SPARQL Query Engine Research Articles

VeriDKG: A Verifiable SPARQL Query Engine for Decentralized Knowledge Graphs

The ability to decentralize knowledge graphs (KG) is important to exploit the full potential of the Semantic Web and realize the Web 3.0 vision. However, decentralization also renders KGs more prone to attacks with adverse effects on data integrity and query verifiability. While existing studies focus on ensuring data integrity, how to ensure query verifiability - thus guarding against incorrect, incomplete, or outdated query results - remains unsolved. We propose VeriDKG, the first SPARQL query engine for decentralized knowledge graphs (DKG) that offers both data integrity and query verifiability guarantees. The core of VeriDKG is the RGB-Trie, a new blockchain-maintained authenticated data structure (ADS) facilitating correctness proofs for SPARQL query results. VeriDKG enables verifiability of subqueries by gathering global index information on subgraphs using the RGB-Trie, which is implemented as a new variant of the Merkle prefix tree with an RGB color model. To enable verifiability of the final query result, the RGB-Trie is integrated with a cryptographic accumulator to support verifiable aggregation operations. A rigorous analysis of query verifiability in VeriDKG is presented, along with evidence from an extensive experimental study demonstrating its state-of-the-art query performance on the largeRDFbench benchmark.

GeoSPARQL query support for scientific raster array data

This paper presents the design of a GeoSPARQL query processing solution for scientific raster array data, called GeoLD. The solution enables the implementation of SPARQL endpoints on top of OGC standard Web Coverage Processing Services (WCPS). Thus, the semantic querying of scientific raster data is supported without the need of specific raster array functions in the language. To achieve this, first Coverage to RDF mapping solutions were defined, based on the well-known W3C standard mappings for relational data. Next, the SPARQL algebra is extended with a new operator that delegates part of the GeoSPARQL query in WCPS services. Query optimization replaces those parts of the SPARQL query plan that may be delegated to a WCPS service by instances of such new WCPS operator. A first prototype has been implemented by extending the ARQ SPARQL query engine of Apache Jena. Petascope was used as the WCPS implementation on top of the Rasdaman raster array database. An initial evaluation with real meteorological data shows, as it was initially expected, that the approach outperforms an existing reference relational database based GeoSPARQL implementation.

A survey of RDF stores & SPARQL engines for querying knowledge graphs

RDF has seen increased adoption in recent years, prompting the standardization of the SPARQL query language for RDF, and the development of local and distributed engines for processing SPARQL queries. This survey paper provides a comprehensive review of techniques and systems for querying RDF knowledge graphs. While other reviews on this topic tend to focus on the distributed setting, the main focus of the work is on providing a comprehensive survey of state-of-the-art storage, indexing and query processing techniques for efficiently evaluating SPARQL queries in a local setting (on one machine). To keep the survey self-contained, we also provide a short discussion on graph partitioning techniques used in the distributed setting. We conclude by discussing contemporary research challenges for further improving SPARQL query engines. An extended version also provides a survey of over one hundred SPARQL query engines and the techniques they use, along with twelve benchmarks and their features.

SPARQL2Flink: Evaluation of SPARQL Queries on Apache Flink

Existing SPARQL query engines and triple stores are continuously improved to handle more massive datasets. Several approaches have been developed in this context proposing the storage and querying of RDF data in a distributed fashion, mainly using the MapReduce Programming Model and Hadoop-based ecosystems. New trends in Big Data technologies have also emerged (e.g., Apache Spark, Apache Flink); they use distributed in-memory processing and promise to deliver higher data processing performance. In this paper, we present a formal interpretation of some PACT transformations implemented in the Apache Flink DataSet API. We use this formalization to provide a mapping to translate a SPARQL query to a Flink program. The mapping was implemented in a prototype used to determine the correctness and performance of the solution. The source code of the project is available in Github under the MIT license.

