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Reasoning is the process of inferring new knowledge and identifying inconsistencies within ontologies. Traditional techniques often prove inadequate when reasoning over large Knowledge Bases containing millions or billions of facts. This article introduces NORA, a persistent and scalable OWL reasoner built on top of Apache Spark, designed to address the challenges of reasoning over extensive and complex ontologies. NORA exploits the scalability of NoSQL databases to effectively apply inference rules to Big Data ontologies with large ABoxes. To facilitate scalable reasoning, OWL data, including class and property hierarchies and instances, are materialized in the Apache Cassandra database. Spark programs are then evaluated iteratively, uncovering new implicit knowledge from the dataset and leading to enhanced performance and more efficient reasoning over large‐scale ontologies. NORA has undergone a thorough evaluation with different benchmarking ontologies of varying sizes to assess the scalability of the developed solution. [ABSTRACT FROM AUTHOR]

In current Open Banking services, the European Payment Services Directive (PSD2) allows the secure collection of bank customer information, on their behalf and with their consent, to analyze their financial status and needs. The PSD2 directive has lead to a massive number of daily transactions between Fintech entities which require the automatic management of the data involved, generally coming from multiple and heterogeneous sources and formats. In this context, one of the main challenges lies in defining and implementing common data integration schemes to easily merge them into knowledge-base repositories, hence allowing data reconciliation and sophisticated analysis. In this sense, Semantic Web technologies constitute a suitable framework for the semantic integration of data that makes linking with external sources possible and enhances systematic querying. With this motivation, an ontology approach is proposed in this work to operate as a semantic data mediator in real-world open banking operations. According to semantic reconciliation mechanisms, the underpinning knowledge graph is populated with data involved in PSD2 open banking transactions, which are aligned with information from invoices. A series of semantic rules is defined in this work to show how the financial solvency classification of client entities and transaction concept suggestions can be inferred from the proposed semantic model. [ABSTRACT FROM AUTHOR]

Abstract Background The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. Methods KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning). Results In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts. Conclusion These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool http://khaos.uma.es/KA-SB, which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases.

Nowadays, the increasing demand of water for electricity production, agricultural and industrial uses are directly affecting the reduction of available quality water for human consumption in the world. Efficient and sustainable maintenance of water reservoirs and supply networks implies a holistic strategy that takes into account, as much as possible, information from the stages of water usage. Next,-generation decision-making software tools, for supporting water management, require the integration of multiple and heterogeneous data sources of different knowledge domains. In this regard, Linked Data and Semantic Web technologies enable harmonization of different data sources, as well as the efficient querying for feeding upper-level Business Intelligence processes. This work investigates the design, implementation and usage of a semantic approach driven by ontology to capture, store, integrate and exploit real-world data concerning water supply networks management. As a main contribution, the proposal helps with obtaining semantically enriched linked data, enhancing the analysis of water network performance. For validation purposes, in the use case, a series of data sources from different measures have been considered, in the scope of an actual water management system of the Mediterranean region of Valencia (Spain), throughout several years of activity. The obtained experience shows the benefits of using the proposed approach to identify possible correlations between the measures such as the supplied water, the water leaks or the population. [ABSTRACT FROM AUTHOR]

Summary: Big data technologies enable people to store, analyze, and utilize large amounts of complex data effectively. In this context, NoSQL (Not only Structured Query Language) databases have emerged as the most commonly used infrastructure for handling big Resource Description Framework data. In this paper, we present our proposal to materialize classified OWL (Web Ontology Language) ontologies in a NoSQL database. This materialization process enables the distributed storage of Resource Description Framework data by exploiting the inherent distribution of the NoSQL database nodes. Furthermore, this approach supposes the first step toward a novel approach to scalable OWL reasoning, which enables scalable Linked Data reasoning. To validate our proposal, we developed a prototype for a tool that stores an OWL ontology in a Cassandra database following our approach. Finally, we introduce our reasoning strategy to compute the ontology closure using this Cassandra database. [ABSTRACT FROM AUTHOR]

Background: The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. Methods: KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning). Results: In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts. Conclusion: These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool http://khaos.uma.es/ KA-SB, which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases. [ABSTRACT FROM AUTHOR]

