Automated weighted aggregation in an ontology matching system

Ontology matching is an important process for integration of heterogeneous data sources. A large number of different matchers for comparing ontologies exist. They can be classified into element-level and structure-level matchers. The element-level matchers compare entities ignoring their relations with other entities, while the structure-level matchers consider these relations. The TF/IDF (term frequency / inverse document frequency) measure is useful for specifying key terms weights in documents. In our matching system we use the TF/IDF measure for comparing documents that store data about ontology entities. However, the TF/IDF does not take synonyms into account, and it may occur that the terms that describe two entities the best are synonyms. In this paper we propose a matcher that combines the TF/IDF measure with synonym recognition when determining key term weights, in order to improve the results of ontology matching. Evaluation of the matcher is performed on case study examples.

Today, there is a rapid increase of the available data because of advances in information and communications technology. Therefore, many mutually heterogeneous data sources that describe the same domain of interest exist. To facilitate the integration of these heterogeneous data sources, an ontology can be used as it enriches the knowledge of a data source by giving a detailed description of entities and their mutual relations within the domain of interest. Ontology matching is a key issue in integrating heterogeneous data sources described by ontologies as it eases the management of data coming from various sources. The ontology matching system consists of several basic matchers. To determine high-quality correspondences between entities of compared ontologies, the matching results of these basic matchers should be aggregated by an aggregation method. In this paper, a new weighted aggregation method for parallel composition of basic matchers based on genetic algorithm is presented. The evaluation has confirmed a high quality of the new aggregation method as this method has improved the process of matching two ontologies by obtaining higher confidence values of correctly found correspondences and thus increasing the quality of matching results.

The paper reports on a case study regarding the integration of heterogeneous data sources, coming from different institutions, needed to support several studies related to the health status of the population of L’Aquila (Italy) after the earthquake of April 6th 2009. In detail, the paper initially describes all the health studies, then the data sources required to support them, finally proposes a simplified federated architecture and a straightforward technological solution to implement it.

As a key representation model of knowledge, ontology has been widely used in a lot of NLP related tasks, such as semantic parsing, information extraction and text mining etc. In this paper, we study the task of ontology matching, which concentrates on finding semantically related entities between different ontologies that describe the same domain, to solve the semantic heterogeneity problem. Previous works exploit different kinds of descriptions of an entity in ontology directly and separately to find the correspondences without considering the higher level correlations between the descriptions. Besides, the structural information of ontology haven’t been utilized adequately for ontology matching. We propose in this paper an ontology matching approach, named ERSOM, which mainly includes an unsupervised representation learning method based on the deep neural networks to learn the general representation of the entities and an iterative similarity propagation method that takes advantage of more abundant structure information of the ontology to discover more mappings. The experimental results on the datasets from Ontology Alignment Evaluation Initiative (OAEI1) show that ERSOM achieves a competitive performance compared to the state-of-the-art ontology matching systems. The OAEI is an international initiative organizing annual campaigns for evaluating ontology matching systems. All of the ontologies provided by OAEI are described in OWL-DL language, and like most of the other participates our ERSOM also manages the OWL ontology in its current version. OAEI: http://oaei.ontologymatching.org/

The mutual identification of spatial objects is a fundamental issue when updating geographic data with other data sets. Representations of spatial objects in different sources may not have the same identifiers, which would unambiguously assign them to each other. Intersections of spatial objects can be used for this purpose, but this does not allow for the detection of possible changes and their quantification. The aim of this paper is to propose a simple, applicable procedure for calculating the shape similarity measure, which should be able to efficiently identify different representations of spatial objects in two data sources, even though they may be changed or generalised. The main result is the aggregated index of shape similarity and instructions for its calculation and implementation. The shape similarity index is based on the calculation of the set similarity, the distance of the boundaries, and the differences in the area, perimeter, and number of the vertices of areal spatial objects. In the case study, the footprints of the building complexes in Dúbravka (part of the city of Bratislava, the capital of Slovakia) are compared using data from OpenStreetMap and INSPIRE (Infrastructure for Spatial Information in Europe) Buildings. A contribution to the quality check of the OpenStreetMap data is then a secondary result. The proposed method can be effectively used in the semi-automatic integration of heterogeneous data sources, updating the data source with other spatial data, or in their quality control.

