The application of ontology has thus far [in 1998] been confined almost exclusively to the field of knowledge representation. Ontology has been applied, for example, in the design of medical databases and in the construction of geographical information systems. One area which is naturally suited to ontological analysis is that of the law and of social institutions in general. -/- Legal systems are composed of legal entities, such as laws, contracts, obligations, and rights. Their application yields new (...) categories of entities such as: corporations, trademarks, marriages, and parcels of real estate. The categorization of these entities by different legal systems has not, by-and-large, been conducted in ways which exploit the tools of modern ontology. Consequently, contradictions and inconsistencies often arise in the law when, for instance, one type of entity is forced into two mutually exclusive categories (e.g., when software is considered both patentable and copyrightable). Papers are invited which consider these and related issues from a philosophical point of view. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer (...) science has always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

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 nontechnical 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. (shrink)

In 2005, IOS Press published the first issue of applied Ontology. At the time, we argued that, at the core of the journal, there was “a desire to understand the nature of reality and how people construe their world”. We declared that ontology was both “fundamental to human thought” and “to translating our thoughts into computational artifacts” (Guarino & Musen,2005). With an editorial board of distinguished scholars representing the fields of computer science, informatics, information science, philosophy, linguistics, (...) psychology, and social science, we had the firm belief that applied Ontologywould fulfill an important academic niche, becoming an essential forum for discussion on topics such as ontological analysis, conceptual modeling, and the role of domain models in building and managing information systems. The facts now show that we were correct. (shrink)

The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists (...) seek to apply ontological tools to solving practical problems of the sort which arise in various extra-philosophical domains, including law and government administration. (shrink)

The institutions we create shape many of the activities we engage insofar as they are pervasive entities in our society. In an era full of new technologies, including the semantic web, there is a movement toward sound conceptual modeling for socio-technical solutions applied to government institutions. To develop these complex solutions, one needs to deepen the ontological status of entities in the institutional domain, because literature is full of ambiguous and ad-hoc hypotheses about distinctions between public and private corporations. (...) We believe we can find better explanations for such distinctions in the interdisciplinary field of library a information science. Within an ongoing semantic web project, we focus on a study case of official documents. First, we analyze theories about public and private corporations, seeking a reliable on‘tological distinction between them; then, by focusing on documents produced by each type of corporation, we hope to provide a well-founded analysis. Second, we adopt the aforementioned theories and the new analysis as recommendations for the improvement for the access and understanding of public documents, through appropriate classification of them within government information systems. This project, ultimately, aims to maximize the transparency of public government documents by favoring retrieval and comprehension by a society with plenty of automated information systems. (shrink)

There have been renewed calls to use phenomenology in psychiatry to improve knowledge about causation, diagnostics, and treatment of mental health conditions. A phenomenological approach aims to elucidate the subjective experiences of mental health, which its advocates claim have been largely neglected by current diagnostic frameworks in psychiatry (eg, DSM-5). The consequence of neglecting rich phenomenological information is a comparatively more constrained approach to theory development, empirical research, and care programmes. Although calls for more phenomenology in psychiatry have been met (...) with enthusiasm, there is still relatively little information on how to practically facilitate this integration. In this Personal View, we argue that phenomenological approaches need a shared semantic framework to drive their innovative potential, thus enabling consistent data capture, exchange, and interoperability with current mental health data and informatics approaches (eg, the Research Domain Criteria project). We show how an applied ontology of phenomenological psychopathology offers a suitable method to address these challenges. (shrink)

This is a short editorial to introduce the double issue of Applied Ontology that celebrates the journal's tenth anniversary. At a time when information technology of all kinds depends on the use of explicit ontologies, our journal addresses the modeling issues that underlie the next generation of computational systems. As the editors of Applied Ontology, we are excited by how far we have come in the past decade and by the opportunities that await our research community.

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel (...) by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives (...) within a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

This paper explores practical application of Heidegger’s fundamental ontology to lived human experience and practical concerns beyond those he addressed, specifically the phenomenon of gender. We are so committed to gender norms that we ostracize or even kill those who violate them, yet rarely question the reasonableness of our expectations. Gender needs to be examined from a phenomenological stance, a) because of the ubiquity of gendering, b) because presuppositions regarding gender go largely unquestioned in most Daseins’ everyday existence, and (...) c) because cases in which actual fact contravenes our expectations offer insight into what it means to be human. (shrink)

Mental health research faces a suite of unresolved challenges that have contributed to a stagnation of research efforts and treatment innovation. One such challenge is how to reliably and validly account for the subjective side of patient symptomatology, that is, the patient’s inner experiences or patient phenomenology. Providing a structured, standardised semantics for patient phenomenology would enable future research in novel directions. In this contribution, we aim at initiating a standardized approach to patient phenomenology by sketching a tentative formalisation within (...) the framework of an applied ontology, in the broader context of existing open-source Open Biomedical Ontologies resources such as the Mental Functioning Ontology. We further discuss a number of prevailing challenges and observations bearing on this task. (shrink)

The aim of this article is to reconstruct Bocheński’s method of philosophical analysis as well as to clarify the purpose of that method and its basic elements. In the second part of the paper I will compare Bocheński’s method with the methods of modern applied ontology.