Gene regulation computational research requires handling and integrating large amounts of heterogeneous data. The Gene Ontology has demonstrated that ontologies play a fundamental role in biological data interoperability and integration. Ontologies help to express data and knowledge in a machine processable way, which enables complex querying and advanced exploitation of distributed data. Contributing to improve data interoperability in gene regulation is a major objective of the GREEKC Consortium, which aims to develop a standardized gene regulation knowledge commons. GREEKC proposes the use of ontologies and semantic tools for developing interoperable gene regulation knowledge models, which should support data annotation. In this work, we study how such knowledge models can be generated from cartoons of gene regulation scenarios. The proposed method consists of generating descriptions in natural language of the cartoons; extracting the entities from the texts; finding those entities in existing ontologies to reuse as much content as possible, especially from well known and maintained ontologies such as the Gene Ontology, the Sequence Ontology, the Relations Ontology and ChEBI; and implementation of the knowledge models. The models have been implemented using Protégé, a general ontology editor, and Noctua, the tool developed by the Gene Ontology Consortium for the development of causal activity models to capture more comprehensive annotations of genes and link their activities in a causal framework for Gene Ontology Annotations. We applied the method to two gene regulation scenarios and illustrate how to apply the models generated to support the annotation of data from research articles. • Development of knowledge models from gene regulation cartoons to support curation. • Gene Ontology Causal Activity Models allow for obtaining interoperable models. • We compare the implementation of the knowledge models using Noctua and Protégé. • Two use cases have been used to evaluate the method proposed. • Experts evaluated if the models supported the annotation of research articles. [ABSTRACT FROM AUTHOR]

E-government services are subject to a growing level of complexity, which requires a disruptive approach that better support the citizen needs concerning the government administration. Nowadays, available information technologies facilitate the description and online execution of administrative tasks, saving time and reducing possible errors. These technologies reduce administrative costs but require a complex electronic government system.We propose using semantic technologies to describe the e-government organisational units and services in the Open Government Data and Services context. The use of semantics improves government management, service delivery and decision-making processes.This article presents an extension of related work, introducing the evolution of the Ontology for Electronic Government (EGO): integrating other existing ontologies, supporting new features to describe e-government services and widening the usage scenarios. This extension enables the use in a real scenario with four use cases: the electronic government in the Province of Misiones (Argentina). However, the use in the domain of electronic government in a provincial context is also a proof of concept that this approach is general enough to expand into superior domains of countries that adopt the republican system of government with the division of government into the executive, legislative and judicial branches. [ABSTRACT FROM AUTHOR]

Gene regulation computational research requires handling and integrating large amounts of heterogeneous data. The Gene Ontology has demonstrated that ontologies play a fundamental role in biological data interoperability and integration. Ontologies help to express data and knowledge in a machine processable way, which enables complex querying and advanced exploitation of distributed data. Contributing to improve data interoperability in gene regulation is a major objective of the GREEKC Consortium, which aims to develop a standardized gene regulation knowledge commons. GREEKC proposes the use of ontologies and semantic tools for developing interoperable gene regulation knowledge models, which should support data annotation. In this work, we study how such knowledge models can be generated from cartoons of gene regulation scenarios. The proposed method consists of generating descriptions in natural language of the cartoons; extracting the entities from the texts; finding those entities in existing ontologies to reuse as much content as possible, especially from well known and maintained ontologies such as the Gene Ontology, the Sequence Ontology, the Relations Ontology and ChEBI; and implementation of the knowledge models. The models have been implemented using Protégé, a general ontology editor, and Noctua, the tool developed by the Gene Ontology Consortium for the development of causal activity models to capture more comprehensive annotations of genes and link their activities in a causal framework for Gene Ontology Annotations. We applied the method to two gene regulation scenarios and illustrate how to apply the models generated to support the annotation of data from research articles., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) has been designed as standard clinical terminology for annotating Electronic Health Records (EHRs). EHRs textual information is used to classify patients' diseases into an International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) category (usually by an expert). Improving the accuracy of classification is the main purpose of using ontologies and OWL representations at the core of classification systems. In the last few years some ontologies and OWL representations for representing ICD-10-CM categories have been developed. However, they were not designed to be the basis for an automatic classification tool nor do they model ICD-10-CM inclusion terms as Web Ontology Language (OWL) axioms, which enables automatic classification. In this context we have developed Dione, an OWL representation of ICD-10-CM., Results: Dione is the first OWL representation of ICD-10-CM, which is logically consistent, whose axioms define the ICD-10-CM inclusion terms by means of a methodology based on SNOMED CT/ICD-10-CM mappings. The ICD-10-CM exclusions are handled with these mappings. Dione currently contains 391,669 classes, 391,720 entity annotation axioms and 11,795 owl:equivalentClass axioms which have been constructed using 104,646 relationships extracted from the SNOMED CT/ICD-10-CM and BioPortal mappings included in Dione using the owl:intersectionOf and the owl:someValuesFrom statements. The resulting OWL representation has been classified and its consistency tested with the ELK reasoner. We have also taken three clinical records from the Virgen de la Victoria Hospital (Málaga, Spain) which have been manually annotated using SNOMED CT. These annotations have been included as instances to be classified by the reasoner. The classified instances show that Dione could be a promising ICD-10-CM OWL representation to support the classification of patients' diseases., Conclusions: Dione is a first step towards the automatic classification of patients' diseases by using SNOMED CT annotations embedded in Electronic Health Records (EHRs). The purpose of Dione is to standardise and formalise a medical terminology, thereby enabling new kinds of tools and new sets of functionalities to be developed. This in turn assists health specialists by providing classified information from EHRs and enables the automatic annotation of patients' diseases with ICD-10-CM codes.