Evaluation Criteria for RDF Triplestores with an Application to Allegrograph
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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. -
Graph Database for Collaborative Communities Rania Soussi, Marie-Aude Aufaure, Hajer Baazaoui
Graph Database for Collaborative Communities Rania Soussi, Marie-Aude Aufaure, Hajer Baazaoui To cite this version: Rania Soussi, Marie-Aude Aufaure, Hajer Baazaoui. Graph Database for Collaborative Communities. Community-Built Databases, Springer, pp.205-234, 2011. hal-00708222 HAL Id: hal-00708222 https://hal.archives-ouvertes.fr/hal-00708222 Submitted on 14 Jun 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Graph Database For collaborative Communities 1, 2 1 Rania Soussi , Marie-Aude Aufaure , Hajer Baazaoui2 1Ecole Centrale Paris, Applied Mathematics & Systems Laboratory (MAS), SAP Business Objects Academic Chair in Business Intelligence 2Riadi-GDL Laboratory, ENSI – Manouba University, Tunis Abstract Data manipulated in an enterprise context are structured data as well as un- structured data such as emails, documents, social networks, etc. Graphs are a natural way of representing and modeling such data in a unified manner (Structured, semi-structured and unstructured ones). The main advantage of such a structure relies in the dynamic aspect and the capability to represent relations, even multiple ones, between objects. Recent database research work shows a growing interest in the definition of graph models and languages to allow a natural way of handling data appearing. -
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 -
Franz's Allegrograph 7.1 Accelerates Complex Reasoning Across
Franz’s AllegroGraph 7.1 Accelerates Complex Reasoning Across Massive, Distributed Knowledge Graphs and Data Fabrics Distributed FedShard Queries Improved 10X. New SPARQL*, RDF* and SHACL Features Added. Lafayette, Calif., February 8, 2021 — Franz Inc., an early innovator in Artificial Intelligence (AI) and leading supplier of Graph Database technology for AI Knowledge Graph Solutions, today announced AllegroGraph 7.1, which provides optimizations for deeply complex queries across FedShard™ deployments – making complex reasoning up to 10X faster. AllegroGraph with FedShard offers a breakthrough solution that allows infinite data integration through a patented approach unifying all data and siloed knowledge into an Entity-Event Knowledge Graph solution for Enterprise scale analytics. AllegroGraph’s unique capabilities drive 360-degree insights and enable complex reasoning across enterprise-wide Knowledge Fabrics in Healthcare, Media, Smart Call Centers, Pharmaceuticals, Financial and much more. “The proliferation of Artificial Intelligence has resulted in the need for increasingly complex queries over more data,” said Dr. Jans Aasman, CEO of Franz Inc. “AllegroGraph 7.1 addresses two of the most daunting challenges in AI – continuous data integration and the ability to query across all the data. With this new version of AllegroGraph, organizations can create Data Fabrics underpinned by AI Knowledge Graphs that take advantage of the infinite data integration capabilities possible with our FedShard technology and the ability to query across -
Using Microsoft Power BI with Allegrograph,Knowledge Graphs Rise
Using Microsoft Power BI with AllegroGraph There are multiple methods to integrate AllegroGraph SPARQL results into Microsoft Power BI. In this document we describe two best practices to automate queries and refresh results if you have a production AllegroGraph database with new streaming data: The first method uses Python scripts to feed Power BI. The second method issues SPARQL queries directly from Power BI using POST requests. Method 1: Python Script: Assuming you know Python and have it installed locally, this is definitely the easiest way to incorporate SPARQL results into Power BI. The basic idea of the method is as follows: First, the Python script enables a connection to your desired AllegroGraph repository. Then we utilize AllegroGraph’s Python API within our script to run a SPARQL query and return it as a Pandas dataframe. When running this script within Power BI Desktop, the Python scripting service recognizes all unique dataframes created, and allows you to import the dataframe into Power BI as a table, which can then be used to create visualizations. Requirements: 1. You must have the AllegroGraph Python API installed. If you do not, installation instructions are here: https://franz.com/agraph/support/documentation/current/p ython/install.html 2. Python scripting must be enabled in Power BI Desktop. Instructions to do so are here: https://docs.microsoft.com/en-us/power-bi/connect-data/d esktop-python-scripts a) As mentioned in the article, pandas and matplotlib must be installed. This can be done with ‘pip install pandas’ and ‘pip install matplotlib’ in your terminal. -
