Ontology Matching Research Articles

Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction

ObjectivesKnowledge graphs and ontologies in the biomedical domain provide rich contextual knowledge for a variety of challenges. Employing that for knowledge-driven NLP tasks such as gene-disease association prediction represents a promising way to increase the predictive power of a model. MethodsWe investigated the power of infusing the embedding of two aligned ontologies as prior knowledge to the NLP models. We evaluated the performance of different models on some large-scale gene-disease association datasets and compared it with a model without incorporating contextualized knowledge (BERT). ResultsThe experiments demonstrated that the knowledge-infused model slightly outperforms BERT by creating a small number of bridges. Thus, indicating that incorporating cross-references across ontologies can enhance the performance of base models without the need for more complex and costly training. However, further research is needed to explore the generalizability of the model. We expected that adding more bridges would bring further improvement based on the trend we observed in the experiments. In addition, the use of state-of-the-art knowledge graph embedding methods on a joint graph from connecting OGG and DOID with bridges also yielded promising results. ConclusionOur work shows that allowing language models to leverage structured knowledge from ontologies does come with clear advantages in the performance. Besides, the annotation stage brought out in this paper is constrained in reasonable complexity.

A Literature Review on Research Opportunities in Ontology Alignment for Quality Standards in Higher Education

Higher education today operates in a globally competitive environment. Competition is increasingly focused on quality. The quality of higher education reflects the relationship of higher education with users. Higher education uses various standards in the internal quality assurance system. It makes improvements in performance, features, suitability, reliability, durability, service, responsiveness, aesthetics, and reputation to support the progress of the quality of its performance. Implementing standards requires excellent effort because it requires quality fulfillment, and the satisfaction of each standard criterion requires internal and external audit processes. Standard alignment is needed for cost efficiency in implementing standards. Standard alignment can be done with ontology alignment technology. However, before applying ontology alignment, each ontology standard is needed. This study aims to explore literature that has implemented ontology and ontology alignment in education. This study aims to find out whether there has been research on the alignment of educational quality standards. The results of this study show that ontology has been applied in education, namely on the topics of curriculum, e-learning, learning assessment, system integration, syllabus, learning style, service, and accreditation. The implementation of ontology alignment has been carried out on the topics of Profile Learning, Learning Design, E-Learning, Curriculum, and System Integration. While the application of ontology or ontology alignment on educational quality standards has yet to be found by research that discusses it, quality standards have been applied to quality management models based on ISO 9000 requirements and software quality standards based on CMMI standards.

Integrating NLP and Ontology Matching into a Unified System for Automated Information Extraction from Geological Hazard Reports

Integrating NLP and Ontology Matching into a Unified System for Automated Information Extraction from Geological Hazard Reports

A novel enhanced flow regime algorithm using opposition-based learning

Metaheuristics are widely used in science and industry because it as a high-level heuristic technique can provide robust or advanced solutions compared to classical search algorithms. Flow Regime Algorithm is a novel physics-based optimization approach recently proposed, and it is one of the candidate algorithms for solving complex optimization problems because of its few parameter configurations, simple coding, and good performance. However, the population that initialized randomly may have poor diversity issues, resulting in insufficient global search, and premature convergence to local optimum. To solve this problem, in this paper, a novel enhanced Flow Regime Algorithm based on opposition learning scheme is proposed. The proposed algorithm introduces the opposition-based learning strategy into the generation of some populations to enhance the global search performance while maintaining a fast convergence rate. In order to verify the performance of the proposed algorithm, 23 benchmark numerical optimization functions were studied experimentally in detail and compared with six well-known algorithms. Experimental results show that the proposed algorithm outperforms all other metaheuristic algorithms in all unimodal functions with higher accuracy, and can obtain competitive results on more multimodal cases. A statistical comparison shows that the proposed algorithm has superiority. Finally, an ontology alignment application study demonstrate that the proposed algorithm can achieve higher quality alignment compared to most other metaheuristic-based systems and OAEI ontology alignment systems.

