Ontology-based Data Research Articles

Use of Semantic Web Technologies to Enhance the Integration and Interoperability of Environmental Geospatial Data: A Framework Based on Ontology-Based Data Access

Abstract: This study addresses the challenges of integrating heterogeneous environmental geospatial data by proposing a framework based on ontology-based data access (OBDA). Geospatial data are important for decision-making in various domains, such as environmental monitoring, disaster management, and urban development. Data integration is a common challenge within these domains due to data heterogeneity and semantic discrepancies. The proposed framework uses semantic web technologies to enhance data interoperability, accessibility, and usability. Several practical examples were demonstrated to validate its effectiveness. These examples were based in Lake Mjøsa, Norway, addressing both spatial and non-spatial scenarios to test the framework’s potential. By extending the GeoSPARQL ontology, the framework supports SPARQL queries to retrieve information based on user requirements. A web-based SPARQL Query Interface (SQI) was developed to execute queries and display the retrieved data in tabular and visual format. Utilizing free and open-source software (FOSS), the framework is easily replicable for stakeholders and researchers. Despite some limitations, the study concludes that the framework is able to enhance cross-domain data integration and semantic querying in various informed decision-making scenarios.

Interweaving academic insights: advancing university knowledge management through a strategic data fabric framework

PurposeEffective knowledge management in large academic institutions is crucial for fostering innovation and improving educational practices. However, these institutions often face challenges, such as data fragmentation, siloed information systems and the complexity of integrating different data sources from various departments with complex hierarchical structures. To address these problems, the authors proposed a data fabric strategic framework that improves and enhances knowledge management by leveraging ontologies and knowledge graphs. This study aims to investigate the potential of knowledge graphs, ontological knowledge modelling and knowledge representation to improve knowledge management in large academic institutions. It also describes how technology can enhance knowledge accessibility and exchanges and improve decision-making processes based on insights from complex educational systems.Design/methodology/approachThis study uses coordination theory as a foundational framework to analyse intricate data systems in preparation for constructing, the Wizard of Oz method to facilitate the systematic organisation and management of information and the execution of an ontology-based data fabric framework and knowledge graphs. The authors propose a data fabric strategic framework aimed at improving knowledge management by leveraging ontologies and knowledge graphs.FindingsThe final evaluation demonstrates that this approach effectively breaks down data silos, promotes research collaboration and improves decision-making processes in large academic settings, offering solution-oriented data fabric technologies applicable to universities and university federations globally.Practical implicationsThe proposed system provides a more efficient way of managing and connecting fragmented academic resources, improving accessibility for both learners and educators. By interconnecting and streaming knowledge management process, the system can reduce not only operational costs but also expenses on doing scientific research.Originality/valueAcademic institutions prioritise time efficiency when acquiring vital data for improved scientific results. This emphasis extends beyond data governance to focus on how collective intelligence might improve organisational performance. The academic community has enhanced data utilisation through the implementation of data fabric technologies to improve data accessibility and data line tracking.

Ontology-based data framework for the digital preservation cultural heritage: A case of Subak

Cultural heritage is increasingly fading due to the influence of globalization and social changes that shift traditional values. Digitalization is critical to addressing the degradation of cultural heritage knowledge by enabling more accessible storage and documentation and facilitating preservation and education efforts for future generations. Subak, as a unique traditional agricultural system in Bali, Indonesia, has a wealth of valuable knowledge and culture, but it is still scattered and unstructured. An ontology-based Knowledge Management System is designed to capture, organize, and utilize knowledge within a domain using ontologies as a fundamental component. Ontologies explicitly represent knowledge by providing meaning, properties, and relationships with related concepts. This paper proposes data modelling with the Ontology Development framework for the knowledge base. The methodological framework consists of knowledge externalization, including identifying and collecting knowledge based on data modelling through interviews and observations. The second steps are modelling and development of ontology, based on the knowledge that has been previously disclosed, including the hierarchical structure, properties, and relationships that form the knowledge base. The third stage is the Implementation and evaluation, which involves evaluating the quality of ontology using onto metrics and implementing the ontology into the KMS. The result of this study is data modeling for the knowledge base and the Ontology Development framework. The data modelling is a form of data mapping based on a combination of traditional philosophy and modern management principles that underlie Subak activities and artefacts, namely Tri Hita Karana, Desa Kala Patra, and POAC. The proposed framework can be a reference in developing new ontologies from scratch on unstructured cultural heritage data.