Practical Semantic Web and Linked Data Applications
Practical Semantic Web and Linked Data Applications Common Lisp Edition Uses the Free Editions of Franz Common Lisp and AllegroGraph Mark Watson Copyright 2010 Mark Watson. All rights reserved. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works Version 3.0 United States License. November 3, 2010 Contents Preface xi 1. Getting started . xi 2. Portable Common Lisp Code Book Examples . xii 3. Using the Common Lisp ASDF Package Manager . xii 4. Information on the Companion Edition to this Book that Covers Java and JVM Languages . xiii 5. AllegroGraph . xiii 6. Software License for Example Code in this Book . xiv 1. Introduction 1 1.1. Who is this Book Written For? . 1 1.2. Why a PDF Copy of this Book is Available Free on the Web . 3 1.3. Book Software . 3 1.4. Why Graph Data Representations are Better than the Relational Database Model for Dealing with Rapidly Changing Data Requirements . 4 1.5. What if You Use Other Programming Languages Other Than Lisp? . 4 2. AllegroGraph Embedded Lisp Quick Start 7 2.1. Starting AllegroGraph . 7 2.2. Working with RDF Data Stores . 8 2.2.1. Creating Repositories . 9 2.2.2. AllegroGraph Lisp Reader Support for RDF . 10 2.2.3. Adding Triples . 10 2.2.4. Fetching Triples by ID . 11 2.2.5. Printing Triples . 11 2.2.6. Using Cursors to Iterate Through Query Results . 13 2.2.7. Saving Triple Stores to Disk as XML, N-Triples, and N3 . 14 2.3. AllegroGraph’s Extensions to RDF . -
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. -
Application of Graph Databases for Static Code Analysis of Web-Applications
Application of Graph Databases for Static Code Analysis of Web-Applications Daniil Sadyrin [0000-0001-5002-3639], Andrey Dergachev [0000-0002-1754-7120], Ivan Loginov [0000-0002-6254-6098], Iurii Korenkov [0000-0002-8948-2776], and Aglaya Ilina [0000-0003-1866-7914] ITMO University, Kronverkskiy prospekt, 49, St. Petersburg, 197101, Russia [email protected], [email protected], [email protected], [email protected], [email protected] Abstract. Graph databases offer a very flexible data model. We present the approach of static code analysis using graph databases. The main stage of the analysis algorithm is the construction of ASG (Abstract Source Graph), which represents relationships between AST (Abstract Syntax Tree) nodes. The ASG is saved to a graph database (like Neo4j) and queries to the database are made to get code properties for analysis. The approach is applied to detect and exploit Object Injection vulnerability in PHP web-applications. This vulnerability occurs when unsanitized user data enters PHP unserialize function. Successful exploitation of this vulnerability means building of “object chain”: a nested object, in the process of deserializing of it, a sequence of methods is being called leading to dangerous function call. In time of deserializing, some “magic” PHP methods (__wakeup or __destruct) are called on the object. To create the “object chain”, it’s necessary to analyze methods of classes declared in web-application, and find sequence of methods called from “magic” methods. The main idea of author’s approach is to save relationships between methods and functions in graph database and use queries to the database on Cypher language to find appropriate method calls. -
Database Software Market: Billy Fitzsimmons +1 312 364 5112