Hetero-GCD2RDF: An Interoperable Solution for Geospatial Climatic Data by Deploying Semantic Web Technologies

Ocean and Land based satellite observation system comprises of various sensors and configurations. The generated Geospatial Climatic Data (GCD) by sensors is transmitted in heterogeneous file formats with heterogeneous vocabularies that lead to semantic heterogeneity of data. Government and public organizations started to publish these datasets to users through climatic web portals. The critical task in handling heterogeneous files is data interpretation and interoperability. This can be handled by facilitating the data to reach semantically structured or linked data. This paper proposes a Hetero-GCD2RDF data retrieval approach that focuses on two aspects (1) Extraction of records from satellite data and represent it as linked data namely Resource Description Framework (RDF) and (2) Implementation of SPARQL query engine to the resultant RDF for data retrieval. Data from Indian Meteorological Satellite INSAT-3D is taken as a typical example to execute the proposed approach. Where, approximately 170 files of about 650 MB in memory containing 1,278,000 records have been converted and queried. Compared to conventional methods the proposed method saves nearly 38.12% of time to represent the data in RDF. Thus, the proposed Hetero-GCD2RDF approach is recognized to be efficient, reliable and suitable for semantic web.

SUMA: A Partial Materialization-Based Scalable Query Answering in OWL 2 DL

Ontology-mediated querying (OMQ) provides a paradigm for query answering according to which users not only query records at the database but also query implicit information inferred from ontology. A key challenge in OMQ is that the implicit information may be infinite, which cannot be stored at the database and queried by off -the -shelf query engine. The commonly adopted technique to deal with infinite entailments is query rewriting, which, however, comes at the cost of query rewriting at runtime. In this work, the partial materialization method is proposed to ensure that the extension is always finite. The partial materialization technology does not rewrite query but instead computes partial consequences entailed by ontology before the online query. Besides, a query analysis algorithm is designed to ensure the completeness of querying rooted and Boolean conjunctive queries over partial materialization. We also soundly and incompletely expand our method to support highly expressive ontology language, OWL 2 DL. Finally, we further optimize the materialization efficiency by role rewriting algorithm and implement our approach as a prototype system SUMA by integrating off-the-shelf efficient SPARQL query engine. The experiments show that SUMA is complete on each test ontology and each test query, which is the same as Pellet and outperforms PAGOdA. Besides, SUMA is highly scalable on large datasets.

An empirical evaluation of cost-based federated SPARQL query processing engines

Finding a good query plan is key to the optimization of query runtime. This holds in particular for cost-based federation engines, which make use of cardinality estimations to achieve this goal. A number of studies compare SPARQL federation engines across different performance metrics, including query runtime, result set completeness and correctness, number of sources selected and number of requests sent. Albeit informative, these metrics are generic and unable to quantify and evaluate the accuracy of the cardinality estimators of cost-based federation engines. To thoroughly evaluate cost-based federation engines, the effect of estimated cardinality errors on the overall query runtime performance must be measured. In this paper, we address this challenge by presenting novel evaluation metrics targeted at a fine-grained benchmarking of cost-based federated SPARQL query engines. We evaluate five cost-based federated SPARQL query engines using existing as well as novel evaluation metrics by using LargeRDFBench queries. Our results provide a detailed analysis of the experimental outcomes that reveal novel insights, useful for the development of future cost-based federated SPARQL query processing engines.

Dataset Characteristics Identification for Federated SPARQL Query

Nowadays, the amount of data published in the RDF format is increasing. Federated SPARQL query engines that can query from multiple distributed SPARQL endpoints have been developed recently. A federated query engine usually has different performance compared to the others. One of the factors that affect the performance of the query engine is the characteristic of the accessed RDF dataset, such as the number of triples, the number of classes, the number of properties, the number of subjects, the number of entities, the number of objects, and the spreading factor of a dataset. The aim of this work is to identify the characteristic of RDF dataset and create a query set for evaluating a federated engine. The study was conducted by identifying 16 datasets that used by ten research papers in Linked Data area.