Ontology-based Data Integration Framework for Smart Pig Farms

Semantic web technology is known to enhance data for the connection of information using a network that can be easily read by machines. This work applies an ontology to integrate data involved in swine farm management towards the development of smart farm for swine. To realize environmental data, IoT devices including sensors, camera, and RFID readers were deployed in a pig farm. Despite differences in data format from different sources, an ontology was crafted to provide semantic annotations that could unify the data and enhance them with tangible relationships based on the domain knowledge. The core concepts of this ontology were sensing data with temporal information and identifiable data to represent relationship between real-time environmental features and the pigs within the pen to improve pig management. The semantically enhanced data can thus be applied with semantic-based queries and inference reasoner. Smart services including monitoring, decision support, alerting, and automatic executing based on the deployed IoT devices are thus enabled to support farm managements towards smart farm for swine. From the results, we found that the integrated sensing information from sensors and knowledge given in the developed ontology with inference rules assists the task of interpretation of monitored information and decision-making to improve swine farm management. The data gathered could be extended by combining two or more factors such as temperature and humidity into heat index using knowledge inference to precisely understand environmental information and activate the relevant machine automatically.

Separability and Its Approximations in Ontology-based Data Management

Given two datasets, i.e., two sets of tuples of constants, representing positive and negative examples, logical separability is the reasoning task of finding a formula in a certain target query language that separates them. As already pointed out in previous works, this task turns out to be relevant in several application scenarios such as concept learning and generating referring expressions. Besides, if we think of the input datasets of positive and negative examples as composed of tuples of constants classified, respectively, positively and negatively by a black-box model, then the separating formula can be used to provide global post-hoc explanations of such a model. In this paper, we study the separability task in the context of Ontology-based Data Management (OBDM), in which a domain ontology provides a high-level, logic-based specification of a domain of interest, semantically linked through suitable mapping assertions to the data source layer of an information system. Since a formula that properly separates (proper separation) two input datasets does not always exist, our first contribution is to propose (best) approximations of the proper separation, called (minimally) complete and (maximally) sound separations. We do this by presenting a general framework for separability in OBDM. Then, in a scenario that uses by far the most popular languages for the OBDM paradigm, our second contribution is a comprehensive study of three natural computational problems associated with the framework, namely Verification (check whether a given formula is a proper, complete, or sound separation of two given datasets), Existence (check whether a proper, or best approximated separation of two given datasets exists at all), and Computation (compute any proper, or any best approximated separation of two given datasets).

Ontology-Based Data Collection for a Hybrid Outbreak Detection Method Using Social Media.

Given the persistent global challenge presented by rapidly spreading diseases, as evidenced notably by the widespread impact of the COVID-19 pandemic on both human health and economies worldwide, the necessity of developing effective infectious disease prediction models has become of utmost importance. In this context, the utilization of online social media platforms as valuable tools in healthcare settings has gained prominence, offering direct avenues for disseminating critical health information to the public in a timely and accessible manner. Propelled by the ubiquitous accessibility of the internet through computers and mobile devices, these platforms promise to revolutionize traditional detection methods, providing more immediate and reliable epidemiological insights. Leveraging this paradigm shift, our proposed framework harnesses Twitter data associated with infectious disease symptoms, employing ontology to identify and curate relevant tweets. Central to our methodology is a hybrid model that integrates XGBoost and Bidirectional Long Short-Term Memory (BiLSTM) architectures. The integration of XGBoost addresses the challenge of handling small dataset sizes, inherent during outbreaks due to limited time series data. XGBoost serves as a cornerstone for minimizing the loss function and identifying optimal features from our multivariate time series data. Subsequently, the combined dataset, comprising original features and predicted values by XGBoost, is channeled into the BiLSTM for further processing. Through extensive experimentation with a dataset spanning multiple infectious disease outbreaks, our hybrid model demonstrates superior predictive performance compared to state-of-the-art and baseline models. By enhancing forecasting accuracy and outbreak tracking capabilities, our model offers promising prospects for assisting health authorities in mitigating fatalities and proactively preparing for potential outbreaks.

