Semantic Data Integration Research Articles

Ontologies in modelling and analysing of big genetic data

To systematize and effectively use the huge volume of experimental data accumulated in the field of bioinformatics and biomedicine, new approaches based on ontologies are needed, including automated methods for semantic integration of heterogeneous experimental data, methods for creating large knowledge bases and self-interpreting methods for analyzing large heterogeneous data based on deep learning. The article briefly presents the features of the subject area (bioinformatics, systems biology, biomedicine), formal definitions of the concept of ontology and knowledge graphs, as well as examples of using ontologies for semantic integration of heterogeneous data and creating large knowledge bases, as well as interpreting the results of deep learning on big data. As an example of a successful project, the Gene Ontology knowledge base is described, which not only includes terminological knowledge and gene ontology annotations (GOA), but also causal influence models (GO-CAM). This makes it useful not only for genomic biology, but also for systems biology, as well as for interpreting large-scale experimental data. An approach to building large ontologies using design patterns is discussed, using the ontology of biological attributes (OBA) as an example. Here, most of the classification is automatically computed based on previously created reference ontologies using automated inference, except for a small number of high-level concepts. One of the main problems of deep learning is the lack of interpretability, since neural networks often function as “black boxes” unable to explain their decisions. This paper describes approaches to creating methods for interpreting deep learning models and presents two examples of self-explanatory ontology-based deep learning models: (1) Deep GONet, which integrates Gene Ontology into a hierarchical neural network architecture, where each neuron represents a biological function. Experiments on cancer diagnostic datasets show that Deep GONet is easily interpretable and has high performance in distinguishing cancerous and non-cancerous samples. (2) ONN4MST, which uses biome ontologies to trace microbial sources of samples whose niches were previously poorly studied or unknown, detecting microbial contaminants. ONN4MST can distinguish samples from ontologically similar biomes, thus offering a quantitative way to characterize the evolution of the human gut microbial community. Both examples demonstrate high performance and interpretability, making them valuable tools for analyzing and interpreting big data in biology.

Concepts for a Semantically Accessible Materials Data Space: Overview over Specific Implementations in Materials Science

This article describes advancements in the ongoing digital transformation in materials science and engineering. It is driven by domain‐specific successes and the development of specialized digital data spaces. There is an evident and increasing need for standardization across various subdomains to support science data exchange across entities. The MaterialDigital Initiative, funded by the German Federal Ministry of Education and Research, takes on a key role in this context, fostering collaborative efforts to establish a unified materials data space. The implementation of digital workflows and Semantic Web technologies, such as ontologies and knowledge graphs, facilitates the semantic integration of heterogeneous data and tools at multiple scales. Central to this effort is the prototyping of a knowledge graph that employs application ontologies tailored to specific data domains, thereby enhancing semantic interoperability. The collaborative approach of the Initiative's community provides significant support infrastructure for understanding and implementing standardized data structures, enhancing the efficiency of data‐driven processes in materials development and discovery. Insights and methodologies developed via the MaterialDigital Initiative emphasize the transformative potential of ontology‐based approaches in materials science, paving the way toward simplified integration into a unified, consolidated data space of high value.

Architectural Suggestions for Ontology Management

Abstract This document describes the steps that required for creating and maintaining an ontology; for exploiting an ontology in order to describe data from one or more data sources; and for developing services and applications that provide unified access and insightful analysis on the data. The document provides the state of the art of the various tools and software components that exist and can be used for carrying out various tasks of the overall process. The components are grouped based on their intended use and for each one of them a concise description, as well as other useful details (i.e. if they are open‐source, their license, etc.), are provided. For each step or task, the involved software components are also described in a table presenting their details with respect to various dimensions (e.g. open‐source, license, available online, key advantages, etc.), in order to enable their quick comparison. Moreover, successful examples of semantic data integration are presented, i.e., for cases where a top‐level ontology is used for integrating data for the cultural and biodiversity domain, and services for large‐scale semantic data integration (including hundreds of datasets from several domains). Furthermore, it provides the high‐level architectural suggestions that can be used as a basis for the actual implementation of any ontology‐based system; the described processes and tools can be exploited for the development of the ontology‐based functionality. Finally, it offers the adaptations of the proposed architecture for the EFSA case studies, by providing details about their components and indicative pipelines and tools.