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these (...) are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

This paper presents use cases for modular development of ontologies using the OWL imports mechanism. Many of the methods are inspired by work in modular development in software engineering. The approach is aimed at developers of large ontologies covering multiple subdomains that make use of OWL reasoners for inference. Such ontologies are common in biomedical sciences, but nothing in the paper is specific to biomedicine. There are four groups of use cases: (i) organisation and factoring of ontologies; (ii) maintaining stable (...) interfaces and bindings between ontologies and between ontologies and software; (iii) localization of ontologies to the requirements of specific sites and (iv) extension of ontologies and encapsulation of modifications. OWL's axiom-oriented import mechanism has many similarities with import mechanisms in object-oriented software but also important differences – in particular, the effects of OWL imports are global, and the order in which modules are imported is irrelevant. The advantages and disadvantages of OWL's axiom-oriented approach are discussed, and suggestions are made for extensions to allow axioms to be filtered out as well as added – a mechanism that we term “adaptation” to distinguish it from the standard import mechanism. Finally we discuss possible alternatives and practical experience with the approaches presented. (shrink)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (...) (ETA). We describe here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (shrink)

We examine how insights made in socio-anthropological and evolutionary schools of thought necessitate us to reevaluate the classic philosophical distinction between epistemology and ontology. We adopt an applied evolutionary epistemological stance and demonstrate that both epistemology and ontology evolve. Epistemology is broadened to include all knowledge and information that all life forms evolve, and ontology encompasses all biologically informed realities that life builds. Through processes such as symbiosis and niche construction, organisms acquire and extend information and (...) knowledge into their offspring, onto unrelated organisms, and onto their niches. Life builds biorealities that change over time. Consequently, knowledge and reality are mutable and truth is spatiotemporally bounded. We conclude that the classic distinction between epistemology and ontology has become superfluous and instead, we argue that the evolving knowledge that comes in the form of organisms and their extended niches equals ontological realities. (shrink)

As is clear in the 2008 report of the President's Council on Bioethics, the brain death debate is plagued by ambiguity in the use of such key terms as ‘integration’ and ‘wholeness’. Addressing this problem, I offer a plausible ontological account of organismal unity drawing on the work of Hoffman and Rosenkrantz, and then apply that account to the case of brain death, concluding that a brain dead body lacks the unity proper to a human organism, and has therefore undergone (...) a substantial change. I also show how my view can explain hard cases better than one in which biological integration is taken to imply ontological wholeness or unity. (shrink)

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 (...) class='Hi'>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. (shrink)

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...) are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (shrink)

ABSTRACT The concept of concrete and abstract entities relates to an ontological specification problem, described by Plato’s Sophist concept of the Gods and Giants and their interpretation of metaphysical reality. Developing an ontology without considering the full metaphysical implications leaves conceptual gaps in the creation of events, change in states and management of thoughts, plans and deceptions. This paper seeks to resolve conceptual gaps in the field of cyberspace representation, enabling both ontological interoperability and the development of more complex (...) artificial intelligence technologies. The beginnings of a new meta-ontology for cyberspace are proposed, based on Stoic metaphysics. A meta-ontology provides high-level construction of meaning, upon which more specific ontologies can be built. Coherence between ontologies is important because cyberspace is a contextually dependent knowledge space within the broader infosphere, with many interdependent concepts. This paper enhances the potential for ontological interoperability and transparency between users, human or machine. (shrink)