UAV, GNSS, Total Station, and Data Management Applied to an Ancient Clay Structure as a Historic Building Information Modeling Proposal: A Case Study of Huaca Arco Iris (Trujillo, Peru)

In light of current risks and environmental impacts, HBIM (historic building information modeling) offers a highly efficient and interactive method for managing historical data and representing the current states of ancient clay structures. In this study, traditional geodetic techniques were employed to digitally locate a structure without compromising its topographic information to create an accurate model. Tools such as total stations, GNSS receivers, and UAVs were utilized to generate detailed topography of the study site and its surroundings. An ontology-based data management structure was also developed to store historical data and site intervention projects, adhering to the ISO 12006-2 standard. This was achieved through automated scripts in Dynamo softwarev.2.18.1. A comparison between the point cloud (279 images) and total station data (600 points) revealed a georeferencing accuracy difference of +/−0.003 m. Consequently, the developed methods can effectively represent similar structures digitally. The proposed ontological structure facilitates automated storage of internal and external information.

Blockchain-Enhanced Traceability Framework for Smart Farming with Integrated Ontology-Based Data Standardization

This paper introduces a new conceptual framework to enhance crop traceability within smart farming environments. The framework merges blockchain technology with ontology-based data standardization to address persistent challenges in traditional traceability systems, such as data fragmentation and inconsistencies. The primary goal is establishing a transparent, reliable, and efficient traceability process from farm to table. The methodology employed in this research follows the Design Science Research Methodology (DSRM), involving iterative cycles of designing, building, and evaluating the proposed framework to ensure its effectiveness in real-world applications. The framework offers a promising solution to improve food safety, quality, regulatory compliance, and data-driven agricultural decision-making by capitalizing on blockchain's immutable and decentralized attributes and leveraging standardized data formats facilitated by ontologies. The proposed framework comprises three key components: ontology development, system integration, and blockchain implementation. Ontology development addresses data fragmentation and inconsistencies by providing a common language and structure for data exchange. Meanwhile, system integration ensures seamless data exchange among stakeholders, and blockchain implementation secures and verifies traceability records to maintain data integrity and trust. This integrated system is expected to foster trust and collaboration among all participants in the agricultural supply chain, thereby advancing the efficiency and sustainability of smart farming practices. Through continuous refinement and validation, this research aims to significantly contribute to the practical implementation of advanced traceability solutions in the agricultural sector, ensuring that these systems are robust, scalable, and adaptable to various farming contexts.

Ontology-Based Data Representation Prototype for Indoor Air Quality, Building Energy Performance, and Health Data Computation

This study investigates the data integration of IoT-enabled sensor networks, emphasizing energy performance and personalized indoor air quality (IAQ) solutions to improve indoor environments, energy efficiency, and sustainability. Ontologies—structured frameworks that standardize data representation and enable interoperability—are the tools for interpreting complex IAQ data for optimal energy rate plans and health situations. Our methodology follows the well-established three-phase engineering approach. We present the design of a prototype with essential classes, which is proposed to integrate IAQ data with health conditions, enhancing real-time monitoring and automated decision making for optimal energy performance for smart buildings. Our research goal is to define the most essential classes, arranging them hierarchically to create a prototype for data computing covering IAQ, energy performance, and health aspects. This ontological framework, covering all three aspects, addresses a current research gap. Results demonstrate the minimum viable product with 78 classes for a smart home IoT system, providing tailored indoor climate control based on user health profiles and energy performance. This prototype represents a significant advancement in sustainable building and IAQ management, promising improved building energy performance, occupant health, and comfort. Future research will validate this framework through extensive testing in real-world environments.

