An Introduction to Ontologies and Ontology Engineering

In the last decades, the use of ontologies in information systems has become more and more popular in various fields, such as web technologies, database integration, multi agent systems, natural language processing, etc. Artificial intelligent researchers have initially borrowed the word “ontology” from Philosophy, then the word spread in many scientific domain and ontologies are now used in several developments. The main goal of this chapter is to answer generic questions about ontologies, such as: Which are the different kinds of ontologies? What is the purpose of the use of ontologies in an application? Which methods can I use to build an ontology

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Ontology-based solutions for interoperability among product lifecycle management systems: A systematic literature review

During recent years, globalization has had an impact on the competitive capacity of industries, forcing them to integrate their productive processes with other, geographically distributed, facilities. This requires the information systems that support such processes to interoperate. Significant attention has been paid to the development of ontology-based solutions, which are meant to tackle issues from inconsistency to semantic interoperability and knowledge reusability. This paper looks into how the available technology, models and ontology-based solutions might interact within the manufacturing industry environment to achieve semantic interoperability among industrial information systems. Through a systematic literature review, this paper has aimed to identify the most relevant elements to consider in the development of an ontology-based solution and how these solutions are being deployed in industry. The research analyzed 54 studies in alignment with the specific requirements of our research questions. The most relevant results show that ontology-based solutions can be set up using OWL as the ontology language, Protégé as the ontology modeling tool, Jena as the application programming interface to interact with the built ontology, and different standards from the International Organization for Standardization Technical Committee 184, Subcommittee 4 or 5, to get the foundational concepts, axioms, and relationships to develop the knowledge base. We believe that the findings of this study make an important contribution to practitioners and researchers as they provide useful information about different projects and choices involved in undertaking projects in the field of industrial ontology application.Fil: Fraga, Alvaro Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Vegetti, Maria Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Leone, Horacio Pascual. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentin

A foundation for ontology modularisation

There has been great interest in realising the Semantic Web. Ontologies are used to define Semantic Web applications. Ontologies have grown to be large and complex to the point where it causes cognitive overload for humans, in understanding and maintaining, and for machines, in processing and reasoning. Furthermore, building ontologies from scratch is time-consuming and not always necessary. Prospective ontology developers could consider using existing ontologies that are of good quality. However, an entire large ontology is not always required for a particular application, but a subset of the knowledge may be relevant. Modularity deals with simplifying an ontology for a particular context or by structure into smaller ontologies, thereby preserving the contextual knowledge. There are a number of benefits in modularising an ontology including simplified maintenance and machine processing, as well as collaborative efforts whereby work can be shared among experts. Modularity has been successfully applied to a number of different ontologies to improve usability and assist with complexity. However, problems exist for modularity that have not been satisfactorily addressed. Currently, modularity tools generate large modules that do not exclusively represent the context. Partitioning tools, which ought to generate disjoint modules, sometimes create overlapping modules. These problems arise from a number of issues: different module types have not been clearly characterised, it is unclear what the properties of a 'good' module are, and it is unclear which evaluation criteria applies to specific module types. In order to successfully solve the problem, a number of theoretical aspects have to be investigated. It is important to determine which ontology module types are the most widely-used and to characterise each such type by distinguishing properties. One must identify properties that a 'good' or 'usable' module meets. In this thesis, we investigate these problems with modularity systematically. We begin by identifying dimensions for modularity to define its foundation: use-case, technique, type, property, and evaluation metric. Each dimension is populated with sub-dimensions as fine-grained values. The dimensions are used to create an empirically-based framework for modularity by classifying a set of ontologies with them, which results in dependencies among the dimensions. The formal framework can be used to guide the user in modularising an ontology and as a starting point in the modularisation process. To solve the problem with module quality, new and existing metrics were implemented into a novel tool TOMM, and an experimental evaluation with a set of modules was performed resulting in dependencies between the metrics and module types. These dependencies can be used to determine whether a module is of good quality. For the issue with existing modularity techniques, we created five new algorithms to improve the current tools and techniques and experimentally evaluate them. The algorithms of the tool, NOMSA, performs as well as other tools for most performance criteria. For NOMSA's generated modules, two of its algorithms' generated modules are good quality when compared to the expected dependencies of the framework. The remaining three algorithms' modules correspond to some of the expected values for the metrics for the ontology set in question. The success of solving the problems with modularity resulted in a formal foundation for modularity which comprises: an exhaustive set of modularity dimensions with dependencies between them, a framework for guiding the modularisation process and annotating module, a way to measure the quality of modules using the novel TOMM tool which has new and existing evaluation metrics, the SUGOI tool for module management that has been investigated for module interchangeability, and an implementation of new algorithms to fill in the gaps of insufficient tools and techniques

Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments

Open Research Knowledge Graph

As we mark the fifth anniversary of the alpha release of the Open Research Knowledge Graph (ORKG), it is both timely and exhilarating to celebrate the significant strides made in this pioneering project. We designed this book as a tribute to the evolution and achievements of the ORKG and as a practical guide encapsulating its essence in a form that resonates with both the general reader and the specialist. The ORKG has opened a new era in the way scholarly knowledge is curated, managed, and disseminated. By transforming vast arrays of unstructured narrative text into structured, machine-processable knowledge, the ORKG has emerged as an essential service with sophisticated functionalities. Over the past five years, our team has developed the ORKG into a vibrant platform that enhances the accessibility and visibility of scientific research. This book serves as a non-technical guide and a comprehensive reference for new and existing users that outlines the ORKG’s approach, technologies, and its role in revolutionizing scholarly communication. By elucidating how the ORKG facilitates the collection, enhancement, and sharing of knowledge, we invite readers to appreciate the value and potential of this groundbreaking digital tool presented in a tangible form. Looking ahead, we are thrilled to announce the upcoming unveiling of promising new features and tools at the fifth-year celebration of the ORKG’s alpha release. These innovations are set to redefine the boundaries of machine assistance enabled by research knowledge graphs. Among these enhancements, you can expect more intuitive interfaces that simplify the user experience, and enhanced machine learning models that improve the automation and accuracy of data curation. We also included a glossary tailored to clarifying key terms and concepts associated with the ORKG to ensure that all readers, regardless of their technical background, can fully engage with and understand the content presented. This book transcends the boundaries of a typical technical report. We crafted this as an inspiration for future applications, a testament to the ongoing evolution in scholarly communication that invites further collaboration and innovation. Let this book serve as both your guide and invitation to explore the ORKG as it continues to grow and shape the landscape of scientific inquiry and communication