BackgroundProtein-protein interaction (PPI) prediction remains a central task in systems biology to achieve a better and holistic understanding of cellular and intracellular processes. Recently, an increasing number of computational methods have shifted from pair-wise prediction to network level prediction. Many of the existing network level methods predict PPIs under the assumption that the training network should be connected. However, this assumption greatly affects the prediction power and limits the application area because the current golden standard PPI networks are usually very sparse and disconnected. Therefore, how to effectively predict PPIs based on a training network that is sparse and disconnected remains a challenge.ResultsIn this work, we developed a novel PPI prediction method based on deep learning neural network and regularized Laplacian kernel. We use a neural network with an autoencoder-like architecture to implicitly simulate the evolutionary processes of a PPI network. Neurons of the output layer correspond to proteins and are labeled with values (1 for interaction and 0 for otherwise) from the adjacency matrix of a sparse disconnected training PPI network. Unlike autoencoder, neurons at the input layer are given all zero input, reflecting an assumption of no a priori knowledge about PPIs, and hidden layers of smaller sizes mimic ancient interactome at different times during evolution. After the training step, an evolved PPI network whose rows are outputs of the neural network can be obtained. We then predict PPIs by applying the regularized Laplacian kernel to the transition matrix that is built upon the evolved PPI network. The results from cross-validation experiments show that the PPI prediction accuracies for yeast data and human data measured as AUC are increased by up to 8.4 and 14.9% respectively, as compared to the baseline. Moreover, the evolved PPI network can also help us leverage complementary information from the disconnected training network and multiple heterogeneous data sources. Tested by the yeast data with six heterogeneous feature kernels, the results show our method can further improve the prediction performance by up to 2%, which is very close to an upper bound that is obtained by an Approximate Bayesian Computation based sampling method.ConclusionsThe proposed evolution deep neural network, coupled with regularized Laplacian kernel, is an effective tool in completing sparse and disconnected PPI networks and in facilitating integration of heterogeneous data sources.

Ontology as the base of semantic web is used in many applications. Different ontologies in the same domain lead some heterogeneities and ontology matching systems are developed for resolved them. Heterogeneities have arisen owing to the fact that these ontologies have been created by various people through diverse methods. Nowadays, using large-scale ontologies in some applications such as medical fields seems inevitable. By using large-scale ontologies, some problems like the shortage of memory consumption and long duration of execution appeared in ontology matching systems. In this paper, large-scale ontology matching systems are studied and proposed a general architecture for them. Then large-scale ontology matching systems classified based on the partitioning large ontologies into several sub-ontologies, as known as the modularization, decomposition, summarization, clustering, and divide and conquer categories. This new classification will be useful for future research works in this field. In order to find out the efficiency of the ontology matching systems the results of OAEI (Ontology Alignment Evaluation Initiative) for the period 2011 to 2015 are compared. In spite of great progress, increasing accuracy is required in some section such as conference and benchmark sections.

COGOM: Cognitive Theory Based Ontology Matching System

The integration of heterogeneous data sources can be done by using data-driven microservices along with Semantic Web technologies. However, it becomes a challenge in cross-domain scenarios, in which data is described by heterogeneous ontologies. This work discusses data integration problems in the context of microservices and proposes an ontology alignment framework aimed at achieving semantic data-driven microservices composition for data integration in multi-ontology scenarios. The proposed framework is evaluated through an experimental design to obtain a suitable statistical analysis of the effects that may be considered for modeling data-driven microservices.

Ontology matching is usually performed to find semantic correspondences between the entity elements of different ontologies to enable interoperability. Current research on ontology matching has largely focused on representation learning. However, there still exist two limitations. Firstly, they are only used in the element level matching phase, ignoring relations of the entity. Secondly, the final alignment threshold is usually determined manually within these methods. It is difficult for an expert to adjust the threshold value and even more for non-expert user. To address these issues, we propose an alternative ontology matching framework, which models the matching process by embedding techniques with jointly encoding ontology terminological description and network structure. We further improve our iterative final alignment method by introducing an automatic adjustment of threshold method. Finally, we perform an experimental evaluation and compare it with state-of-the-art ontology matching systems on four Ontology Alignment Evaluation Initiative (OAEI) datasets. Our approach performs better than most of the systems and achieves a competitive performance. Moreover, we obtained F-measure values of 93.8% and 90.8% on the OAEI Large Biomedical Ontologies FMA-NCI and FMA-SNOMED subtasks.

