SPARQL Query Language Research Articles

Application of a Question Answering System in the Ontology-Based Health Domain and Question Templates to Improve the Quality of Answers

Developing an effective Question Answering System (QAS) to address a wide range of health-related inquiries presents a significant challenge. This study introduces an innovative approach using an ontology-based QAS within the health domain, leveraging the Resource Description Framework (RDF) and SPARQL query language. By utilizing ontology, the system can more accurately map health concepts, improving the relevance and precision of its responses. Additionally, the incorporation of structured Question Templates enhances the system’s ability to understand and respond to diverse user queries. The system's performance was evaluated using Black Box Testing, which demonstrated that it consistently provides accurate and relevant answers. The system achieved a Mean Average Precision (MAP) of 79.6%, indicating its potential to effectively address a broad spectrum of health issues.

Automated SPARQL Template for Flexible Question Answering

The knowledge bases required the query language SPARQL, which consists of subject, property, and object. SPARQL is a structured query language and is difficult to understand. That issue becomes a problem in natural language processing queries. One situation in question answering is how to translate natural language into a structural SPARQL. This work aims to develop an automated SPARQL template algorithm regardless of the pattern structure of the query triples. It provides a more varied SPARQL query for data retrieval named Flexible SPARQL. This approach initially lies in combining elements of RDF with basic techniques of natural language processing to generate a template of SPARQL. In this work, the approach to making automatic templates is proposed without regard to the pattern of the triple structure or the location of the subject and object. Template-based research that exists today still uses rules to determine the position of subjects, objects, and properties in the SPARQL structure. Therefore, this work used the QALD 7 question set and DBpedia dataset. The previous systems utilized the same questions and data sets. Despite the simple proposed approaches that do not use complex, sophisticated techniques, they have shown promising results compared to the previous systems. The accuracy result from 215 questions is 73% and micro-Recall 0.701, micro-Precision 0.664, micro-F-Measure 0.682, macro-Recall 0.711, macro-Precision 0.592, macro-F-Measure 0.646. Overall, the Flexible SPARQL system has higher results on several measurements that define a promising approach. However, it's important to note that Flexible SPARQL generally tends to fail at generating complex SPARQL, which is a limitation of the system.

An Efficient Approach to Extract and Store Big Semantic Web Data Using Hadoop and Apache Spark GraphX

The volume of data is growing at an astonishingly high speed. Traditional techniques for storing and processing data, such as relational and centralized databases, have become inefficient and time-consuming. Linked data and the Semantic Web make internet data machine-readable. Because of the increasing volume of linked data and Semantic Web data, storing and working with them using traditional approaches is not enough, and this causes limited hardware resources. To solve this problem, storing datasets using distributed and clustered methods is essential. Hadoop can store datasets because it can use many hard disks for distributed data clustering; Apache Spark can be used for parallel data processing more efficiently than Hadoop MapReduce because Spark uses memory instead of the hard disk. Semantic Web data has been stored and processed in this paper using Apache Spark GraphX and the Hadoop Distributed File System (HDFS). Spark's in-memory processing and distributed computing enable efficient data analysis of massive datasets stored in HDFS. Spark GraphX allows graph-based semantic web data processing. The fundamental objective of this work is to provide a way for efficiently combining Semantic Web and big data technologies to utilize their combined strengths in data analysis and processing. First, the proposed approach uses the SPARQL query language to extract Semantic Web data from DBpedia datasets. DBpedia is a hugely available Semantic Web dataset built on Wikipedia. Secondly, the extracted Semantic Web data was converted to the GraphX data format; vertices and edges files were generated. The conversion process is implemented using Apache Spark GraphX. Third, both vertices and edge tables are stored in HDFS and are available for visualization and analysis operations. Furthermore, the proposed techniques improve the data storage efficiency by reducing the amount of storage space by half when converting from Semantic Web Data to a GraphX file, meaning the RDF size is around 133.8 and GraphX is 75.3. Adopting parallel data processing provided by Apache Spark in the proposed technique reduces the required data processing and analysis time. This article concludes that Apache Spark GraphX can enhance Semantic Web and Big Data technologies. We minimize data size and processing time by converting Semantic Web data to GraphX format, enabling efficient data management and seamless integration.