Ontologies and Case Studies

Abstract Ontologies define the main concepts and relations of a domain and can play the role of common language between domain experts, software developers and computer systems, allowing for easier and more comprehensive data management. Ontologies can provide a structure and context for data, enabling better analysis and decision‐making. Ontologies can be leveraged for improving various Machine Learning‐based tasks (they can be used for improving the accuracy and consistency of training data, and we can combine ML‐based predictions with ontology‐based reasoning). Ontologies are key components for achieving semantic data integration. In the context of this deliverable, we have surveyed 40 ontologies and 7 other knowledge organization systems related to food safety and we have categorized them according to a set of appropriate criteria. Subsequently we analysed the 18 case studies, that could involve ontologies, and for each one we have described the possible use of ontologies and what would be the benefit. Finally the identified case studies have been evaluated with respect to a set of criteria regarding benefits, cost and maturity.

Embedding AI-Enabled Data Infrastructures for Sustainability in Agri-Food: Soft-Fruit and Brewery Use Case Perspectives.

The agri-food sector is undergoing a comprehensive transformation as it transitions towards net zero. To achieve this, fundamental changes and innovations are required, including changes in how food is produced and delivered to customers, new technologies, data and physical infrastructures, and algorithmic advancements. In this paper, we explore the opportunities and challenges of deploying AI-based data infrastructures for sustainability in the agri-food sector by focusing on two case studies: soft-fruit production and brewery operations. We investigate the potential benefits of incorporating Internet of Things (IoT) sensors and AI technologies for improving the use of resources, reducing carbon footprints, and enhancing decision-making. We identify user engagement with new technologies as a key challenge, together with issues in data quality arising from environmental volatility, difficulties in generalising models, including those designed for carbon calculators, and socio-technical barriers to adoption. We highlight and advocate for user engagement, more granular availability of sensor, production, and emissions data, and more transparent carbon footprint calculations. Our proposed future directions include semantic data integration to enhance interoperability, the generation of synthetic data to overcome the lack of real-world farm data, and multi-objective optimisation systems to model the competing interests between yield and sustainability goals. In general, we argue that AI is not a silver bullet for net zero challenges in the agri-food industry, but at the same time, AI solutions, when appropriately designed and deployed, can be a useful tool when operating in synergy with other approaches.

Efficient Small Object Detection You Only Look Once: A Small Object Detection Algorithm for Aerial Images.

Aerial images have distinct characteristics, such as varying target scales, complex backgrounds, severe occlusion, small targets, and dense distribution. As a result, object detection in aerial images faces challenges like difficulty in extracting small target information and poor integration of spatial and semantic data. Moreover, existing object detection algorithms have a large number of parameters, posing a challenge for deployment on drones with limited hardware resources. We propose an efficient small-object YOLO detection model (ESOD-YOLO) based on YOLOv8n for Unmanned Aerial Vehicle (UAV) object detection. Firstly, we propose that the Reparameterized Multi-scale Inverted Blocks (RepNIBMS) module is implemented to replace the C2f module of the Yolov8n backbone extraction network to enhance the information extraction capability of small objects. Secondly, a cross-level multi-scale feature fusion structure, wave feature pyramid network (WFPN), is designed to enhance the model's capacity to integrate spatial and semantic information. Meanwhile, a small-object detection head is incorporated to augment the model's ability to identify small objects. Finally, a tri-focal loss function is proposed to address the issue of imbalanced samples in aerial images in a straightforward and effective manner. In the VisDrone2019 test set, when the input size is uniformly 640 × 640 pixels, the parameters of ESOD-YOLO are 4.46 M, and the average mean accuracy of detection reaches 29.3%, which is 3.6% higher than the baseline method YOLOv8n. Compared with other detection methods, it also achieves higher detection accuracy with lower parameters.

Interdisciplinary semantic integration of battery electric vehicle charging infrastructure data

Interdisciplinary semantic integration of battery electric vehicle charging infrastructure data

Ontology-Guided Generation of Mechanized Construction Plan for Power Grid Construction Project

Mechanized construction is being fully implemented in the electric power infrastructure domain to ensure construction safety, enhance project quality, and improve efficiency. Traditional methods of designing mechanized construction plans are often inefficient due to their labor-intensive processes and heavy reliance on human expertise. This study introduces and evaluates an ontology-guided system designed to automate mechanized construction planning for power grid projects. The developed ontology effectively models domain-specific knowledge, enabling the semantic integration of data from various sources. By leveraging SPARQL queries, the ontology-guided system incorporates knowledge reasoning capabilities that facilitate the automated selection of construction equipment and the generation of comprehensive construction plans. A prototype system incorporating an ontology-guided mechanism has been developed, showcasing marked enhancements in efficiency and accuracy over traditional manual methods, as evidenced by case studies and expert evaluations. The research results emphasize the potential of ontology-guided systems in innovating architectural planning, providing an extensible and standardized approach. Expert evaluation indicates that the system achieves 71.38% effectiveness in generating mechanized construction plans.