Mapping method for complex mechatronic equipment relationship data to contextual semantic-constrained knowledge graphs

Complex mechatronic equipment’s complete life cycle information model includes multidimensional data on structure, qualities, behavior, and limitations. The data are diverse, derived from multiple sources, and include both streaming and non-streaming cyber-physical data. The product data system’s structured relational model, which is represented by the XBOM (X Bill of Material), is primarily where this data is stored. However, with the growing amount of equipment information, this relatively isolated and redundant architecture poses challenges. Within relational models, the growing intricacy of inner-outer key joins impedes effective data mining and retrieval for dynamic digital twin business applications. In response, this study proposes a knowledge graph transformation method that takes into account the semantic restrictions of the business application context to translate relational data to entities and semantic expressions. The method builds a knowledge context constraint meta-model by classifying data according to context semantics into one-hop entities, multi-hop entities, and abstract classes. Additionally, an ontology-based data extraction transformation method and an ontology-based mapping algorithm based on relational schema transformation are introduced in this article. This strategy significantly minimizes knowledge redundancy and enhances retrieval performance, as demonstrated by experimental verification through the development of a relational data mapping tool software.

Predicting an Optimal Virtual Data Model for Uniform Access to Large Heterogeneous Data

ABSTRACT The growth of generated data in the industry requires new efficient big data integration approaches for uniform data access by end-users to perform better business operations. Data virtualization systems, including Ontology-Based Data Access (ODBA) query data on-the-fly against the original data sources without any prior data materialization. Existing approaches by design use a fixed model e.g., TABULAR as the only Virtual Data Model — a uniform schema built on-the-fly to load, transform, and join relevant data. While other data models, such as GRAPH or DOCUMENT, are more flexible and, thus, can be more suitable for some common types of queries, such as join or nested queries. Those queries are hard to predict because they depend on many criteria, such as query plan, data model, data size, and operations. To address the problem of selecting the optimal virtual data model for queries on large datasets, we present a new approach that (1) builds on the principal of OBDA to query and join large heterogeneous data in a distributed manner and (2) calls a deep learning method to predict the optimal virtual data model using features extracted from SPARQL queries. OPTIMA — implementation of our approach currently leverages state-of-the-art Big Data technologies, Apache-Spark and Graphx, and implements two virtual data models, GRAPH and TABULAR, and supports out-of-the-box five data sources models: property graph, document-based, e.g., wide-columnar, relational, and tabular, stored in Neo4j, MongoDB, Cassandra, MySQL, and CSV respectively. Extensive experiments show that our approach is returning the optimal virtual model with an accuracy of 0.831, thus, a reduction in query execution time of over 40% for the tabular model selection and over 30% for the graph model selection.

A survey on semantic data management as intersection of ontology-based data access, semantic modeling and data lakes

In recent years, data lakes emerged as a way to manage large amounts of heterogeneous data for modern data analytics. One way to prevent data lakes from turning into inoperable data swamps is semantic data management. Such approaches propose the linkage of metadata to knowledge graphs based on the Linked Data principles to provide more meaning and semantics to the data in the lake. Such a semantic layer may be utilized not only for data management but also to tackle the problem of data integration from heterogeneous sources, in order to make data access more expressive and interoperable. In this survey, we review recent approaches with a specific focus on the application within data lake systems and scalability to Big Data. We classify the approaches into (i) basic semantic data management, (ii) semantic modeling approaches for enriching metadata in data lakes, and (iii) methods for ontology-based data access. In each category, we cover the main techniques and their background, and compare latest research. Finally, we point out challenges for future work in this research area, which needs a closer integration of Big Data and Semantic Web technologies.

Ontology-Based Data Preparation in Healthcare: The Case of the AMD-STITCH Project

Ontology-Based Data Preparation in Healthcare: The Case of the AMD-STITCH Project

Dataset Constrution through Ontology-Based Data Requirements Analysis

Machine learning (ML) technology is rapidly evolving, and the quality of ML systems is becoming an increasingly focal point of attention. Since the ML system is shaped by the dataset it learns from, its quality largely depends on the quality of the dataset. However, the dataset is often collected in a non-standardized process and few requirements and analysis methods are given to assist in identifying the needed dataset. This leads to no guarantee for the quality of dataset, affecting the generalization ability of model and resulting in low training efficiency. To address these issues, this paper proposes an ontology-based requirement analysis method where ontology integrates domain knowledge into the process of data requirements analysis and the coverage criteria on ontology are given for specifying data requirements which can later be used to guide the high-quality construction of the dataset. We held an experiment on an image recognition system in the field of autonomous driving to validate our approach. The result shows that the ML system trained by the dataset constructed through our data requirements analysis method has a better performance.

