approach to validation than existing schema languages: Schematron uses a tree pattern based paradigm, rather than the regular grammars used in DTDs and XML schemas. As an extensible, easy to use, open source tool Schematron is an extremely useful addition to the XML developers toolkit. The initial section of this paper conducts a brief overview of tree pattern validation, and some of the advantages it has in comparison to a regular grammar approach. This is followed by an outline of Schematron and the intended uses which have guided its design. The Schematron language is then discussed, covering all major elements in the language with examples of their 1 of 14 Schematron: validating XML using XSLT usage. -
Schema Declaration in Xml Document
Schema Declaration In Xml Document Is Darin varying or propellant when cluck some suffusion motive melodically? When Anton interdepend his titters reap not gyrally enough, is Parsifal malnourished? Styled Winnie scollop confoundedly, he reincreasing his stopple very refreshfully. When a uri that they come back into account only applies when sales orders that document in order to the design Must understand attribute Should I define a global attribute that will indicate to implementation the criticality of extension elements? Create a DOM parser to use for the validation of an instance document. As such, the XML Schema namespace, and provides a mapping between NIEM concepts and the RDF model. It is a convention to use XSD or XS as a prefix for the XML Schema namespace, et al. XML documents have sufficient structure to guarantee that they can be represented as a hierarchical tree. Are expanded names universally unique? DOC format for easy reading. This site uses cookies. This schema fragment shows the definition of an association type that defines a relationship between a person and a telephone number. Furthermore, such as Adobe Acrobat Reader. In some cases, if any. The idea behind using URIs for namespace names are that URIs are designed to be unique and persistent. Note: The material discussed in this section also applies to validating when using the SAX parser. Finally, Relax NG Schema, even when the elements and attributes defined by Microsoft are present. The XML representation for assertions. Developers of domain schemas and other schemas that build on and extend the NIEM release schemas need to be able to define additional characteristics of common types. -
Open Web Ontobud: an Open Source RDF4J Frontend
Open Web Ontobud: An Open Source RDF4J Frontend Francisco José Moreira Oliveira University of Minho, Braga, Portugal [email protected] José Carlos Ramalho Department of Informatics, University of Minho, Braga, Portugal [email protected] Abstract Nowadays, we deal with increasing volumes of data. A few years ago, data was isolated, which did not allow communication or sharing between datasets. We live in a world where everything is connected, and our data mimics this. Data model focus changed from a square structure like the relational model to a model centered on the relations. Knowledge graphs are the new paradigm to represent and manage this new kind of information structure. Along with this new paradigm, a new kind of database emerged to support the new needs, graph databases! Although there is an increasing interest in this field, only a few native solutions are available. Most of these are commercial, and the ones that are open source have poor interfaces, and for that, they are a little distant from end-users. In this article, we introduce Ontobud, and discuss its design and development. A Web application that intends to improve the interface for one of the most interesting frameworks in this area: RDF4J. RDF4J is a Java framework to deal with RDF triples storage and management. Open Web Ontobud is an open source RDF4J web frontend, created to reduce the gap between end users and the RDF4J backend. We have created a web interface that enables users with a basic knowledge of OWL and SPARQL to explore ontologies and extract information from them. -
A Performance Study of RDF Stores for Linked Sensor Data
Semantic Web 1 (0) 1–5 1 IOS Press 1 1 2 2 3 3 4 A Performance Study of RDF Stores for 4 5 5 6 Linked Sensor Data 6 7 7 8 Hoan Nguyen Mau Quoc a,*, Martin Serrano b, Han Nguyen Mau c, John G. Breslin d , Danh Le Phuoc e 8 9 a Insight Centre for Data Analytics, National University of Ireland Galway, Ireland 9 10 E-mail: [email protected] 10 11 b Insight Centre for Data Analytics, National University of Ireland Galway, Ireland 11 12 E-mail: [email protected] 12 13 c Information Technology Department, Hue University, Viet Nam 13 14 E-mail: [email protected] 14 15 d Confirm Centre for Smart Manufacturing and Insight Centre for Data Analytics, National University of Ireland 15 16 Galway, Ireland 16 17 E-mail: [email protected] 17 18 e Open Distributed Systems, Technical University of Berlin, Germany 18 19 E-mail: [email protected] 19 20 20 21 21 Editors: First Editor, University or Company name, Country; Second Editor, University or Company name, Country 22 Solicited reviews: First Solicited Reviewer, University or Company name, Country; Second Solicited Reviewer, University or Company name, 22 23 Country 23 24 Open reviews: First Open Reviewer, University or Company name, Country; Second Open Reviewer, University or Company name, Country 24 25 25 26 26 27 27 28 28 29 Abstract. The ever-increasing amount of Internet of Things (IoT) data emanating from sensor and mobile devices is creating 29 30 new capabilities and unprecedented economic opportunity for individuals, organisations and states. -
Instruction for Using XML Notepad
Using XML Notepad to Read, Edit, and Parse FGDC-CSDGM XML Metadata. Currently many tools exist that allow a user to work with XML metadata files. However, most of the main metadata creation/editing tools do not provide a means of validating a metadata record for compliance with the FGDC-CSDGM standard or its variants, such as the Biological Data Profile (BDP) standard. One of the most reliable ways to validate metadata files (that is, check files for completion and/or errors) is with the USGS Metadata Parser (MP) utilities. The MP tool and the other tools distributed in the package were developed by Peter Schweitzer and are freely available online (http://geology.usgs.gov/tools/metadata/tools/doc/mp.html). Once configured properly, MP can process metadata files and be used to produce a text file with a list of all errors found. A user can then use this list of errors to find and correct the problems using a text editor or the metadata editor of their choice. The challenge with this method is that finding and correcting the error within a metadata editor based solely on the error message from MP can be confusing and frustrating. Additionally, if there are many errors or complex problems to correct, the process will require multiple iterations of running MP and subsequently correcting errors in a metadata editor. All in all, the process can be fairly time consuming and onerous, especially for those without a detailed understanding of the FGDC-CSDGM standard. The methodology for metadata editing and validation described in this document tries to address some of these problems with an alternative approach.