SPARQL Optimization Using Re-ordering Joining Patterns with Surrogate Key Concept and Subset Patterns

Semantic web data resides on the web in the form of knowledge graphs known as RDF graphs and searching around the web has been always a crucial task. For the data retrieval of RDF data of the semantic web, SPARQL query language has been used which in turn is based on triple patterns and joins. Optimization of SPARQL query has been a problematic concern for decades due to the large amount of triple patterns associated with RDF data. Although several researchers have put a lot of effort into the optimization of SPARQL query, it is difficult to understand the concept from scratch due to its diversified nature. This paper analyses various optimization techniques for the SPARQL query used with the semantic web to process knowledge graphs. These techniques include join-based, heuristic-based, rule-based, and indexing-based approaches for optimization. This paper will help researchers in this domain to easily get into the core concept of SPARQL execution along with various optimization approaches used for query processing, which can help in various other domains like linked open data and information retrieval. In this paper, an optimization algorithm HSOA (hybrid SPARQL optimization algorithm) has been proposed, which comprises the features of index-based, cost-based, and triple reordering-based optimization approaches. The proposed hybrid algorithm has been designed specifically for n-triple RDF data, which comprises subset patterns, and surrogate key concepts. The results produced by the proposed algorithm are encouraging and have also been tested and compared with the benchmark dataset and SPARQL queries like LUBM, BSBM, and SP2Bench.

Tuning fuzzy SPARQL queries

During the last years, the study of fuzzy database query languages has attracted the attention of many researchers. In this line of research, our group has proposed and developed FSA-SPARQL (Fuzzy Sets and Aggregators based SPARQL), which is a fuzzy extension of the Semantic Web query language SPARQL. FSA-SPARQL works with fuzzy RDF datasets and allows the definition of fuzzy queries involving fuzzy conditions through fuzzy connectives and aggregators. However, there are two main challenges to be solved for the practical applicability of FSA-SPARQL. The first problem is the lack of fuzzy RDF data sources. The second is how to customize fuzzy queries on fuzzy RDF data sources. Our research group has also recently proposed a fuzzy logic programming language called FASILL that offers powerful tuning capabilities that can accept applications in many fields. The purpose of this paper is to show how the FASILL tuning capabilities serve to accomplish in a unified framework both challenges in FSA-SPARQL: data fuzzification and query customization. More concretely, from a FSA-SPARQL to FASILL transformation, data fuzzification and query customization in FSA-SPARQL become FASILL tuning problems. We have validated the approach with queries against datasets from online communities.

The IDSM mass spectrometry extension: searching mass spectra using SPARQL.

The Integrated Database of Small Molecules (IDSM) integrates data from small-molecule datasets, making them accessible through the SPARQL query language. Its unique feature is the ability to search for compounds through SPARQL based on their molecular structure. We extended IDSM to enable mass spectra databases to be integrated and searched for based on mass spectrum similarity. As sources of mass spectra, we employed the MassBank of North America database and the In Silico Spectral Database of natural products. The extension is an integral part of IDSM, which is available at https://idsm.elixir-czech.cz. The manual and usage examples are available at https://idsm.elixir-czech.cz/docs/ms. The source codes of all IDSM parts are available under open-source licences at https://github.com/idsm-src.

