Building Ontologies With Basic Formal Ontology

An introduction to the field of applied ontology with examples derived particularly from biomedicine, covering theoretical components, design practices, and practical applications. In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

An introduction to the field of applied ontology with examples derived particularly from biomedicine, covering theoretical components, design practices, and practical applications. In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

FOIS is the flagship conference of the International Association for Ontology and its Applications (IAOA). Its interdisciplinary research focus lies at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science, as well as in the applications of ontological analysis to conceptual modeling, knowledge engineering, knowledge management, information-systems development, library and information science, scientific research, and semantic technologies in general. This volume presents the proceedings of FOIS 2018, held in Cape Town, South Africa, from 19-21 September. It was the 10th edition and 20th anniversary of the conference series. The volume contains 19 papers grouped into 4 sections: Foundations (7 papers), Agents and Properties (4 papers), Methods and Tools (4 papers), and Applications (4 papers). Regarding the applications of ontologies, a broad spectrum of areas is covered, including in particular biology and medicine, IoT, engineering and linguistics. Formal Ontology in Information Systems - Proceedings of the 10th International Conference (FOIS 2018) will be of interest to researchers from all disciplines with an interest in formal ontology.

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called ‘ontologies,’ for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a non-technical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends.

Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL, Second Edition, discusses the capabilities of Semantic Web modeling languages, such as RDFS (Resource Description Framework Schema) and OWL (Web Ontology Language). Organized into 16 chapters, the book provides examples to illustrate the use of Semantic Web technologies in solving common modeling problems. It uses the life and works of William Shakespeare to demonstrate some of the most basic capabilities of the Semantic Web. The book first provides an overview of the Semantic Web and aspects of the Web. It then discusses semantic modeling and how it can support the development from chaotic information gathering to one characterized by information sharing, cooperation, and collaboration. It also explains the use of RDF to implement the Semantic Web by allowing information to be distributed over the Web, along with the use of SPARQL to access RDF data. Moreover, the reader is introduced to components that make up a Semantic Web deployment and how they fit together, the concept of inferencing in the Semantic Web, and how RDFS differs from other schema languages. Finally, the book considers the use of SKOS (Simple Knowledge Organization System) to manage vocabularies by taking advantage of the inferencing structure of RDFS-Plus. This book is intended for the working ontologist who is trying to create a domain model on the Semantic Web. Updated with the latest developments and advances in Semantic Web technologies for organizing, querying, and processing information, including SPARQL, RDF and RDFS, OWL 2.0, and SKOS Detailed information on the ontologies used in today's key web applications, including ecommerce, social networking, data mining, using government data, and more Even more illustrative examples and case studies that demonstrate what semantic technologies are and how they work together to solve real-world problems

The philosophical study of what exists and what it means for something to exist is one of the core concerns of metaphysics. This introduction to ontology provides readers with a comprehensive account of the central ideas of the subject of being. This book is divided into two parts. The first part explores questions of pure philosophical ontology: what is meant by the concept of being, why there exists something rather than nothing, and why there is only one logically contingent actual world. Dale Jacquette shows how logic provides the only possible answers to these fundamental problems. The second part of the book examines issues of applied scientific ontology. Jacquette offers a critical survey of some of the most influential traditional ontologies, such as the distinction between appearance and reality, and the categories of substance and transcendence. The ontology of physical entities - space, time, matter and causation - is examined as well as the ontology of abstract entities such as sets, numbers, properties, relations and propositions. The special problems posed by the subjectivity of mind and of postulating a god are also explored in detail. The final chapter examines the ontology of culture, language and art.

Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications.The first part of the book defines ontology and bio-ontologies. It also explains the importan

This posthumous work by Gustav Bergmann was essentially complete before his death in 1987. In it, he proposes a systematic ontological system that would account for all the basic areas of human thought and experience within an extended framework of logical atomism. Bergmann's approach to traditional problems of ontology seeks to balance the competing demands of phenomenology, which emphasizes the reality presented to us by experience, and of metaphysics, which delineates the most general kinds of existents given in experience and the most general kinds of relationships they bear to one another. Beginning with atomic facts composed of phenomenally presented qualities, Bergmann goes on to develop an ontology that can account for the ordinary objects of everyday experience, the mental states through which we become aware of and acquire knowledge of these objects, and even the truths of logic and mathematics that allow us to extend our thought and discourse about ordinary objects beyond what may be phenomenally apparent. Many ontologists will be particularly interested in the attention Bergmann pays to the concept of logical form. In his earlier works, Bergmann claimed that "the form of the world is in the world"; the "fact" that a thing or a complex has a certain logical or syntactic form, he argued, is itself one more fact of our experienced reality, rather than a contribution of the mind or of linguistic conventions. Critics of this claim have suggested that paradoxes and contradictions result from it. In New Foundations of Ontology Bergmann responds, arguing that his concept of logical form does not necessarily create the problems noted in earlier critiques.