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. (shrink)

A generalized Wittgensteinian semantics for propositional languages is presented, based on a lattice of elementary situations. Of these, maximal ones are possible worlds, constituting a logical space; minimal ones are logical atoms, partitioned into its dimensions. A verifier of a proposition is an elementary situation such that if real it makes true. The reference (or objective) of a proposition is a situation, which is the set of all its minimal verifiers. (Maximal ones constitute its locus.) Situations are shown to form (...) a Boolean algebra, and the Boolean set algebra of loci is its representation. Wittgenstein's is a special case, admitting binary dimensions only. (shrink)

This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present - in other words, virtually any area of activity. The conceptualization relies on recent philosophical and psychological research on artefacts, having resulted in a largely consensual theoretical basis. Furthermore, this ontology of artefacts extends the foundational DOLCE ontology and supplements its axiomatization. The conceptual primitives are as follows: (...) artificial entity, intentional production of entities, (state of) capacity, capacity to play a role in actions of a given type, function and functional object. These primitives enable artefacts in general to be characterized as intentionally and successfully produced entities, and isolate an important subclass of “technical” artefacts to which a function is ascribed. Lastly, we emphasize the novelty of this ontology by comparing it with other works with similar objectives. (shrink)

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we (...) aim to move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (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)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of (...) the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between concrete objects and (...) object-pieces, but also relations between what we shall call dependent parts or moments. A two-dimensional formal language is canvassed for the resultant ontological theory, a language which owes more to the tradition of Euler, Boole and Venn than to the quantifier-centred languages which have predominated amongst analytic philosophers since the time of Frege and Russell. Analytic philosophical arguments against moments, and against the entire project of a formal ontology, are considered and rejected. The paper concludes with a brief account of some applications of the theory presented. (shrink)

There are two main ways, philosophically, of characterizing the business of ontology. On one account, made popular by Quine, ontology is concerned with the material question of what there is. On the other, which made its way into our times through Brentano and his pupils, ontology is concerned with the task of laying bare the formal structure of all there is, whatever it is. My question, here, is whether one can pursue one sort of theory without (...) also engaging in the other—whether, or to what extent, the tasks of material ontology presuppose the backing of some formal-ontological theory, and whether or to what extent formal ontology can be, in the material sense of the term, ontologically neutral. (shrink)

Revised version of chapter in J. N. Mohanty and W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, Lanham: University Press of America, 1989, 29–67. -/- Logic for Husserl is a science of science, a science of what all sciences have in common in their modes of validation. Thus logic deals with universal laws relating to truth, to deduction, to verification and falsification, and with laws relating to theory as such, and to what makes for theoretical unity, both on the side of (...) the propositions of a theory and on the side of the domain of objects to which these propositions refer. This essay presents a systematic overview of Husserl’s views on these matters as put forward in his Logical Investigations. It shows how Husserl’s theory of linguistic meanings as species of mental acts, his formal ontology of part, whole and dependence, his theory of meaning categories, and his theory of categorial intuition combine with his theory of science to form a single whole. Finally, it explores the ways in which Husserl’s ideas on these matters can be put to use in solving problems in the philosophy of language, logic and mathematics in a way which does justice to the role of mental activity in each of these domains while at the same time avoiding the pitfalls of psychologism. (shrink)

Just as ontology developed over the centuries as part of philosophy, so in recent years ontology has become intertwined with the development of the information sciences. Researchers in various fields have come to realize that a solid foundation for their projects calls for an explicit theorization of the types of entities and relations that make up their respective domains of inquiry, and as the need for integrating such projects arises, so does the need to identify common ontological principles (...) over ad hoc, case-based solutions. This volume collects the papers presented at the third international conference devoted to current research in this area, including invited papers by P. Gärdenfors and A. L. Thomasson. (shrink)