LUBM4OBDA: Benchmarking OBDA Systems with Inference and Meta Knowledge

Ontology-based data access focuses on enabling query evaluation over heterogeneous relational databases according to the model represented by an ontology. The relationships between the ontology and the data sources are commonly defined with declarative mappings, which are used by systems to perform SPARQL-to-SQL query translation or to generate RDF dumps from the relational databases. Besides the potential homogenization of data because of using an ontology, some additional advantages of this paradigm are that it may allow applying reasoning thanks to the ontology, as well as querying for meta knowledge, which describes statements with information such as provenance or certainty. In this paper, (i) we adapt a widely used RDF graph store benchmark, namely LUBM, for ontology-based data access, (ii) extend the benchmark for the evaluation of queries that exploit meta knowledge, and (iii) apply it for performance evaluation of state-of-the-art declarative mapping systems. Our proposal, the LUBM4OBDA Benchmark, considers inference capabilities that are not covered by previous ontology-based data access benchmarks, and it is the first one for the evaluation of meta knowledge and the RDF-star data model. The experimental evaluation shows that current virtualization systems cannot handle some advanced inference tasks, and that optimizations are needed to scale RDF-star materialization.

Integrating data and knowledge to support the selection of service plant species in agroecology

There is a crucial need for tools to help researchers, technicians and farmers designing sustainable agroecosystems based on agroecology Indeed, such agroecosystems are inherently complex and their design requires to integrate various data and unstabilised scientific knowledge. In this paper, we consider the issue of selecting service plant species according to their potential to provide ecosystem services. To tackle that issue, we adopt an approach based both on a formalized representation of domain knowledge, which enables reasoning, and on the exploitation of available data, collected independently of the targeted application. More specifically, we rely on the one hand on recent scientific results in agronomy linking functional traits (i.e., measurable characteristics of plant species) to ecosystem services, and on the other hand on data about functional traits collected by the research community in ecology. The architecture of our system is inspired by the ontology-based data access paradigm, which allows to combine data and knowledge in a principled way. We provide a methodology to acquire scientific knowledge in the form of diagrams linked to data sources, as well as a formalization in a logical rule-based language. Importantly, our rules are independent from specific diagrams and data, to ensure genericity and facilitate the evolution of the system. We detail the construction of a knowledge base devoted to vine grassing, i.e., installing herbaceous service plants in vineyards, and present an evaluation of the system’s results on this use case. We finally discuss the lessons learned and further challenges to be met.

Living without Beth and Craig: Definitions and Interpolants in Description and Modal Logics with Nominals and Role Inclusions

The Craig interpolation property (CIP) states that an interpolant for an implication exists iff it is valid. The projective Beth definability property (PBDP) states that an explicit definition exists iff a formula stating implicit definability is valid. Thus, the CIP and PBDP reduce potentially hard existence problems to entailment in the underlying logic. Description (and modal) logics with nominals and/or role inclusions do not enjoy the CIP nor the PBDP, but interpolants and explicit definitions have many applications, in particular in concept learning, ontology engineering, and ontology-based data management. In this article, we show that, even without Beth and Craig, the existence of interpolants and explicit definitions is decidable in description logics with nominals and/or role inclusions such as 𝒜ℒ𝒞𝒪, 𝒜ℒ𝒞ℋ, and 𝒜ℒ𝒞ℋ𝒪ℐ and corresponding hybrid modal logics. However, living without Beth and Craig makes these problems harder than entailment: the existence problems become 2ExpTime -complete in the presence of an ontology or the universal modality, and coNExpTime -complete otherwise. We also analyze explicit definition existence if all symbols (except the one that is defined) are admitted in the definition. In this case, the complexity depends on whether one considers individual or concept names. Finally, we consider the problem of computing interpolants and explicit definitions if they exist and turn the complexity upper bound proof into an algorithm computing them, at least for description logics with role inclusions.

