Some Experiments on the Usage of a Deductive Database for RDFS Querying and Reasoning
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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. -
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. -
A Fuzzy Datalog Deductive Database System 1
A FUZZY DATALOG DEDUCTIVE DATABASE SYSTEM 1 A Fuzzy Datalog Deductive Database System Pascual Julian-Iranzo,´ Fernando Saenz-P´ erez´ Abstract—This paper describes a proposal for a deduc- particular, non-logic constructors are disallowed, as the cut), tive database system with fuzzy Datalog as its query lan- but it is not Turing-complete as it is meant as a database query guage. Concepts supporting the fuzzy logic programming sys- language. tem Bousi∼Prolog are tailored to the needs of the deductive database system DES. We develop a version of fuzzy Datalog Fuzzy Datalog [9] is an extension of Datalog-like languages where programs and queries are compiled to the DES core using lower bounds of uncertainty degrees in facts and rules. Datalog language. Weak unification and weak SLD resolution are Akin proposals as [10], [11] explicitly include the computation adapted for this setting, and extended to allow rules with truth de- of the rule degree, as well as an additional argument to gree annotations. We provide a public implementation in Prolog represent this degree. However, and similar to Bousi∼Prolog, which is open-source, multiplatform, portable, and in-memory, featuring a graphical user interface. A distinctive feature of this we are interested in removing this burden from the user system is that, unlike others, we have formally demonstrated with an automatic rule transformation that elides both the that our implementation techniques fit the proposed operational degree argument and the explicit call to fuzzy connective semantics. We also study the efficiency of these implementation computations in user rules. In addition, we provide support for techniques through a series of detailed experiments. -
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 -
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. -
A Deductive Database with Datalog and SQL Query Languages
A Deductive Database with Datalog and SQL Query Languages FernandoFernando SSááenzenz PPéérez,rez, RafaelRafael CaballeroCaballero andand YolandaYolanda GarcGarcííaa--RuizRuiz GrupoGrupo dede ProgramaciProgramacióónn DeclarativaDeclarativa (GPD)(GPD) UniversidadUniversidad ComplutenseComplutense dede MadridMadrid (Spain)(Spain) 12/5/2011 APLAS 2011 1 ~ ContentsContents 1.1. IntroductionIntroduction 2.2. QueryQuery LanguagesLanguages 3.3. IntegrityIntegrity ConstraintsConstraints 4.4. DuplicatesDuplicates 5.5. OuterOuter JoinsJoins 6.6. AggregatesAggregates 7.7. DebuggersDebuggers andand TracersTracers 8.8. SQLSQL TestTest CaseCase GeneratorGenerator 9.9. ConclusionsConclusions 12/5/2011 APLAS 2011 2 ~ 1.1. IntroductionIntroduction SomeSome concepts:concepts: DatabaseDatabase (DB)(DB) DatabaseDatabase ManagementManagement SystemSystem (DBMS)(DBMS) DataData modelmodel (Abstract) data structures Operations Constraints 12/5/2011 APLAS 2011 3 ~ IntroductionIntroduction DeDe--factofacto standardstandard technologiestechnologies inin databases:databases: “Relational” model SQL But,But, aa currentcurrent trendtrend towardstowards deductivedeductive databases:databases: Datalog 2.0 Conference The resurgence of Datalog inin academiaacademia andand industryindustry Ontologies Semantic Web Social networks Policy languages 12/5/2011 APLAS 2011 4 ~ Introduction.Introduction. SystemsSystems Classic academic deductive systems: LDL++ (UCLA) CORAL (Univ. of Wisconsin) NAIL! (Stanford University) Ongoing developments Recent commercial -
Comparative Study of Database Modeling Approaches
COMPARATIVE STUDY OF DATABASE MODELING APPROACHES Department of Computer Science Algoma University APRIL 2014 Advisor Dr. Simon Xu By Mohammed Aljarallah ABSTRACT An overview and comparative study of different database modeling approaches have been conducted in the thesis. The foundation of every structure is important and if the foundation is weak the whole system can collapse and database is the foundation of every software system. The complexity and simplicity of this core area of software development is also a very important issue as different modeling techniques are used according to the requirements of software and evaluation of these techniques is necessary. The approach of the thesis is a literature survey and background of data modeling techniques. All the requirements of data modeling and