The term ‘formal ontology’ was first used by the philosopher Edmund Husserl in his Logical Investigations to signify the study of those formal structures and relations – above all relations of part and whole – which are exemplified in the subject-matters of the different material sciences. We follow Husserl in presenting the basic concepts of formal ontology as falling into three groups: the theory of part and whole, the theory of dependence, and the theory of (...) boundary, continuity and contact. These basic concepts are presented in relation to the problem of providing an account of the formal ontology of the mesoscopic realm of everyday experience, and specifically of providing an account of the concept of individual substance. (shrink)

There are many ontologies of the world or of specific phenomena such as time, matter, space, and quantum mechanics1. However, ontologies of information are rather rare. One of the reasons behind this is that information is most frequently associated with communication and computing, and not with ‘the furniture of the world’. But what would be the nature of an ontology of information? For it to be of significant import it should be amenable to formalization in a logico-grammatical formalism. A (...) candidate ontology satisfying such a requirement can be found in some of the ideas of K. Turek, presented in this paper. Turek outlines the ontology of information conceived of as a part of nature, and provides the ‘missing link’ to the Z axiomatic set theory, offering a proposal for developing a formal ontology of information both in its philosophical and logicogrammatical representations. (shrink)

There are many ontologies of the world or of specific phenomena such as time, matter, space, and quantum mechanics1. However, ontologies of information are rather rare. One of the reasons behind this is that information is most frequently associated with communication and computing, and not with ‘the furniture of the world’. But what would be the nature of an ontology of information? For it to be of significant import it should be amenable to formalization in a logico-grammatical formalism. A (...) candidate ontology satisfying such a requirement can be found in some of the ideas of K. Turek, presented in this paper. Turek outlines the ontology of information conceived of as a part of nature, and provides the ‘missing link’ to the Z axiomatic set theory, offering a proposal for developing a formal ontology of information both in its philosophical and logicogrammatical representations. (shrink)

As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an (...) account of what might be involved in this new discipline, an account which is illustrated in application to the formal-ontological problems raised by negative states of affairs. (shrink)

Revised version published as Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, (...) and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

The current resurgence of interest in cognition and in the nature of cognitive processing has brought with it also a renewed interest in the early work of Husserl, which contains one of the most sustained attempts to come to grips with the problems of logic from a cognitive point of view. Logic, for Husserl, is a theory of science; but it is a theory which takes seriously the idea that scientific theories are constituted by the mental acts of cognitive subjects. (...) The present essay begins with an exposition of Husserl's act-based conception of what a science is, and goes on to consider his account of the role of linguistic meanings, of the ontology of scientific objects, and of evidence and truth. The essay concentrates almost exclusively on the Logical Investigations of 1900/01. This is not only because this work, which is surely Husserl's single most important masterpiece, has been overshadowed first of all by his Ideas I and then later by the Crisis. It is also because the Investigations contain, in a peculiarly clear and pregnant form, a whole panoply of ideas on logic and cognitive theory which either simply disappeared in Husserl's own later writings or became obfuscated by an admixture of that great mystery which is 'transcendental phenomenology'. (shrink)

The concept of formal ontology was first developed by Husserl. It concerns problems relating to the notions of object, substance, property, part, whole, predication, nominalization, etc. The idea of formal ontology is present in many of Husserl?s works, with minor changes. This paper provides a reconstruction of such an idea. Husserl?s proposal is faced with contemporary logical orthodoxy and it is presented also an interpretative hypothesis, namely that the original difference between the general perspective of usual (...) model theory and formal ontology is grounded in the fact that this latter starts from an intended interpretation and not from the set of all the possible interpretations. (shrink)

Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.

This is a critical discussion of Nino B. Cocchiarella’s book “Formal Ontology and Conceptual Realism.” It focuses on paradoxes of hyperintensionality that may arise in formal systems of intensional logic.

This volume collects the papers presented at the 9th edition of the Formal Ontology in Information Systems conference, FOIS 2016, held July 6–9, 2016, in Annecy, France. As in the previous editions, FOIS 2016 included keynote addresses, full paper presentations, an Ontology Competition, an Early Career Symposium in its scientific program and was preceded by the Interdisciplinary Summer School on Ontological Analysis, now at its third edition and held June 27–July 1 in Bolzano-Bozen, Italy.