Data integration of heterogeneous sources is still an active research problem. This topic is especially crucial on enterprises that deal with new and different kinds of data as new services are provided. However, even though research efforts have been applied to the information integration, there is a lack of practical approaches ready to be implemented for real use cases. In this paper, we present a web-based framework and system built upon ontologies and other semantic techniques for the integration of heterogeneous data sources. The example scenario used to demonstrate the utility of the framework consists of a use case with the actual data of a telecom company.

The multi-national MIDAS (Meaningful Integration of Data Analytics and Services) project is developing a big data platform to facilitate the utilisation of a wide range of health and social care data. The platform will enable the integration of heterogeneous data sources, providing privacy-preserving analytics, forecasting tools and bespoke visualisations of actionable epidemiological data. An evaluation framework starting with a logic model and using the principles of realist evaluation developed working with users, and software developers. The tools used are a series of parallel case studies to address the requirements of stakeholder groups at critical time points during the project to ensure IT systems development is in line with user’s requirements. The process includes longitudinal interviews with stakeholders, regular feedback to users and developers, and measurement of stakeholder’s attitudes to the project using Q-methodology.

A method and software framework for enriching private biomedical sources with data from public online repositories

In recent years, research on digital twins in the construction sector has grown significantly, particularly since 2018. However, most studies focus on isolated lifecycle phases and give limited attention to developing practices that address all stages of the building lifecycle. Current applications of digital twins in construction are largely concentrated on design and engineering, where Building Information Modeling (BIM) serves as the primary input. This dominance stems from BIM's role as an existing digital representation of built assets, which can be extended into a digital twin. One of the major barriers to wider implementation lies in data integration and interoperability—specifically, the challenge of consolidating information from diverse sources, formats, and lifecycle stages. Future research should prioritize the standardization of data formats, protocols, and application programming interfaces (APIs) to facilitate seamless exchange across digital twin systems. Additionally, the development of advanced data governance frameworks is essential to ensure accuracy, completeness, and security of information. Greater exploration into semantic data modeling and ontologies will also support the integration of heterogeneous data sources. Beyond technical issues, it is equally important to investigate the costs, benefits, and potential drawbacks of adopting digital twins across the entire building lifecycle. Expanding the scope of applications beyond design and engineering to include construction, operation and maintenance, as well as demolition and recovery phases, will be crucial. This paper therefore outlines the current state of digital twin research in construction, identifies critical challenges, and highlights key directions for future development.

Businesses find it hard to combine data from different systems, formats, and sources. Some examples of these sources are structured data in relational databases, semi-structured data like JSON or XML, and unstructured data like text or multimedia files. Businesses need to be able to handle and mix all of these different types of data in order to get the most out of them. You can now utilize an architecture to put together data from languages that are distinct. This framework is meant to help you find a way to handle a lot of various types of data and sources without slowing down or losing consistency. Cloud storage, APIs, and machine learning are just a few of the cutting-edge technologies that the framework leverages to make sure that data systems can work together without any hassles. It allows businesses to combine their data while ensuring that all of their systems are accurate and high-quality. The platform also solves the problem of scalability, which means that companies can simply handle more and more data without any issues or delays. This plan helps businesses maintain better track of their data, which makes it easier to put together and less likely to make mistakes. Companies should always be able to see their data in the same way, no matter where it comes from or what format it is in. This makes it easier to choose. The answer also helps with data governance since it allows people ways to keep track of data history, set security standards, and make sure they follow the rules. When you have to interact with diverse kinds of data, the polyglot data integration framework is an excellent method to deal with problems that come up. In a world where data is king, it helps businesses get the most out of their data, keep things running smoothly, and remain ahead of the competition