Equity Research Technology, Media, & Communications | Enterprise and Cloud Infrastructure March 22, 2019 Industry Report Jason Ader +1 617 235 7519 [email protected] Database Software Market: Billy Fitzsimmons +1 312 364 5112 The Long-Awaited Shake-up [email protected] Naji +1 212 245 6508 [email protected] Please refer to important disclosures on pages 70 and 71. Analyst certification is on page 70. William Blair or an affiliate does and seeks to do business with companies covered in its research reports. As a result, investors should be aware that the firm may have a conflict of interest that could affect the objectivity of this report. This report is not intended to provide personal investment advice. The opinions and recommendations here- in do not take into account individual client circumstances, objectives, or needs and are not intended as recommen- dations of particular securities, financial instruments, or strategies to particular clients. The recipient of this report must make its own independent decisions regarding any securities or financial instruments mentioned herein. William Blair Contents Key Findings ......................................................................................................................3 Introduction .......................................................................................................................5 Database Market History ...................................................................................................7 Market Definitions -
Gábor Melis to Keynote European Lisp Symposium
Gábor Melis to Keynote European Lisp Symposium OAKLAND, Calif. — April 14, 2014 —Franz Inc.’s Senior Engineer, Gábor Melis, will be a keynote speaker at the 7th annual European Lisp Symposium (ELS’14) this May in Paris, France. The European Lisp Symposium provides a forum for the discussion and dissemination of all aspects of design, implementationand application of any of the Lisp and Lisp- inspired dialects, including Common Lisp, Scheme, Emacs Lisp, AutoLisp, ISLISP, Dylan, Clojure, ACL2, ECMAScript, Racket, SKILL, Hop etc. Sending Beams into the Parallel Cube A pop-scientific look through the Lisp lens at machine learning, parallelism, software, and prize fighting We send probes into the topic hypercube bounded by machine learning, parallelism, software and contests, demonstrate existing and sketch future Lisp infrastructure, pin the future and foreign arrays down. We take a seemingly random walk along the different paths, watch the scenery of pairwise interactions unfold and piece a puzzle together. In the purely speculative thread, we compare models of parallel computation, keeping an eye on their applicability and lisp support. In the the Python and R envy thread, we detail why lisp could be a better vehicle for scientific programming and how high performance computing is eroding lisp’s largely unrealized competitive advantages. Switching to constructive mode, a basic data structure is proposed as a first step. In the machine learning thread, lisp’s unparalleled interactive capabilities meet contests, neural networks cross threads and all get in the way of the presentation. Video Presentation About Gábor Melis Gábor Melis is a consultant at Franz Inc. -
Evaluation of Current RDF Database Solutions
Evaluation of Current RDF Database Solutions Florian Stegmaier1, Udo Gr¨obner1, Mario D¨oller1, Harald Kosch1 and Gero Baese2 1 Chair of Distributed Information Systems University of Passau Passau, Germany [email protected] 2 Corporate Technology Siemens AG Munich, Germany [email protected] Abstract. Unstructured data (e.g., digital still images) is generated, distributed and stored worldwide at an ever increasing rate. In order to provide efficient annotation, storage and search capabilities among this data and XML based description formats, data stores and query languages have been introduced. As XML lacks on expressing semantic meanings and coherences, it has been enhanced by the Resource Descrip- tion Format (RDF) and the associated query language SPARQL. In this context, the paper evaluates currently existing RDF databases that support the SPARQL query language by the following means: gen- eral features such as details about software producer and license infor- mation, architectural comparison and efficiency comparison of the inter- pretation of SPARQL queries on a scalable test data set. 1 Introduction The production of unstructured data especially in the multimedia domain is overwhelming. For instance, recent studies3 report that 60% of today's mobile multimedia devices equipped with an image sensor, audio support and video playback have basic multimedia functionalities, almost nine out of ten in the year 2011. In this context, the annotation of unstructured data has become a necessity in order to increase retrieval efficiency during search. In the last couple of years, the Extensible Markup Language (XML) [16], due to its interoperability features, has become a de-facto standard as a basis for the use of description formats in various domains.