SPARQL-QA-v2 system for Knowledge Base Question Answering

Accessing the large volumes of information available in public knowledge bases might be complicated for those users unfamiliar with formal languages, such as the SPARQL query language and the ontology definition languages. This issue can be overcome by providing systems able to answer questions posed in natural language on a knowledge base, a task that is called Knowledge Base Question Answering (KBQA) in the literature. More in detail, many KBQA systems aim at translating automatically questions into the corresponding SPARQL queries to be executed over the knowledge base to get the answers. Effective state-of-the-art KBQA systems are based on neural-machine translation but easily fail to recognize words that are Out Of the Vocabulary (OOV) of the training set. This is a serious issue while querying large ontologies where the list of entities is huge and easily evolves over time. In this paper, we present the SPARQL-QA-v2 system that combines in an innovative way Named Entity Linking, Named Entity Recognition, and Neural Machine Translation for addressing the problem of generating SPARQL queries from questions posed in natural language. We demonstrate empirically that SPARQL-QA-v2 is effective and resilient to OOV words and delivers state-of-the-art performance in well-known datasets for question answering over DBpedia and Wikidata knowledge bases.

Data quality and patient characteristics in European ANCA-associated vasculitis registries: data retrieval by federated querying

ObjectivesThis study aims to describe the data structure and harmonisation process, explore data quality and define characteristics, treatment, and outcomes of patients across six federated antineutrophil cytoplasmic antibody-associated vasculitis (AAV)...

The SIB Swiss Institute of Bioinformatics Semantic Web of data.

The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international life science community in academia and industry has been accessing the freely available databases provided by SIB since its inception in 1998. In this paper we present the 11 databases which currently offer semantically enriched data in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable), as well as the Swiss Personalized Health Network initiative (SPHN) which also employs this enrichment. The semantic enrichment facilitates the manipulation of large data sets from public databases and private data sets. Examples are provided to illustrate that the data from the SIB databases can not only be queried using precise criteria individually, but also across multiple databases, including a variety of non-SIB databases. Data manipulation, be it exploration, extraction, annotation, combination, and publication, is possible using the SPARQL query language. Providing documentation, tutorials and sample queries makes it easier to navigate this web of semantic data. Through this paper, the reader will discover how the existing SIB knowledge graphs can be leveraged to tackle the complex biological or clinical questions that are being addressed today.

Knowledge Graph Construction with a Façade : A Unified Method to Access Heterogeneous Data Sources on the Web

Data integration is the dominant use case for RDF Knowledge Graphs. However, Web resources come in formats with weak semantics (for example, CSV and JSON), or formats specific to a given application (for example, BibTex, HTML, and Markdown). To solve this problem, Knowledge Graph Construction (KGC) is gaining momentum due to its focus on supporting users in transforming data into RDF. However, using existing KGC frameworks result in complex data processing pipelines, which mix structural and semantic mappings, whose development and maintenance constitute a significant bottleneck for KG engineers. Such frameworks force users to rely on different tools, sometimes based on heterogeneous languages, for inspecting sources, designing mappings, and generating triples, thus making the process unnecessarily complicated. We argue that it is possible and desirable to equip KG engineers with the ability of interacting with Web data formats by relying on their expertise in RDF and the well-established SPARQL query language [ 2 ]. In this article, we study a unified method for data access to heterogeneous data sources with Facade-X, a meta-model implemented in a new data integration system called SPARQL Anything. We demonstrate that our approach is theoretically sound, since it allows a single meta-model, based on RDF, to represent data from (a) any file format expressible in BNF syntax, as well as (b) any relational database. We compare our method to state-of-the-art approaches in terms of usability (cognitive complexity of the mappings) and general performance. Finally, we discuss the benefits and challenges of this novel approach by engaging with the reference user community.