Analysis and implementation of the DynDiff tool when comparing versions of ontology

BackgroundOntologies play a key role in the management of medical knowledge because they have the properties to support a wide range of knowledge-intensive tasks. The dynamic nature of knowledge requires frequent changes to the ontologies to keep them up-to-date. The challenge is to understand and manage these changes and their impact on depending systems well in order to handle the growing volume of data annotated with ontologies and the limited documentation describing the changes.MethodsWe present a method to detect and characterize the changes occurring between different versions of an ontology together with an ontology of changes entitled DynDiffOnto, designed according to Semantic Web best practices and FAIR principles. We further describe the implementation of the method and the evaluation of the tool with different ontologies from the biomedical domain (i.e. ICD9-CM, MeSH, NCIt, SNOMEDCT, GO, IOBC and CIDO), showing its performance in terms of time execution and capacity to classify ontological changes, compared with other state-of-the-art approaches.ResultsThe experiments show a top-level performance of DynDiff for large ontologies and a good performance for smaller ones, with respect to execution time and capability to identify complex changes. In this paper, we further highlight the impact of ontology matchers on the diff computation and the possibility to parameterize the matcher in DynDiff, enabling the possibility of benefits from state-of-the-art matchers.ConclusionDynDiff is an efficient tool to compute differences between ontology versions and classify these differences according to DynDiffOnto concepts. This work also contributes to a better understanding of ontological changes through DynDiffOnto, which was designed to express the semantics of the changes between versions of an ontology and can be used to document the evolution of an ontology.

Augmented intelligence facilitates concept mapping across different electronic health records

IntroductionWith the advent of artificial intelligence, the secondary use of routinely collected medical data from electronic healthcare records (EHR) has become increasingly popular. However, different EHR systems typically use different names for the same medical concepts. This obviously hampers scalable model development and subsequent clinical implementation for decision support. Therefore, converting original parameter names to a so-called ontology, a standardized set of predefined concepts, is necessary but time-consuming and labor-intensive. We therefore propose an augmented intelligence approach to facilitate ontology alignment by predicting correct concepts based on parameter names from raw electronic health record data exports. MethodsWe used the manually mapped parameter names from the multicenter “Dutch ICU data warehouse against COVID-19” sourced from three types of EHR systems to train machine learning models for concept mapping. Data from 29 intensive care units on 38,824 parameters mapped to 1,679 relevant and unique concepts and 38,069 parameters labeled as irrelevant were used for model development and validation. We used the Natural Language Toolkit (NLTK) to preprocess the parameter names based on WordNet cognitive synonyms transformed by term-frequency inverse document frequency (TF-IDF), yielding numeric features. We then trained linear classifiers using stochastic gradient descent for multi-class prediction. Finally, we fine-tuned these predictions using information on distributions of the data associated with each parameter name through similarity score and skewness comparisons. ResultsThe initial model, trained using data from one hospital organization for each of three EHR systems, scored an overall top 1 precision of 0.744, recall of 0.771, and F1-score of 0.737 on a total of 58,804 parameters. Leave-one-hospital-out analysis returned an average top 1 recall of 0.680 for relevant parameters, which increased to 0.905 for the top 5 predictions. When reducing the training dataset to only include relevant parameters, top 1 recall was 0.811 and top 5 recall was 0.914 for relevant parameters. Performance improvement based on similarity score or skewness comparisons affected at most 5.23% of numeric parameters. ConclusionAugmented intelligence is a promising method to improve concept mapping of parameter names from raw electronic health record data exports. We propose a robust method for mapping data across various domains, facilitating the integration of diverse data sources. However, recall is not perfect, and therefore manual validation of mapping remains essential.

Terminologies in RDM for Engineering – a Service Approach

The frameworks which have been established since the start of the NFDI allow for a coordinated development of RDM services, which include the introduction of community specific Terminology Services. To address the challenge of alignment and re-use of established ontologies and terminologies in the engineering domain, a Terminology Service (TS) was set-up for the NFDI4Ing initiative: https://terminology.nfdi4ing.de. The NFDI4Ing TS provides a single point of access to relevant research concepts and offers the building blocks for (meta-) data schemata and data annotation. As an open source platform, it features more than 50 ontologies, 147,000 terms and over 5,800 properties from a range of engineering-related terminology collections. The use of the NFDI4Ing TS fosters interoperability and reuse in a FAIR data context.

A Secure and Privacy-Preserving Blockchain-Based XAI-Justice System

Pursuing “intelligent justice” necessitates an impartial, productive, and technologically driven methodology for judicial determinations. This scholarly composition proposes a framework that harnesses Artificial Intelligence (AI) innovations such as Natural Language Processing (NLP), ChatGPT, ontological alignment, and the semantic web, in conjunction with blockchain and privacy techniques, to examine, deduce, and proffer recommendations for the administration of justice. Specifically, through the integration of blockchain technology, the system affords a secure and transparent infrastructure for the management of legal documentation and transactions while preserving data confidentiality. Privacy approaches, including differential privacy and homomorphic encryption techniques, are further employed to safeguard sensitive data and uphold discretion. The advantages of the suggested framework encompass heightened efficiency and expediency, diminished error propensity, a more uniform approach to judicial determinations, and augmented security and privacy. Additionally, by utilizing explainable AI methodologies, the ethical and legal ramifications of deploying intelligent algorithms and blockchain technologies within the legal domain are scrupulously contemplated, ensuring a secure, efficient, and transparent justice system that concurrently protects sensitive information upholds privacy.