DESERT: A Continuous SPARQL Query Engine for On-Demand Query Answering

The Internet of Things (IoT) has been rapidly adopted in many domains ranging from household appliances e.g. ventilation, lighting, and heating, to industrial manufacturing and transport networks. Despite the, enormous benefits of optimization, monitoring, and maintenance rendered by IoT devices, an ample amount of data is generated continuously. Semantically describing IoT generated data using ontologies enables a precise interpretation of this data. However, ontology-based descriptions tremendously increase the size of IoT data and in presence of repeated sensor measurements, a large amount of the data are duplicates that do not contribute to new insights during query processing or IoT data analytics. In order to ensure that only required ontology-based descriptions are generated, we devise a knowledge-driven approach named DESERT that is able to on-[Formula: see text]emand factoriz[Formula: see text] and [Formula: see text]emantically [Formula: see text]nrich st[Formula: see text]eam da[Formula: see text]a. DESERT resorts to a knowledge graph to describe IoT stream data; it utilizes only the data that is required to answer an input continuous SPARQL query and applies a novel method of data factorization to reduce duplicated measurements in the knowledge graph. The performance of DESERT is empirically studied on a collection of continuous SPARQL queries from SRBench, a benchmark of IoT stream data and continuous SPARQL queries. Furthermore, data streams with various combinations of uniform and varying data stream speeds and streaming window size dimensions are considered in the study. Experimental results suggest that DESERT is capable of speeding up continuous query processing while creates knowledge graphs that include no replications.

A SPARQL query engine for binary-formatted IFC building models

Abstract To date, widely implemented and full-featured query languages for building models in their native exchange formats do not exist. While interesting proposals exist for querying Industry Foundation Classes (IFC) models, their functionality is often incomplete and their semantics not precisely defined. With the introduction of the ifcOWL ontology as an equivalent to the IFC schema in the Web Ontology Language (OWL), an option to represent such models in RDF (Resource Description Framework, a general information modeling method) is provided, and such models can be queried using SPARQL (SPARQL Protocol and RDF Query Language). The size of data sets in complex building projects, however, renders the use of clear-text encoded RDF infeasible in many cases. A SPARQL implementation, compatible with ifcOWL, is proposed, directly atop a standardized binary serialization format for IFC building models. This novel format is the binary equivalent of traditional IFC serialization formats but with more compact storage and less overhead than the graph serialization in RDF. The format is based on ISO 10303-26 and relies on an open standard for organizing large amounts of data: Hierarchical Data Format version 5 (HDF5). Due to hierarchical partitioning and fixed-length records, only small subsets of the data are read to answer queries, improving efficiency. A prototypical implementation of the query engine is provided in the Python programming language. In several realistic use cases, the proposed system performs equivalent to or better than the state of the art in SPARQL querying on building models. For large datasets, the proposed storage format results in files that are 2–3 times smaller than the current, most concise, RDF databases while offering a platform-neutral, containerized exchange file.

CostFed: Cost-Based Query Optimization for SPARQL Endpoint Federation

The runtime optimization of federated SPARQL query engines is of central importance to ensure the usability of the Web of Data in real-world applications. The efficient selection of sources (SPARQL endpoints in our case) as well as the generation of optimized query plans belong to the most important optimization steps in this respect. This paper presents CostFed, an index-assisted federation engine for federated SPARQL query processing. CostFed makes use of statistical information collected from endpoints to perform efficient source selection and cost-based query planning. In contrast to the state of the art, it relies on a non-linear model for the estimation of the selectivity of joins. Therewith, it is able to generate better plans than the state-of-the-art federation engines. Our experiments on the FedBench benchmark shows that CostFed is 3 to 121 times faster than the current federation engines.

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

BackgroundPubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as an increasingly important approach to distribute and integrate scientific data. Exposing PubChem data to Semantic Web services may help enable automated data integration and management, as well as facilitate interoperable web applications.DescriptionThis work, one of a series covering the PubChemRDF project, describes an approach to translate PubChem Substance and Compound information into Resource Description Framework (RDF) format. Basic examples are provided to demonstrate its use. The aim of this effort is to provide two new primary benefits to researchers in a cost-effective manner. Firstly, we aim to remove the inherent limitations of using the web-based resource PubChem by allowing a researcher to use readily available semantic technologies (namely, RDF triple stores and their corresponding SPARQL query engines) to query and analyze PubChem data on local computing resources. Secondly, this work intends to help improve data sharing, analysis, and integration of PubChem data to resources external to NCBI and across scientific domains, by means of the association of PubChem data to existing ontological frameworks, including CHEMical INFormation ontology, Semanticscience Integrated Ontology, and others.ConclusionsWith the goal of semantically describing information available in the PubChem archive, pre-existing ontological frameworks were used, rather than creating new ones. Semantic relationships between compounds and substances, chemical descriptors associated with compounds and substances, interrelationships between chemicals, as well as provenance and attribute metadata of substances are described.Graphical abstract:Schematic representation of the semantic links for PubChem compounds and substances.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0084-4) contains supplementary material, which is available to authorized users.