ONTOLOGICAL MODELING OF INFORMATION DATA OF DIGITAL CRIMINAL CRIME

In the article, an ontological model of information data of a digital criminal offense is formed and researched. Ontological modeling made it possible to conceptualize knowledge and effectively overcome the problems of insufficient structure, ambiguity and inconsistency of data and knowledge in the field of digital forensics. On the basis of the conducted classification, five main classes (Digital Crime, Digital Traces, Types of Crimes, Criminal and Criminal Liability) were identified, which include multiple user and non-user instances, including relevant articles of the Criminal Code of Ukraine and international law. The user creates instances of three classes: Digital Crime, Digital Traces, and Criminal. They contain personal information about digital crime and are the main data of the user part of the ontological model as a knowledge base. The Crime Types and Criminal Liability classes are non-user and can only be modified by model support specialists. The ontology model is implemented in Protege in the OWL language, which is an informal standard for creating and sharing ontologies. Of the selected seven relationships between entities, only three are entered into the ontology by the user, the others are formed automatically based on the developed SWRL rules. Using the SPARQL query language, real-time information search, filtering, and analysis patterns are provided to help discover complex relationships between objects and generate new ontological knowledge. The results of the study highlight the importance of ontology modeling in the field of digital forensics and how SPARQL queries can be used to improve data processing, analysis and understanding of knowledge in this field.

Creating Bengali Freebase Using Wikidata

Freebase is a large collaborative knowledge base and database of general, structured information for public use. Its structured data had been harvested from many sources, including individual, user-submitted wiki contributions. Its aim is to create a global resource so that people (and machines) can access common information more effectively which is mostly available in English. In this research work, we have tried to build the technique of creating the Freebase for Bengali language. Today the number of Bengali articles on the internet is growing day by day. So it has become a necessary to have a structured data store in Bengali. It consists of different types of concepts (topics) and relationships between those topics. These include different types of areas like popular culture (e.g. films, music, books, sports, television), location information (restaurants, geolocations, businesses), scholarly information (linguistics, biology, astronomy), birth place of (poets, politicians, actor, actress) and general knowledge (Wikipedia). It will be much more helpful for relation extraction or any kind of Natural Language Processing (NLP) works on Bengali language. In this work, we identified the technique of creating the Bengali Freebase and made a collection of Bengali data. We applied SPARQL query language to extract information from natural language (Bengali) documents such as Wikidata which is typically in RDF (Resource Description Format) triple format.

Fetching Automatic Authority Data in ILS from Wikidata via OpenRefine

Authority data is vital for effective library and information services. It serves a major purpose in realizing the collocation function of library catalogues and indexes. Unfortunately, however, authority control has been neglected in library catalogues and other bibliographic databases in India. This paper seeks to demonstrate how authority data can be fetched automatically from Wikidata, a sibling project of Wikipedia. For this purpose, the query language SPARQL is required to formulate the names of persons of Indian origin along with their date of birth and place in Wikidata. The collected datasets are processed and implemented as MARC21-based authority data in KOHA, an open-source library management software. The ways in which the library and information science community can use these free, open-source platforms to gather, organize and share data and how they enhance the retrieval efficiency are shown.

Solving the SPARQL query containment problem with SpeCS

The query containment problem is a fundamental computer science problem which was originally defined for relational queries. With the growing popularity of the sparql query language, it became relevant and important in this new context: reliable and efficient sparql query containment solvers may have various applications within static analysis of queries, especially in the area of query optimizations and refactoring. In this paper, we present a new approach for solving the query containment problem in sparql. The approach is based on reducing the query containment problem to the satisfiability problem in first order logic. It covers a wide range of the sparql language constructs, including union of conjunctive queries, blank nodes, projections, subqueries, clauses from, filter, optional, graph, etc. It also covers containment under rdf schema entailment regime, and it can deal with the subsumption relation. We describe an implementation of the approach, an open source solver SpeCS and its thorough experimental evaluation on two relevant benchmarks, Query Containment Benchmark and SQCFramework. As a side result, SpeCS identified incorrect test cases within both benchmarks, which were manually checked, confirmed and fixed, resulting in better and more reliable benchmarks. The evaluation also shows that SpeCS is highly efficient and that compared to the state-of-the-art solvers, it gives more precise results in a shorter amount of time. In addition, SpeCS has the highest coverage of the supported language constructs.