A Novel Accurate and Time Efficient Map Reduce Approach for Biomedical Ontology Alignment

A Novel Accurate and Time Efficient Map Reduce Approach for Biomedical Ontology Alignment

Ontology alignment with semantic and structural embeddings

Ontology alignment is essential for data integration and interoperability across multiple applications across diverse disciplines. In recent decades, significant advancements have been made in the development of advanced methods and systems for ontology alignment. Empirical results have suggested that ontological semantics can be effectively employed to enhance the alignment process. Besides, structural information is crucial for ontology alignment as it reflects the relations among adjacent concepts in the ontology. Previous works are mainly based on external lexicon and predefined rules based on ontological structure. Recently, deep learning has imposed positive impacts on ontology alignment and obtained substantial improvement.This paper proposes a new method based on ontology embedding incorporating the semantic and structural features. It utilizes the distance between the embedding of two ontological concepts to be aligned as the criterion for alignment. The proposed method is used to align two widely used food ontologies and three Chinese food classification ontologies. The experimental results show that our method enhances the performance compared to several state-of-the-art alignment systems, demonstrating the importance of learning semantic representation and structural representation. Furthermore, the proposed method is evaluated on several different tracks of the Ontology Alignment Evaluation Initiative (OAEI), and experimental results show that our method outperforms other baselines in effectiveness. The data and code can be obtained from: https://github.com/haozhigang1111/Ontology-Alignment.git.

Hybridizing Fuzzy String Matching and Machine Learning for Improved Ontology Alignment

Ontology alignment has become an important process for identifying similarities and differences between ontologies, to facilitate their integration and reuse. To this end, fuzzy string-matching algorithms have been developed for strings similarity detection and have been used in ontology alignment. However, a significant limitation of existing fuzzy string-matching algorithms is their reliance on lexical/syntactic contents of ontology only, which do not capture semantic features of ontologies. To address this limitation, this paper proposed a novel method that hybridizes fuzzy string-matching algorithms and the Deep Bidirectional Transformer (BERT) deep learning model with three machine learning regression classifiers, namely, K-Nearest Neighbor Regression (kNN), Decision Tree Regression (DTR), and Support Vector Regression (SVR), to perform the alignment of ontologies. The use of the kNN, SVR, and DTR classifiers in the proposed method resulted in the building of three similarity models (SM), encoded SM-kNN, SM-SVR, and SM-DTR, respectively. The experiments were conducted on a dataset obtained from the anatomy track in the Ontology Alignment and Evaluation Initiative 2022 (OAEI 2022). The performances of the SM-kNN, SM-SVR, and SM-DTR models were evaluated using various metrics including precision, recall, F1-score, and accuracy at thresholds 0.70, 0.80, and 0.90, as well as error rates and running times. The experimental results revealed that the SM-SVR model achieved the best recall of 1.0, while the SM-DTR model exhibited the best precision, accuracy, and F1-score of 0.98, 0.97, and 0.98, respectively. Furthermore, the results showed that the SM-kNN, SM-SVR, and SM-DTR models outperformed state-of-the-art alignment systems that participated in the OAEI 2022 challenge, indicating the superior capability of the proposed method.

AgreementMakerLight

Ontology matching establishes correspondences between entities of related ontologies, with applications ranging from enabling semantic interoperability to supporting ontology and knowledge graph development. Its demand within the Semantic Web community is on the rise, as the popularity of knowledge graph supporting information systems or artificial intelligence applications continues to increase. In this article, we showcase AgreementMakerLight (AML), an ontology matching system in continuous development since 2013, with demonstrated performance over nine editions of the Ontology Alignment Evaluation Initiative (OAEI), and a history of real-world applications across a variety of domains. We overview AML’s architecture and algorithms, its user interfaces and functionalities, its performance, and its impact. AML has participated in more OAEI tracks since 2013 than any other matching system, has a median rank by F-measure between 1 and 2 across all tracks in every year since 2014, and a rank by run time between 3 and 4. Thus, it offers a combination of range, quality and efficiency that few matching systems can rival. Moreover, AML’s impact can be gauged by the 263 (non-self) publications that cite one or more of its papers, among which we count 34 real-world applications.