database systems are encapsulated here along with the structure of database. The foundation of the thesis is developed by discussing some of the cases studies regarding the database models from the practical field to develop an understanding of database systems, models and techniques from the practical perspective. The study of database system and most of the models are investigated in the thesis to establish a scenario in which these modeling approaches could be compared in a more innovative and better way. Relational database modeling approach is one of the important techniques used to develop the database system and the technique that could be used as replacement of relational model as single or in hybrid way is also an interesting aspect of survey. The comparisons of traditional and modern database modeling methodologies are also discussed here to highlight the features of current database management systems. -
A Digital Library for Plant Information with Performance Comparison Between a Relational Database and a Nosql Database (RDF Triple Store)
Grand Valley State University ScholarWorks@GVSU Technical Library School of Computing and Information Systems 2015 A Digital Library for Plant Information with Performance Comparison between a Relational Database and a NoSQL Database (RDF Triple Store) Md Arman Ullah Grand Valley State University Follow this and additional works at: https://scholarworks.gvsu.edu/cistechlib ScholarWorks Citation Ullah, Md Arman, "A Digital Library for Plant Information with Performance Comparison between a Relational Database and a NoSQL Database (RDF Triple Store)" (2015). Technical Library. 205. https://scholarworks.gvsu.edu/cistechlib/205 This Project is brought to you for free and open access by the School of Computing and Information Systems at ScholarWorks@GVSU. It has been accepted for inclusion in Technical Library by an authorized administrator of ScholarWorks@GVSU. For more information, please contact [email protected]. A Digital Library for Plant Information with Performance Comparison between a Relational Database and a NoSQL Database (RDF Triple Store) By Md Arman Ullah A project submitted in partial fulfillment of the requirements for the degree of Master of Science in Computer Information System at Grand Valley State University April, 2015 Dr. Tao Yonglei Date Abstract This project is to develop a digital library that allows the user to browse, search, and retrieve information about plants. It uses plant information acquired from the United States Department of Agriculture (USDA), which contains native and naturalized plants in North American territories. In addition, the user is allowed to contribute information and the administrator is able to add or edit plant information. This project is built by using a relational database and also a NoSQL database (RDF Triple Store), allowing to compare performance between the two databases. -
Combining Unstructured, Fully Structured and Semi-Structured Information in Semantic Wikis
Combining Unstructured, Fully Structured and Semi-Structured Information in Semantic Wikis Rolf Sint1, Sebastian Schaffert1, Stephanie Stroka1 and Roland Ferstl2 1 [email protected] Salzburg Research Jakob Haringer Str. 5/3 5020 Salzburg Austria 2 [email protected] Siemens AG (Siemens IT Solutions and Services) Werner von Siemens-Platz 1 5020 Salzburg Austria Abstract. The growing impact of Semantic Wikis deduces the impor- tance of finding a strategy to store textual articles, semantic metadata and management data. Due to their different characteristics, each data type requires a specialized storing system, as inappropriate storing re- duces performance, robustness, flexibility and scalability. Hence, it is important to identify a sophisticated strategy for storing and synchro- nizing different types of data structures in a way they provide the best mix of the previously mentioned properties. In this paper we compare fully structured, semi-structured and unstruc- tured data and present their typical appliance. Moreover, we discuss how all data structures can be combined and stored for one application and consider three synchronization design alternatives to keep the dis- tributed data storages consistent. Furthermore, we present the semantic wiki KiWi, which uses an RDF triplestore in combination with a re- lational database as basis for the persistence of data, and discuss its concrete implementation and design decisions. 1 Introduction Although the promise of effective knowledge management has had the indus- try abuzz for well over a decade, the reality of available systems fails to meet the expectations. The EU-funded project KiWi - Knowledge in a Wiki project sets out to combine the wiki method of collaborative content creation with the technologies of the Semantic Web to bring knowledge management to the next level. -