Semantic sensor data integration for talent development via hybrid multi‐objective evolutionary algorithm

AbstractIn this work, we propose a new hybrid Multi‐Objective Evolutionary Algorithm (hMOEA) specifically designed for semantic sensor data integration, targeting talent development within the burgeoning field of the Semantic Internet of Things (SIoT). Our approach synergizes the capabilities of Multi‐Objective Particle Swarm Optimization and Genetic Algorithms to tackle the sophisticated challenges inherent in Sensor Ontology Matching (SOM). This innovative hMOEA framework is adapt at discerning precise semantic correlations among diverse ontologies, thereby facilitating seamless interoperability and enhancing the functionality of IoT applications. Central to our contributions are the development of an advanced multi‐objective optimization model that underpins the SOM process, the implementation of the hMOEA framework which sets a new benchmark for accurate semantic sensor data integration, and the rigorous validation of hMOEA's superiority through extensive testing in varied real‐world SOM scenarios. This research not only marks a significant advancement in SOM but also highlights the critical role of cutting‐edge SOM methodologies in educational curricula, for example, the new business subject education proposed by China in recent years, aimed at equipping future professionals with the necessary skills to innovate and lead in the SIoT and SW domains.

Semantic integration of diverse data in materials science: Assessing Orowan strengthening

This study applies Semantic Web technologies to advance Materials Science and Engineering (MSE) through the integration of diverse datasets. Focusing on a 2000 series age-hardenable aluminum alloy, we correlate mechanical and microstructural properties derived from tensile tests and dark-field transmission electron microscopy across varied aging times. An expandable knowledge graph, constructed using the Tensile Test and Precipitate Geometry Ontologies aligned with the PMD Core Ontology, facilitates this integration. This approach adheres to FAIR principles and enables sophisticated analysis via SPARQL queries, revealing correlations consistent with the Orowan mechanism. The study highlights the potential of semantic data integration in MSE, offering a new approach for data-centric research and enhanced analytical capabilities.

Semantic Data Integration and Querying: A Survey and Challenges

Digital revolution produces massive, heterogeneous and isolated data. These latter remain underutilized, unsuitable for integrated querying and knowledge discovering. Hence the importance of this survey on data integration which identifies challenging issues and trends. First, an overview of the different generations and basics of data integration is given. Then, semantic data integration is focused, since it semantically links data allowing wider insights and decision-making. More than thirty works are reviewed. The goal is to help analysts to identify relevant criteria to compare then choose among semantic data integration approaches, focusing on the category (materialized, virtual or hybrid) and querying techniques.

Research on the Exposure Risk Analysis of Wildfires with a Spatiotemporal Knowledge Graph

This study focuses on constructions that are vulnerable to fire hazards during wildfire events, and these constructions are known as ‘exposures’, which are an increasingly significant area of disaster research. A key challenge lies in estimating dynamically and comprehensively the risk that individuals are exposed to during wildfire spread. Here, ‘exposure risk’ denotes the potential threat to exposed constructions from fires within a future timeframe. This paper introduces a novel method that integrates a spatiotemporal knowledge graph with wildfire spread data and an exposure risk analysis model to address this issue. This approach enables the semantic integration of varied and heterogeneous spatiotemporal data, capturing the dynamic nature of wildfire propagation for precise risk analysis. Empirical tests are employed for the study area of Xichang, Sichuan Province, using real-world data to validate the method’s efficacy in merging multiple data sources and enhancing the accuracy of exposure risk analysis. Notably, this approach also reduces the time complexity from O (m×n×p) to O (m×n).

Multimodal information fusion method in emotion recognition in the background of artificial intelligence

AbstractRecent advances in Semantic IoT data integration have highlighted the importance of multimodal fusion in emotion recognition systems. Human emotions, formed through innate learning and communication, are often revealed through speech and facial expressions. In response, this study proposes a hidden Markov model‐based multimodal fusion emotion detection system, combining speech recognition with facial expressions to enhance emotion recognition rates. The integration of such emotion recognition systems with Semantic IoT data can offer unprecedented insights into human behavior and sentiment analysis, contributing to the advancement of data integration techniques in the context of the Internet of Things. Experimental findings indicate that in single‐modal emotion detection, speech recognition achieves a 76% accuracy rate, while facial expression recognition achieves 78%. However, when state information fusion is applied, the recognition rate increases to 95%, surpassing the national average by 19% and 17% for speech and facial expressions, respectively. This demonstrates the effectiveness of multimodal fusion in emotion recognition, leading to higher recognition rates and reduced workload compared to single‐modal approaches.