Integrating Sensor Ontologies with Niching Multi-Objective Particle Swarm Optimization Algorithm.

Sensor ontology provides a standardized semantic representation for information sharing between sensor devices. However, due to the varied descriptions of sensor devices at the semantic level by designers in different fields, data exchange between sensor devices is hindered. Sensor ontology matching achieves data integration and sharing between sensors by establishing semantic relationships between sensor devices. Therefore, a niching multi-objective particle swarm optimization algorithm (NMOPSO) is proposed to effectively solve the sensor ontology matching problem. As the sensor ontology meta-matching problem is essentially a multi-modal optimization problem (MMOP), a niching strategy is introduced into MOPSO to enable the algorithm to find more global optimal solutions that meet the needs of different decision makers. In addition, a diversity-enhancing strategy and an opposition-based learning (OBL) strategy are introduced into the evolution process of NMOPSO to improve the quality of sensor ontology matching and ensure the solutions converge to the real Pareto fronts (PFs). The experimental results demonstrate the effectiveness of NMOPSO in comparison to MOPSO-based matching techniques and participants of the Ontology Alignment Evaluation Initiative (OAEI).

Fast and Accurate Framework for Ontology Matching in Web of Things

The Web of Things (WoT) can help with knowledge discovery and interoperability issues in many Internet of Things (IoT) applications. This article focuses on semantic modeling of WoT and proposes a new approach called Decomposition for Ontology Matching (DOM) to discover relevant knowledge by exploring correlations between WoT data using decomposition strategies. The DOM technique adopts several decomposition techniques to order highly linked ontologies of WoT data into similar groups. The main idea is to decompose the instances of each ontology into similar groups and then match instances of similar groups instead of entire instances of two ontologies. Three main algorithms for decomposition have been developed. The first algorithm is based on radar scanning, which determines the distribution of distances between each instance and all other instances to determine the cluster centroid. The second algorithm is based on adaptive grid clustering, where it focuses on distribution information and the construction of spanning trees. The third algorithm is based on split index clustering, where instances are divided into groups of cells from which noise is removed during the merging process. Several studies were conducted with different ontology databases to illustrate the use of the DOM technique. The results show that DOM outperforms state-of-the-art ontology matching models in terms of computational cost while maintaining the quality of the matching. Moreover, these results demonstrate that DOM is capable of handling various large datasets in WoT contexts.

Methods of managing the evolution of ontologies and their alignments

Nowadays, none can expect that knowledge about some part of reality will not change. Consequently, a representation of such evolving knowledge (for example, ontologies) also changes. Such changes entail that applications incorporating such knowledge may become compromised and yield wrong results. An example of such an application is ontology alignment which can be informally described as a set of connections between two ontologies. Those connections mark elements from two ontologies that relate to the same parts of reality. In changing one of the corresponding ontologies, such connections may become invalid. One may designate the ontology alignment once again from scratch for altered ontologies. However, such an approach is time and resource-consuming. The paper comprehensively presents our ontology evolution and alignment maintenance framework. It can be used to preserve the validity of ontology alignment using only the analysis of changes introduced to maintained ontologies. The precise definition of ontologies is provided, along with a definition of the ontology change log. A set of algorithms that allow revalidating ontology alignments have been built based on such elements.

A systematic comparison and evaluation of building ontologies for deploying data-driven analytics in smart buildings

Ontologies play a critical role in data exchange, information integration, and knowledge sharing across diverse smart building applications. Yet, semantic differences between the prevailing building ontologies hamper their purpose of bringing data interoperability and restrict the ability to reuse building ontologies in real-world applications. In this paper, we propose and adopt a framework to conduct a systematic comparison and evaluation of four popular building ontologies (Brick Schema, RealEstateCore, Project Haystack, and Digital Buildings) from both axiomatic design and assertions in a use case, namely the Terminological Box (TBox) evaluation and the Assertion Box (ABox) evaluation. In the TBox evaluation, we use the SQuaRE-based Ontology Quality Evaluation (OQuaRE) framework and concede that Project Haystack and Brick Schema are more compact with respect to the ontology axiomatic design. In the ABox evaluation, we apply an empirical study with sample building data that suggests Brick Schema and RealEstateCore have greater completeness and expressiveness in capturing the main concepts and relations within the building domain. The results indicate that there is no universal building ontology for integrating Linked Building Data (LBD). We also discuss ontology compatibility and investigate building ontology design patterns (ODPs) to support ontology matching, alignment, and harmonisation.

