An ontology is a description (like a formal specification of a program) of concepts and relationships that can exist for an agent or a community of agents. The concept is important for the purpose of enabling knowledge sharing and reuse. The Handbook on Ontologies provides a comprehensive overview of the current status and future prospectives of the field of ontologies. The handbook demonstrates standards that have been created recently, it surveys methods that have been developed and it shows how to bring both into practice of ontology infrastructures and applications that are the best of their kind.

An ontology is a formal description of concepts and relationships that can exist for a community of human and/or machine agents. The notion of ontologies is crucial for the purpose of enabling knowledge sharing and reuse. The Handbook on Ontologies provides a comprehensive overview of the current status and future prospectives of the field of ontologies considering ontology languages, ontology engineering methods, example ontologies, infrastructures and technologies for ontologies, and how to bring this all into ontology-based infrastructures and applications that are among the best of their kind. The field of ontologies has tremendously developed and grown in the five years since the first edition of the "Handbook on Ontologies". Therefore, its revision includes 21 completely new chapters as well as a major re-working of 15 chapters transferred to this second edition.

This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of the Methods in Molecular Biology book series, there is an emphasis throughout the chapters on providing practical guidance and troubleshooting advice. Authoritative and accessible, The Gene Ontology Handbook serves non-experts as well as seasoned GO users as a thorough guide to this powerful knowledge system. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Metadata research has emerged as a discipline cross-cutting many domains, focused on the provision of distributed descriptions (often called annotations) to Web resources or applications. Such associated descriptions are supposed to serve as a foundation for advanced services in many application areas, including search and location, personalization, federation of repositories and automated delivery of information. Indeed, the Semantic Web is in itself a concrete technological framework for ontology-based metadata. For example, Web-based social networking requires metadata describing people and their interrelations, and large databases with biological information use complex and detailed metadata schemas for more precise and informed search strategies.There is a wide diversity in the languages and idioms used for providing meta-descriptions, from simple structured text in metadata schemas to formal annotations using ontologies, and the technologies for storing, sharing and exploiting meta-descriptions are also diverse and evolve rapidly. In addition, there is a proliferation of schemas and standards related to metadata, resulting in a complex and moving technological landscape — hence, the need for specialized knowledge and skills in this area.The Handbook of Metadata, Semantics and Ontologies is intended as an authoritative reference for students, practitioners and researchers, serving as a roadmap for the variety of metadata schemas and ontologies available in a number of key domain areas, including culture, biology, education, healthcare, engineering and library science.

Ontology, or the nature of being, has been a focal area of study in the philosophical disciplines for a long time. Interpreted simply, the term ontology refers to the question what kinds of things exist? to a philosopher, while a computer scientist grapples with the question what kinds of things should we capture and represent? Together, research on the two questions yield a broad framework for the analysis of a discourse universe, its representation in some abstract form and the development of organizations and systems within the universe. The philosophical perspective on ontology provides a description of the essential properties and relations of all beings in the universe, while this notion has been expanded as well as specialized in the fields of computer science and artificial intelligence. The AI/CS communities now use this notion to refer to not one but multiple ontologies. In the AI/CS perspective, an ontology refers to the specification of knowledge about entities, and their relationships and interactions in a bounded universe of discourse only. As a result, a number of bounded-universe ontologies have been created over the last decade. These include the Chemicals ontology in the chemistry area, the TOVE and Enterprise ontologies for enterprise modeling, the REA ontology in the accounting area, organizational knowledge ontology in the knowledge management area, an ontology of air campaign planning in the defense area, and the GALEN ontology in the medical informatics area."

"This book explores how social software and developing community ontologies are challenging the way we operate in a performative space"--Provided by publisher.

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.

Ontology was once understood to be the philosophical inquiry into the structure of reality: the analysis and categorization of ‘what there is’. Recently, however, a field called ‘ontology’ has become part of the rapidly growing research industry in information technology. The two fields have more in common than just their name. Theory and Applications of Ontology is a two-volume anthology that aims to further an informed discussion about the relationship between ontology in philosophy and ontology in information technology. It fills an important lacuna in cutting-edge research on ontology in both fields, supplying stage-setting overview articles on history and method, presenting directions of current research in either field, and highlighting areas of productive interdisciplinary contact. Theory and Applications of Ontology: Philosophical Perspectives presents ontology in philosophy in ways that computer scientists are not likely to find elsewhere. The volume offers an overview of current research traditions in ontology, contrasting analytical, phenomenological, and hermeneutic approaches. It introduces the reader to current philosophical research on those categories of everyday and scientific reasoning that are most relevant to present and future research in information technology.

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.