Real-Time Semantic Data Integration and Reasoning in Life- and Time-Critical Decision Support Systems

Natural disasters such as earthquakes, floods, and forest fires involve critical situations in which human lives and infrastructures are in jeopardy. People are often injured and/or trapped without being able to be assisted by first responders on time. Moreover, in most cases, the harsh environment jeopardizes first responders by significantly increasing the difficulty of their mission. In such scenarios, time is crucial and often of vital importance. First responders must have a clear and complete view of the current situation every few seconds/minutes to efficiently and timely tackle emerging challenges, ensuring the safety of both victims and personnel. Advances in related technology including robots, drones, and Internet of Things (IoT)-enabled equipment have increased their usability and importance in life- and time-critical decision support systems such as the ones designed and developed for Search and Rescue (SAR) missions. Such systems depend on efficiency in their ability to integrate large volumes of heterogeneous and streaming data and reason with this data in (near) real time. In addition, real-time critical data integration and reasoning need to be performed on edge devices that reside near the missions, instead of using cloud infrastructure. The aim of this paper is twofold: (a) to review technologies and approaches related to real-time semantic data integration and reasoning on IoT-enabled collaborative entities and edge devices in life- and time-critical decision support systems, with a focus on systems designed for SAR missions and (b) to identify open issues and challenges focusing on the specific topic. In addition, this paper proposes a novel approach that will go beyond the state-of-the-art in efficiently recognizing time-critical high-level events, supporting commanders and first responders with meaningful and life-critical insights about the current and predicted state of the environment in which they operate.

KD SENSO-MERGER: An architecture for semantic integration of heterogeneous data

This paper presents KD SENSO-MERGER, a novel Knowledge Discovery (KD) architecture that is capable of semantically integrating heterogeneous data from various sources of structured and unstructured data (i.e. geolocations, demographic, socio-economic, user reviews, and comments). This goal drives the main design approach of the architecture. It works by building internal representations that adapt and merge knowledge across multiple domains, ensuring that the knowledge base is continuously updated. To deal with the challenge of integrating heterogeneous data, this proposal puts forward the corresponding solutions: (i) knowledge extraction, addressed via a plugin-based architecture of knowledge sensors; (ii) data integrity, tackled by an architecture designed to deal with uncertain or noisy information; (iii) scalability, this is also supported by the plugin-based architecture as only relevant knowledge to the scenario is integrated by switching-off non-relevant sensors. Also, we minimize the expert knowledge required, which may pose a bottleneck when integrating a fast-paced stream of new sources. As proof of concept, we developed a case study that deploys the architecture to integrate population census and economic data, municipal cartography, and Google Reviews to analyze the socio-economic contexts of educational institutions. The knowledge discovered enables us to answer questions that are not possible through individual sources. Thus, companies or public entities can discover patterns of behavior or relationships that would otherwise not be visible and this would allow extracting valuable information for the decision-making process.

Empowering Electronic Health Record Systems (EHRs) with Cloud Storage Management

We present a novel method for building cloud based interoperable electronic health record (EHR) systems. All members of the healthcare ecosystem, including patients, providers, and payers, can benefit from cloud computing in a number of ways. The exchange of healthcare information among diverse stakeholders has been significantly hampered by the lack of standardised data interoperability. In order to solve this problem, semantic interoperability is used. With the use of a reference model that outlines a common set of data structures and an archetype model that details the characteristics of clinical data, we employ a general design technique. The loosely connected, asynchronously communicating components of the application are created utilising the cloud component model technique. This article discusses our methods for attaining semantic interoperability, data integration, and high-level architecture of our EHR system.

Semantic Integration of BPMN Models and FHIR Data to Enable Personalized Decision Support for Malignant Melanoma

With digital patient data increasing due to new diagnostic methods and technology, showing the right data in the context of decision support at the point of care becomes an even greater challenge. Standard operating procedures (SOPs) modeled in BPMN (Business Process Model and Notation) contain evidence-based treatment guidance for all phases of a certain diagnosis, while physicians need the parts relevant to a specific patient at a specific point in the clinical process. Therefore, integration of patient data from electronic health records (EHRs) providing context to clinicians is needed, which is stored and communicated in HL7 (Health Level Seven) FHIR (Fast Healthcare Interoperability Resources). To address this issue, we propose a method combining an integration of stored data into BPMN and a loss-free transformation from BPMN into FHIR, and vice versa. Based on that method, an identification of the next necessary decision point in a specific patient context is possible. We verified the method for treatment of malignant melanoma by using an extract of a formalized SOP document with predefined decision points and validated FHIR references with real EHR data. The patient data could be stored and integrated into the BPMN element ‘DataStoreReference’. Our loss-free transformation process therefore is the foundation for combining evidence-based knowledge from formalized clinical guidelines or SOPs and patient data from EHRs stored in FHIR. Processing the SOP with the available patient data can then lead to the next upcoming decision point, which will be displayed to the physician integrated with the corresponding data.