Two-stage Detection of Semantic Redundancies in RDF Data

With the enrichment of the RDF (resource description framework), integrating diverse data sources may result in RDF data duplication. Failure to effectively detect the duplicates brings redundancies into the integrated RDF datasets. This not only increases unnecessarily the size of the datasets, but also reduces the dataset quality. Traditionally a similarity calculation is applied to detect if a pair of candidates contains duplicates. For massive RDF data, a simple similarity calculation may lead to extremely low efficiency. To detect duplicates in the massive RDF data, in this paper we propose a detection approach based on RDF data clustering and similarity measurements. We first propose a clustering method based on locality sensitive hashing (LSH), which can efficiently select candidate pairs in RDF data. Then, a similarity calculation is performed on the selected candidate pairs. We finally obtain the duplicate candidates. We show through experiments that our approach can quickly extract the duplicate candidates in RDF datasets. Our approach had the highest F score and time performance in the OAEI (Ontology Alignment Evaluation Initiative) 2019 competition.

Systematic Approach for Measuring Semantic Relatedness between Ontologies

Measuring ontology matching is a critical issue in knowledge engineering and supports knowledge sharing and knowledge evolution. Recently, linguistic scientists have defined semantic relatedness as being more significant than semantic similarities in measuring ontology matching. Semantic relatedness is measured using synonyms and hypernym–hyponym relationships. In this paper, a systematic approach for measuring ontology semantic relatedness is proposed. The proposed approach is developed with a clear and fully described methodology, with illustrative examples used to demonstrate the proposed approach. The relatedness between ontologies has been measured based on class level by using lexical features, defining semantic similarity of concepts based on hypernym–hyponym relationships. For evaluating our proposed approach against similar works, benchmarks are generated using five properties: related meaning features, lexical features, providing technical descriptions, proving applicability, and accuracy. Technical implementation is carried out in order to demonstrate the applicability of our approach. The results demonstrate an achieved accuracy of 99%. The contributions are further highlighted by benchmarking against recent related works.

Integrating Heterogeneous Ontologies in Asian Languages Through Compact Genetic Algorithm with Annealing Re-sample Inheritance Mechanism

An ontology is a state-of-the-art knowledge modeling technique in the natural language domain, which has been widely used to overcome the linguistic barriers in Asian and European countries’ intelligent applications. However, due to the different knowledge backgrounds of ontology developers, the entities in the ontologies could be defined in different ways, which hamper the communications among the intelligent applications built on them. How to find the semantic relationships among the entities that are lexicalized in different languages is called the Cross-lingual Ontology Matching problem (COM), which is a challenge problem in the ontology matching domain. To face this challenge, being inspired by the success of the Genetic Algorithm (GA) in the ontology matching domain, this work proposes a Compact GA with Annealing Re-sample Inheritance mechanism (CGA-ARI) to efficiently address the COM problem. In particular, a Cross-lingual Similarity Metric (CSM) is presented to distinguish two cross-lingual entities, a discrete optimal model is built to define the COM problem, and the compact encoding mechanism and the Annealing Re-sample Inheritance mechanism (ARI) are introduced to improve CGA’s searching performance. The experiment uses Multifarm track to test CGA-ARI’s performance, which includes 45 ontology pairs in different languages. The experimental results show that CGA-ARI is able to significantly improve the performance of GA and CGA and determine better alignments than state-of-the-art ontology matching systems.

SALON ontology for the formal description of sequence alignments

BackgroundInformation provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and their context. Sequence alignment is a bioinformatics approach to identifying regions of similarity in DNA, RNA, or protein sequences. However, there is no consensus about the specific common terminology and representation for sequence alignments. Thus, automatically linking the wide existing knowledge about the sequences with the alignments is challenging.ResultsThe Sequence Alignment Ontology (SALON) defines a helpful vocabulary for representing and semantically annotating pairwise and multiple sequence alignments. SALON is an OWL 2 ontology that supports automated reasoning for alignments validation and retrieving complementary information from public databases under the Open Linked Data approach. This will reduce the effort needed by scientists to interpret the sequence alignment results.ConclusionsSALON defines a full range of controlled terminology in the domain of sequence alignments. It can be used as a mediated schema to integrate data from different sources and validate acquired knowledge.