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, (...) we aim to move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

General and Formal Ontology Paolo Valore The word ontology derives from tÕ Ôn ( tò òn), which is the neutral participle of e„m. ...

I have supposed that we need a formal system to represent and explain humans' conceptions of the world. According to this research, such a formal system is representable based on a Conception Language (CL) that is a terminological knowledge representation formalism. In this research, I will offer a formal ontology for conception representation in terminological systems. Such a CL-based ontology will specify the conceptualization of humans' conceptions as well as of the effects of their conceptions (...) on the world. (shrink)

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to (...) maximize reasoning efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

In this paper I will discuss Barry Smith’s and Kevin Mulligan’s revision of Husserl’s phenomenology, starting from the fact that many Italian scholars seem to follow them in a sense, by dealing with phenomenology as a sort of a priori ontology. Therefore, I will first reconstruct Smith’s and Mulligan’s attempt and its objectives, then I will show how it is rooted in the school of Brentano and, in particular, in Husserl’s phenomenology. Finally, I will provide some arguments against this (...) attempt : first of all that it does not attain a better description of the world, secondly that phenomenology does the job of formal ontology better than the latter. (shrink)

What primitive concepts does formal ontology require? Forsaking as too indirect the linguistic way of discerning the categories of being, this paper considers what primitives might be required for representing things in themselves (noumena) and representations of them in a thoroughly crafted large autonomous multi-purpose database. Leaving logical concepts and material ontology aside, the resulting 32 categories in 13 families range from the obvious (identity/difference, existence/non-existence) through the fairly obvious (part/whole, one/many, sequential order) and the surprisingly familiar (...) (illocutionary modes, mass/count, indexical/descriptive) to the controversial (moment/fundament, transparent/opaque) and the arcane (modes of class delimitation, taxonomic rank, aspects of designators). Any such list is speculative and tentative, but the test of this one will be in its implementation, a new departure for philosophical category theories. (shrink)

What primitive concepts does formal ontology require? Forsaking as too indirect the linguistic way of discerning the categories of being, this paper considers what primitives might be required for representing things in themselves and representations of them in a thoroughly crafted large autonomous multi-purpose database. Leaving logical concepts and material ontology aside, the resulting 32 categories in 13 families range from the obvious through the fairly obvious and the surprisingly familiar to the controversial and the arcane. Any (...) such list is speculative and tentative, but the test of this one will be in its implementation, a new departure for philosophical category theories. (shrink)

It is accepted that certain mereological concepts and phenomenological conceptualisations presented in Carl Stumpf’s Über den psychologischen Ursprung der Raumvorstellung and Tonpsychologie played an important role in the development of the Husserlian formal ontology. In the third Logical Investigation, which displays the formal relations between part and whole and among parts that make out a whole, one of the main concepts of contemporary formal ontology and metaphysics is settled: ontological dependence or foundation. My main objective (...) is to display Stumpf’s concepts of partial content, independent content, spatial wholes, sound wholes, and the different kinds of connection among parts, in particular, fusion. Second, I will show how Husserl improved this background, in particular with regards to the exact nature of the theory of manifolds, in discussion with Georg Cantor, the father of set theory. Third, I will focus on Ingarden’s use of formal ontology and on the different modes of being that can be justified by appealing to the concept of ontological dependence in its Ingardenian variations. If my interpretation is adequate, it should be inferred that formal ontology is the operative theory of phenomenological philosophy, and this must be acknowledged in its full significance with respect to the supposed independence of the phenomenological method since 1913. A further consequence, not developed in this essay, is that formal ontology can be mathematised. (shrink)

This paper develops — within an axiomatic theory of properties, relations, and propositions which accords them well-defined existence and identity conditions — a sententialist-functionalist account of belief as a symbolically mediated relation to a special kind of propositional entity, theproxy-encoding abstract proposition. It is then shown how, in terms of this account, the truth conditions of English belief reports may be captured in a formally precise and empirically adequate way that accords genuinely semantic status to familiar opacity data.