A knowledge graph-based data harmonization framework for secondary data reuse

Background and objectiveThe adoption of new technologies in clinical care systems has propitiated the availability of a great amount of valuable data. However, this data is usually heterogeneous, requiring its harmonization to be integrated and analysed. We propose a semantic-driven harmonization framework that (1) enables the meaningful sharing and integration of healthcare data across institutions and (2) facilitates the analysis and exploitation of the shared data. MethodsThe framework includes an ontology-based common data model (i.e. SCDM), a data transformation pipeline and a semantic query system. Heterogeneous datasets, mapped to different terminologies, are integrated by using an ontology-based infrastructure rooted in a top-level ontology. A graph database is generated by using these mappings, and web-based semantic query system facilitates data exploration. ResultsSeveral datasets from different European institutions have been integrated by using the framework in the context of the European H2020 Precise4Q project. Through the query system, data scientists were able to explore data and use it for building machine learning models. ConclusionsThe flexible data representation using RDF, together with the formal semantic underpinning provided by the SCDM, have enabled the semantic integration, query and advanced exploitation of heterogeneous data in the context of the Precise4Q project.

Semantic Modelling of Archaeological Excavation Data. A review of the current state of the art and a roadmap of activities

Archaeological data repositories usually manage excavation data collections as project-level entities with restricted capacities to facilitate search or aggregation of excavation data at the sub-collection level (trenches, finds, season reports or excavation diaries etc.). More granular access to excavation data collections would enable layered querying across their informational content. In the past decade, several attempts to adapt CIDOC CRM in order to provide more explicit descriptions of the excavation universe have resulted in the use of domain-specific model extensions (e.g. CRMarchaeo, CRMsci, CRMba). Each focuses on corresponding aspects of the excavation research process, while their combined usage has potential to support expressive data mappings at the sub-collection level. As part of the ARIADNEplus project, several CIDOC CRM developers and domain experts have collaborated to undertake conceptual mapping exercises, to address the practicalities of bringing excavation data descriptions together and to link these to our overall aspirations in terms of excavation data discoverability and reusability. In this contribution, we discuss the current state and future directions of the field of semantic representation of archaeological excavation data and consider several issues that constrain the applicability of existing solutions. We identify five key enabling technologies or research areas (Conceptual models and semantic data structures, Conceptual modelling patterns, Data mapping workflows and tools, Learning technologies and Semantic queries) and assign readiness levels to assess their level of technological maturity. Our research demonstrates that while the existing models and domain-specific extensions are deemed adequate, there is a need for more user-friendly methods and tools to structure data in meaningful and interoperable ways. The next steps involve consolidating relevant semantic structures, improving modelling implementation guidance, adhering to consistent workflows, developing engaging curricula, and documenting real-case examples to demonstrate the benefits and results of semantic data integration.

An Ontology-Based Framework for Geospatial Integration and Querying of Raster Data Cube Using Virtual Knowledge Graphs

The integration of the raster data cube alongside another form of geospatial data (e.g., vector data) raises considerable challenges when it comes to managing and representing it using knowledge graphs. Such integration can play an invaluable role in handling the heterogeneity of geospatial data and linking the raster data cube to semantic technology standards. Many recent approaches have been attempted to address this issue, but they often lack robust formal elaboration or solely concentrate on integrating raster data cubes without considering the inclusion of semantic spatial entities along with their spatial relationships. This may constitute a major shortcoming when it comes to performing advanced geospatial queries and semantically enriching geospatial models. In this paper, we propose a framework that can enable such semantic integration and advanced querying of raster data cubes based on the virtual knowledge graph (VKG) paradigm. This framework defines a semantic representation model for raster data cubes that extends the GeoSPARQL ontology. With such a model, we can combine the semantics of raster data cubes with features-based models that involve geometries as well as spatial and topological relationships. This could allow us to formulate spatiotemporal queries using SPARQL in a natural way by using ontological concepts at an appropriate level of abstraction. We propose an implementation of the proposed framework based on a VKG system architecture. In addition, we perform an experimental evaluation to compare our framework with other existing systems in terms of performance and scalability. Finally, we show the potential and the limitations of our implementation and we discuss several possible future works.