DES: a Deductive Database System Des.Sourceforge.Net
DES: A Deductive Database System des.sourceforge.net FernandoFernando SSááenzenz PPéérezrez GrupoGrupo dede ProgramaciProgramacióónn DeclarativaDeclarativa (GPD)(GPD) DeptDept.. IngenierIngenierííaa deldel SoftwareSoftware ee InteligenciaInteligencia ArtificialArtificial UniversidadUniversidad ComplutenseComplutense dede MadridMadrid FacultadFacultad dede InformInformááticatica PROLE 2010 10/9/2010 1 / 30 ContentsContents 1.1. IntroductionIntroduction 2.2. FeaturesFeatures 3.3. QueryQuery LanguagesLanguages 4.4. OuterOuter JoinsJoins 5.5. AggregatesAggregates 6.6. DESDES asas aa TestTest--BedBed forfor ResearchResearch 7.7. ImpactImpact FactorFactor 8.8. ConclusionsConclusions PROLE 2010 10/9/2010 2 / 30 1.1. IntroductionIntroduction Databases:Databases: FromFrom relationalrelational toto deductivedeductive (Declarative)(Declarative) QueryQuery Languages:Languages: FromFrom SQLSQL toto DatalogDatalog PROLE 2010 10/9/2010 3 / 30 1.1. Introduction:Introduction: DatalogDatalog AA databasedatabase queryquery languagelanguage stemmingstemming fromfrom PrologProlog PrologProlog DatalogDatalog PredicatePredicate RelationRelation GoalGoal QueryQuery MeaningMeaning ofof aa predicatepredicate ((Multi)setMulti)set ofof derivablederivable factsfacts Intensionally (Rules or Clauses) Extensionally (Facts) PROLE 2010 10/9/2010 4 / 30 1.1. Introduction:Introduction: DatalogDatalog WhatWhat aa typicaltypical databasedatabase useruser wouldwould expectexpect fromfrom aa queryquery language?language? FiniteFinite data,data, finitefinite computationscomputations -
Tilburg University a Deductive Database Management System in Prolog Gelsing, P.P
Tilburg University A deductive database management system in Prolog Gelsing, P.P. Publication date: 1989 Document Version Publisher's PDF, also known as Version of record Link to publication in Tilburg University Research Portal Citation for published version (APA): Gelsing, P. P. (1989). A deductive database management system in Prolog. (ITK Research Memo). Institute for Language Technology and Artifical IntelIigence, Tilburg University. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 27. sep. 2021 i CBM ~~ R ~~ , r ~~~: `j 8419 ~`~~~ ~~~` 1989 J~~~ ~ iiiiiiiuiiiiiuiiuiiuiiiuiiiiiiiui ~ C I N 0 0 2 8 3~ 4 INSTITUTE FOR LANGUAGE TECHNOLOGY AND ARTIFICIAL INTELLIGENCE INSTITUUT VOOR TAAL- EN KENNISTECHNOLOGIE r~~. , `-,~ d i~;~!í;'~:.1l.B. ~ ~,,~~'.;, ~:~; ! 7T!-!-~K J~ , TtL~i~1:-y!(à I.T.K. Research Memo no. 4 November 1989 A Deductive Database Management System in Prolog Paul P. Gelsing Institute for Language Technology and Artificizl Intelligence, Tilburg University, The Netherlands Table of Contents Introduction . -
A Basis for Deductive Database Systems Ii
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector J. LOGIC PROGRAMMING 1986:1:55-67 55 A BASIS FOR DEDUCTIVE DATABASE SYSTEMS II J. W. LLOYD AND R. W. TOPOR* D This paper is the third in a series providing a theoretical basis for deductive database systems. A deductive database consists of closed typed first order logic formulas of the form A + W, where A is an atom and W is a typed first order formula. A typed first order formula can be used as a query, and a closed typed first order formula can be used as an integrity constraint. Functions are allowed to appear in formulas. Such a deductive database system can be implemented using a PROLOG system. The main results of this paper are concerned with the nonfloundering and completeness of query evaluation. We also introduce an alternative query evaluation process and show that corresponding versions of the earlier results can be obtained. Finally, we summarize the results of the three papers and discuss the attractive properties of the deductive database system approach based on first order logic. a 1. INTRODUCTION The use of deductive database systems based on first order logic has recently received considerable interest because of their many attractive properties [3-6,131. In particular, first order logic has a well-developed theory and can be used as a uniform language for data, programs, queries, views, and integrity constraints. One promising approach to implementing deductive database systems is to use a PROLOG system as the query evaluator [2,7,9-11,15,16].