Infrastructure tools to support an effective Radiation Oncology Learning Health System.

Radiation Oncology Learning Health System (RO-LHS) is a promising approach to improve the quality of care by integrating clinical, dosimetry, treatment delivery, research data in real-time. This paper describes a novel set of tools to support the development of a RO-LHS and the current challenges they can address. We present a knowledge graph-based approach to map radiotherapy data from clinical databases to an ontology-based data repository using FAIR concepts. This strategy ensures that the data are easily discoverable, accessible, and can be used by other clinical decision support systems. It allows for visualization, presentation, and data analyses of valuable information to identify trends and patterns in patient outcomes. We designed a search engine that utilizes ontology-based keyword searching, synonym-based term matching that leverages the hierarchical nature of ontologies to retrieve patient records based on parent and children classes, connects to the Bioportal database for relevant clinical attributes retrieval. To identify similar patients, a method involving text corpus creation and vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) are employed, using cosine similarity and distance metrics. The data pipeline and tool were tested with 1660 patient clinical and dosimetry records resulting in 504180 RDF (Resource Description Framework) tuples and visualized data relationships using graph-based representations. Patient similarity analysis using embedding models showed that the Word2Vec model had the highest mean cosine similarity, while the GloVe model exhibited more compact embeddings with lower Euclidean and Manhattan distances. The framework and tools described support the development of a RO-LHS. By integrating diverse data sources and facilitating data discovery and analysis, they contribute to continuous learning and improvement in patient care. The tools enhance the quality of care by enabling the identification of cohorts, clinical decision support, and the development of clinical studies and machine learning programs in radiation oncology.

The notion of Abstraction in Ontology-based Data Management

We study a novel reasoning task in Ontology-based Data Management (OBDM), called Abstraction, which aims at associating formal semantic descriptions to data services. In OBDM a domain ontology is used to provide a semantic layer mapped to the data sources of an organization. The basic idea of the work presented in this paper is to explain the semantics of a data service in terms of a query over the ontology. We illustrate a formal framework for this problem, based on three different notions of abstraction, called sound, complete, and perfect, respectively. We present a thorough complexity analysis of two computational problems, namely verification (checking whether a query is an abstraction of a given data service), and computation (computing an abstraction of a given data service).

Finite Materialisability of Datalog Programs with Metric Temporal Operators

DatalogMTL is an extension of Datalog with metric temporal operators that has recently found applications in stream reasoning and temporal ontology-based data access. In contrast to plain Datalog, where materialisation (a.k.a. forward chaining) naturally terminates in finitely many steps, reaching a fixpoint in DatalogMTL may require infinitely many rounds of rule applications. As a result, existing reasoning systems resort to other approaches, such as constructing large Büchi automata, whose implementations turn out to be highly inefficient in practice. In this paper, we propose and study finitely materialisable DatalogMTL programs, for which forward chaining reasoning is guaranteed to terminate. We consider a data-dependent notion of finite materialisability of a program, where termination is guaranteed for a given dataset, as well as a data-independent notion, where termination is guaranteed regardless of the dataset. We show that, for bounded programs (a natural DatalogMTL fragment for which reasoning is as hard as in the full language), checking data-dependent finite materialisability is ExpSpace-complete in combined complexity and PSpace-complete in data complexity; furthermore, we propose a practical materialisation-based decision procedure that works in doubly exponential time. We show that checking data-independent finite materialisability for bounded progams is computationally easier, namely ExpTime-complete; moreover, we propose sufficient conditions for data-indenpendent finite materialisability that can be efficiently checked. We provide also the complexity landscape of fact entailment for different classes of finitely materialisable programs; surprisingly, we could identify a large class of finitely materialisable programs, called MTL-acyclic programs, for which fact entailment has exactly the same data and combined complexity as in plain Datalog, which makes this fragment especially well suited for big-scale applications.