A Decision Support System (DSS) for Colorectal Cancer Follow-Up Program via a Semantic Framework

This paper offers insights into evolving a decision support system (DSS) to aid primary care physicians and/or nurses in the post-surgical care of patients with Colorectal Cancer in a clinical setting. Presently, the oncologists in the cancer center, who are familiar with the Clinical Practice Guidelines (CPGs), are primarily responsible for the provision of follow-up care to their patients on the basis of the CPGs; in contrast, the attending primary care physician and/or nurse assisting the oncologist may be unfamiliar with these guidelines. These caregivers would, therefore, either require hardcopies of the CPGs or can be aided via a DSS for them to be able to provide the appropriate follow-up care for the respective cancer patients. Clearly, the Colorectal Cancer follow-up CPGs have to be analyzed and the ontology representing the knowledge embedded in the guidelines designed prior to realizing such a DSS. The designed ontology is often coded into Web Ontology Language (OWL) as a standard ontology that can be accessed through the Web. The authors' research team designed and presented the semantic framework of the web application, using the designed ontology that combines the current Web technology with database storage to achieve a unified development of the DSS. The authors also designed a user-friendly interface of the Web application to provide medical practitioners the functionality of the CPGs and the flexibility to customize the desired follow-up care schedule. The resulting DSS provides the physicians with follow-up program for the Colorectal Cancer patients based on the CPGs. The system was built using the semantic framework for the follow-up program and queries on the system are executed through SPARQL query engine.

Extended Query Pattern Graph and Heuristics - based SPARQL Query Planning

SPARQL query language plays a significant role in developing semantic web and web intelligence. In order to deal with large data query execution over RDF, SPARQL query optimizer is an essential component in the SPARQL query engine for improving query execution performance. This paper proposes an approach for performing query planning and optimization based on an extended query pattern graph and heuristics. First, this paper generalizes SPARQL query statement representation by taking other expressions into account, aiming at overcoming the limitations of only using basic query triple patterns. Second, this paper presents the heuristics for estimating the cost of executing query triple pattern. The proposed query planning methods are implemented within Corese query engine and are evaluated using BSBM benchmark. The results suggest that the proposed methods can optimize effectively the query execution time of SPARQL query engine.

GStore: a graph-based SPARQL query engine

We address efficient processing of SPARQL queries over RDF datasets. The proposed techniques, incorporated into the gStore system, handle, in a uniform and scalable manner, SPARQL queries with wildcards and aggregate operators over dynamic RDF datasets. Our approach is graph based. We store RDF data as a large graph and also represent a SPARQL query as a query graph. Thus, the query answering problem is converted into a subgraph matching problem. To achieve efficient and scalable query processing, we develop an index, together with effective pruning rules and efficient search algorithms. We propose techniques that use this infrastructure to answer aggregation queries. We also propose an effective maintenance algorithm to handle online updates over RDF repositories. Extensive experiments confirm the efficiency and effectiveness of our solutions.

Representing and querying multiple ontologies with Contextual Logic Programming

The system presented in this paper uses Contextual Logic Programming as a computational hub for representing and reasoning over knowledge modeled by web ontologies, integrating the approach with similar mechanisms which we already developed. As a result of its Logic Programming heritage, the system may also recursively interrogate other ontologies or data repositories, providing a semantic integration of multiple sources. The components required to behave as a SPARQL query engine are explained and examples of integration of deferent sources are shown - in particular, the case of multiple OWL ontologies is discussed. .