Fuzzy Spatiotemporal Data Modeling and Operations in RDF

With the emergence of a large number of fuzzy spatiotemporal data on the Web, how to represent and operate fuzzy spatiotemporal data has become an important research issue. Meanwhile, the Resource Description Framework (RDF) is a standard data and knowledge description language of the Semantic Web and has been applied in many application areas, such as geographic information systems and meteorological systems. In this paper, a model for representing fuzzy spatiotemporal data is proposed and a set of algebraic operations for the model are investigated. First, a representation method of fuzzy spatiotemporal RDF data and a fuzzy spatiotemporal RDF graph model are proposed. In addition, a formal fuzzy spatiotemporal RDF algebra is proposed and a set of algebraic operations for manipulating fuzzy spatiotemporal RDF data are developed. The algebraic operations include: set operation, selection operation, projection operation, join operation, and construction operation. Finally, the existing SPARQL query language is extended and an example that shows how to apply the proposed algebraic operations to capture the queries expressed by the extended SPARQL query language is given.

Medieval Manuscripts and Their Migrations: Using SPARQL to Investigate the Research Potential of an Aggregated Knowledge Graph

Although the RDF query language SPARQL has a reputation for being opaque and difficult for traditional humanists to learn, it holds great potential for opening up vast amounts of Linked Open Data to researchers willing to take on its challenges. This is especially true in the field of premodern manuscripts studies as more and more datasets relating to the study of manuscript culture are made available online. This paper explores the results of a two-year long process of collaborative learning and knowledge transfer between the computer scientists and humanities researchers from the Mapping Manuscript Migrations (MMM) project to learn and apply SPARQL to the MMM dataset. The process developed into a wider investigation of the use of SPARQL to analyse the data, refine research questions, and assess the research potential of the MMM aggregated dataset and its Knowledge Graph. Through an examination of a series of six SPARQL query case studies, this paper will demonstrate how the process of learning and applying SPARQL to query the MMM dataset returned three important and unexpected results: 1) a better understanding of a complex and imperfect dataset in a Linked Open Data environment, 2) a better understanding of how manuscript description and associated data involving the people and institutions involved in the production, reception, and trade of premodern manuscripts needs to be presented to better facilitate computational research, and 3) an awareness of need to further develop data literacy skills among researchers in order to take full advantage of the wealth of unexplored data now available to them in the Semantic Web.

A Semantic Approach for Building System Operations: Knowledge Representation and Reasoning

Artificial intelligence is set to transform the next generation of intelligent buildings through the application of information and semantic data models and machine learning algorithms. Semantic data models enable the understanding of real-world data for building automation, integration and control applications. This article explored the use of semantic models, a subfield of artificial intelligence, for knowledge representation and reasoning (KRR) across a wide variety of applications in building control, automation and analytics. These KRR-enabled applications include context-aware control of mechanical systems, building energy auditing and commissioning, indoor air monitoring, fault detection and diagnostics (FDD) of mechanical equipment and systems and building-to-grid integration. To this end, this work employed the Apache Jena Application Programming Interface (API) to develop KRR and integrate it with some domain-specific ontologies expressed in the Resource Description Framework (RDF) and Web Ontology Language (OWL). The ontology-driven rules were represented using Jena rule formalisms to enable the inference of implicit information from data asserted in the ontologies. Moreover, SPARQL (SPARQL Query Language for RDF) was used to query the knowledge graph and obtain useful information for a variety of building applications. This approach enhances building analytics through multi-domain knowledge integration; spatial and temporal reasoning for monitoring building operations, and control systems and devices; and the performance of compliance checking. We show that existing studies have not leveraged state-of-the-art ontologies to infer information from different domains. While the proposed semantic infrastructure and methods in this study demonstrated benefits for different building applications applicable to mechanical systems, the approach also has great potential for lighting, shading and security applications. Multi-domain knowledge integration that includes spatial and temporal reasoning allows the optimization of the performance of building equipment and systems.

NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.

Semantic annotation is a crucial step to assure reusability and reproducibility of biosimulation models in biology and physiology. For this purpose, the COmputational Modeling in BIology NEtwork (COMBINE) community recommends the use of the Resource Description Framework (RDF). This grounding in RDF provides the flexibility to enable searching for entities within models (e.g., variables, equations, or entire models) by utilizing the RDF query language SPARQL. However, the rigidity and complexity of the SPARQL syntax and the nature of the tree-like structure of semantic annotations, are challenging for users. Therefore, we propose NLIMED, an interface that converts natural language queries into SPARQL. We use this interface to query and discover model entities from repositories of biosimulation models. NLIMED works with the Physiome Model Repository (PMR) and the BioModels database and potentially other repositories annotated using RDF. Natural language queries are first “chunked” into phrases and annotated against ontology classes and predicates utilizing different natural language processing tools. Then, the ontology classes and predicates are composed as SPARQL and finally ranked using our SPARQL Composer and our indexing system. We demonstrate that NLIMED's approach for chunking and annotating queries is more effective than the NCBO Annotator for identifying relevant ontology classes in natural language queries.Comparison of NLIMED's behavior against historical query records in the PMR shows that it can adapt appropriately to queries associated with well-annotated models.

Creating RESTful APIs over SPARQL endpoints using RAMOSE

Semantic Web technologies are widely used for storing RDF data and making them available on the Web through SPARQL endpoints, queryable using the SPARQL query language. While the use of SPARQL endpoints is strongly supported by Semantic Web experts, it hinders broader use of RDF data by common Web users, engineers and developers unfamiliar with Semantic Web technologies, who normally rely on Web RESTful APIs for querying Web-available data and creating applications over them. To solve this problem, we have developed RAMOSE, a generic tool developed in Python to create REST APIs over SPARQL endpoints. Through the creation of source-specific textual configuration files, RAMOSE enables the querying of SPARQL endpoints via simple Web RESTful API calls that return either JSON or CSV-formatted data, thus hiding all the intrinsic complexities of SPARQL and RDF from common Web users. We provide evidence that the use of RAMOSE to provide REST API access to RDF data within OpenCitations triplestores is beneficial in terms of the number of queries made by external users of such RDF data using the RAMOSE API, compared with the direct access via the SPARQL endpoint. Our findings show the importance for suppliers of RDF data of having an alternative API access service, which enables its use by those with no (or little) experience in Semantic Web technologies and the SPARQL query language. RAMOSE can be used both to query any SPARQL endpoint and to query any other Web API, and thus it represents an easy generic technical solution for service providers who wish to create an API service to access Linked Data stored as RDF in a triplestore.

Building Quranic stories ontology using MappingMaster domain-specific language

<p>The Holy Quran, due to it is full of many inspiring stories and multiple lessons that need to understand it requires additional attention when it comes to searching issues and information retrieval. Many works were carried out in the Holy Quran field, but some of these dealt with a part of the Quran or covered it in general, and some of them did not support semantic research techniques and the possibility of understanding the Quranic knowledge by the people and computers. As for others, techniques of data analysis, processing, and ontology were adopted, which led to directed these to linguistic aspects more than semantic. Another weakness in the previous works, they have adopted the method manually entering ontology, which is costly and time-consuming. In this paper, we constructed the ontology of Quranic stories. This ontology depended in its construction on the MappingMaster domain-specific language (MappingMaster DSL)technology, through which concepts and individuals can be created and linked automatically to the ontology from Excel sheets. The conceptual structure was built using the object role modeling (ORM) modeling language. SPARQL query language used to test and evaluate the propsed ontology by asking many competency questions and as a result, the ontology answered all these questions well.</p>