This book is written in homage to Nicola Guarino. It is a tribute to his many scientific contributions to the new discipline, applied ontology, he struggled to establish. Nicola Guarino is widely recognized as one of the pioneers in formal and applied ontology. Renow – and sometimes even criticized – for his deep interest for the subtlest details of theoretical analysis, all throughout his career he has held the conviction that all science has to be for (...) the benefit of society at large, hence his motto that ontologies are not just for making information systems interoperable, but also – and more importantly – for making people (users of the systems) understand each other. He was among the first to realize that, to capture the intended meaning of the terms used by an information system, applied ontology has necessarily to be an interdisciplinary enterprise. Nicola’s early career developed in the areas of data systems and expert systems in physics and biomedical engineering. The lack of methodologies in expert systems led him to turn to philosophical logic as a source of inspiration, prompting him to attend the meetings of the analytic philosophy group at the University of Padua, and to discover a whole new world. It was the end of the 1980s and in that period the term ‘ontology’ started to be used to indicate a shared vocabulary across a community. Recognizing the potentials of this idea, Nicola began studying philosophical work. Knowing that language remains one of the pivotal elements in knowledge acquisition and representation, he paired it with the study of linguistic analysis. The combination of the two fields proved to be fundamental to shape his research vision, which could be summarized as: ontological analysis is hard, yet unavoidable to address the pervasive need for explicit, meaningful and transparent information systems. In other words, ontology makes sense. (shrink)

Disagreement about the nature of ‘addiction’, such as whether it is a brain disease, arises in part because the label is applied to a wide range of phenomena. This creates conceptual and definitional confusions and misunderstandings, often leading to researchers talking past one another. Ontologies have been successfully implemented in other fields to help solve these problems by creating unifying frameworks that can accommodate divergence while clarifying the basis for it. We argue that ontologies can help transform the way (...) we think and communicate about addiction as well, providing a basis for a shared understanding of the domain and a shared means for communicating and achieving that understanding. -/- We introduce the use of ontologies in science and medicine and show how they can unify differing perspectives on addiction. We also show how ontologies provide a practical tool for organizing our collective knowledge in this field, even, and especially, when that knowledge is garnered through distinct disciplinary approaches adopting disparate methodologies or perspectives (e.g., neurobiological, psychological, sociological, etc.). In the end, we believe that ontologies can help to avoid letting questions like “Is addiction a brain disease?” divide the field, hamper communication, or otherwise disrupt the ability to make meaningful progress. (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by (...) philosophers, the term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

Researchers in areas such as artificial intelligence, formal and computational linguistics, biomedical informatics, conceptual modeling, knowledge engineering and information retrieval have come to realise that a solid foundation for their research calls for serious work in ontology, understood as a general theory of the types of entities and relations that make up their respective domains of inquiry. In all these areas, attention is now being focused on the content of information rather than on just the formats and languages used (...) to represent information. The clearest example of this development is provided by the many initiatives growing up around the project of the Semantic Web. And, as the need for integrating research in these different fields arises, so does the realisation that strong principles for building well-founded ontologies might provide significant advantages over ad hoc, case-based solutions. The tools of formal ontology address precisely these needs, but a real effort is required in order to apply such philosophical tools to the domain of information systems. Reciprocally, research in the information sciences raises specific ontological questions which call for further philosophical investigations. The purpose of FOIS is to provide a forum for genuine interdisciplinary exchange in the spirit of a unified effort towards solving the problems of ontology, with an eye to both theoretical issues and concrete applications. This book contains a wide range of areas, all of which are important to the development of formal ontologies. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing (...) the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

Metaphysics can be used to help us understand the world, and has applications both within philosophy and beyond. Within philosophy, metaphysical questions arise whether we are thinking about ethics, art, religion, or science. Beyond philosophy, there are many areas where metaphysics can be applied. Case studies in this chapter include applied ontology in information science, social ontology in both philosophy and the social sciences, and questions about classification and kinds in psychiatry.

Nicola Guarino is widely recognized as one of the founders of applied ontology. His deep interest in the subtlest details of theoretical analysis and his vision of ontology as the Rosetta Stone for semantic interoperability guided the development and understanding of this domain. His motivations in research stem from the conviction that all science must be for the benefit of society at large, and his motto has always been that ontologies are not just for making information systems (...) interoperable, but – more importantly – for ensuring that systems’ users understand each other. He was among the first to recognize that applied ontology must be an interdisciplinary enterprise if it is to capture the intended meaning of the terms used by an information system. (shrink)

The paper is concerned with the way in which “ontology” and “realism” are to be interpreted and applied so as to give us a deeper philosophical understanding of mathematical theories and practice. Rather than argue for or against some particular realistic position, I shall be concerned with possible coherent positions, their strengths and weaknesses. I shall also discuss related but different aspects of these problems. The terms in the title are the common thread that connects the various sections.

The aim of this paper is to summarize a particular approach of doing metaphysics through physics - the primitive ontology approach. The idea is that any fundamental physical theory has a well-defined architecture, to the foundation of which there is the primitive ontology, which represents matter. According to the framework provided by this approach when applied to quantum mechanics, the wave function is not suitable to represent matter. Rather, the wave function has a nomological character, given that (...) its role in the theory is to implement the law of evolution for the primitive ontology. (shrink)