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)

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)

Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go hand-in-hand, (...) and were essentially inseparable in medieval thought. This constitutes the foundation for a bridge, and this article analyzes the causality-based ontology of the late medieval philosopher Dietrich of Freiberg from the viewpoint of today's upper-ontology engineering. In this bridging attempt, it offers a translation into English of the first part of Dietrich's De origine (abbreviated title) that is a compromise between traditional scholarly translations of medieval Latin philosophical texts and contemporary ontology. (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)

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)

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)

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)

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.

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)

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)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

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)

We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds (...) of representation in order to provide a more rational basis for using ontologies and related artifacts to advance integration of data and enhance interoperability of associated reasoning systems. We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies as long as the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models. (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)

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)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...) In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

Genera, typically hand-in-hand with their branching species, are essential elements of vocabulary-based information constructs, in particular scientific taxonomies. Should they also feature in formal ontologies, the highest of such constructs? I argue in this article that the answer is “Yes” and that the question posed in its title also has a Yes-answer: The way medieval ontologists sliced up the world into genera does matter to formal ontology. More specifically, the way Dietrich of Freiberg, a Latin scholastic, conceived (...) and applied strictly generic criteria to slice up the world into its entities can provide some guidelines to the field of formal ontology with respect to not only its contents, but also its scope. In particular, Dietrich's information criterion plays here a central role. (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.

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)

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.

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)

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.

In this paper, I elaborate on the Strong Nuclear Theory (SNT) of tropes and substances, which I have defended elsewhere, using my metatheory about formal ontology and especially fundamental ontological form. According to my metatheory, for an entity to have an ontological form is for it to be a relatum of a formal ontological relation or relations jointly in an order. The full fundamental ontological form is generically identical to a simple formal ontological relation or relations (...) jointly in an order. Regarding generic identity, I follow Fabrice Correia and Alexander Skiles, who consider it a form of generalized identity as distinguished from numerical identity. The SNT states that for any trope to have the full fundamental ontological form is for it to be a strongly rigidly or generically (existentially) dependent individual simple part. Therefore, the common dichotomous set-up of asking whether tropes are fundamentally properties rather than objects or vice versa is a non-starter to me in formal ontological terms. The elaboration of the SNT also supplies me with the resources to respond to the arguments against tropes by Douglas Ehring, Robert K. Garcia and Herbert Hochberg. Finally, I argue that non-fundamentally but necessarily, every trope is a proper part of a substance and is concrete in the SNT. (shrink)

In this paper, we argue that formal ontological relations avoid Bradley's reductio of relations, including his famous relation regress.

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper (...) class='Hi'>ontology descending from BFO. The axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

Formal ontologies are nowadays widely considered a standard tool for knowledge representation and reasoning in the Semantic Web. In this context, they are expected to play an important role in helping automated processes to access information. Namely: they are expected to provide a formal structure able to explicate the relationships between different concepts/terms, thus allowing intelligent agents to interpret, correctly, the semantics of the web resources improving the performances of the search technologies. Here we take into account a (...) problem regarding Knowledge Representation in general, and ontology based representations in particular; namely: the fact that knowledge modeling seems to be constrained between conflicting requirements, such as compositionality, on the one hand and the need to represent prototypical information on the other. In particular, most common sense concepts seem not to be captured by the stringent semantics expressed by such formalisms as, for example, Description Logics (which are the formalisms on which the ontology languages have been built). The aim of this work is to analyse this problem, suggesting a possible solution suitable for formal ontologies and semantic web representations. The questions guiding this research, in fact, have been: is it possible to provide a formal representational framework which, for the same concept, combines both the classical modelling view (accounting for compositional information) and defeasible, prototypical knowledge ? Is it possible to propose a modelling architecture able to provide different type of reasoning (e.g. classical deductive reasoning for the compositional component and a non monotonic reasoning for the prototypical one)? We suggest a possible answer to these questions proposing a modelling framework able to represent, within the semantic web languages, a multilevel representation of conceptual information, integrating both classical and non classical (typicality based) information. Within this framework we hypothesise, at least in principle, the coexistence of multiple reasoning processes involving the different levels of representation. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to (...) extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (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)

ABSTRACT: In its strongest unqualified form, the principle of wholistic reference is that in any given discourse, each proposition refers to the whole universe of that discourse, regardless of how limited the referents of its non-logical or content terms. According to this principle every proposition of number theory, even an equation such as "5 + 7 = 12", refers not only to the individual numbers that it happens to mention but to the whole universe of numbers. This principle, its history, (...) and its relevance to some of Oswaldo Chateaubriand's work are discussed in my 2004 paper "The Principle of Wholistic Reference" in Essays on Chateaubriand's "Logical Forms". In Chateaubriand's réplica (reply), which is printed with my paper, he raised several important additional issues including the three I focus on in this tréplica (reply to his reply): truth-values, universes of discourse, and formal ontology. This paper is self-contained: it is not necessary to have read the above-mentioned works. The principle of wholistic reference (PWR) was first put forth by George Boole in 1847 when he espoused a monistic fixed-universe viewpoint similar to the one Frege and Russell espoused throughout their careers. Later, Boole elaborated PWR in 1854 from the pluralistic multiple-universes perspective. (shrink)

Description logics and other formal devices are frequently used as means for preventing or detecting mistakes in ontologies. Some of these devices are also capable of inferring the existence of inter-concept relationships that have not been explicitly entered into an ontology. A prerequisite, however, is that this information can be derived from those formal definitions of concepts and relationships which are included within the ontology. In this paper, we present a novel algorithm that is able to (...) suggest relationships among existing concepts in a formal ontology that are not derivable from such formal definitions. The algorithm exploits cross-lingual information that is implicitly present in the collection of terms used in various languages to denote the concepts and relationships at issue. By using a specific experimental design, we are able to quantify the impact of cross-lingual information in coping with underspecification in formal ontologies. (shrink)

The philosophy of science of Patrick Suppes is centered on two important notions that are part of the title of his recent book (Suppes 2002): Representation and Invariance. Representation is important because when we embrace a theory we implicitly choose a way to represent the phenomenon we are studying. Invariance is important because, since invariants are the only things that are constant in a theory, in a way they give the “objective” meaning of that theory. Every scientific theory gives a (...) representation of a class of structures and studies the invariant properties holding in that class of structures. In Suppes’ view, the best way to define this class of structures is via axiomatization. This is because a class of structures is given by a definition, and this same definition establishes which are the properties that a single structure must possess in order to belong to the class. These properties correspond to the axioms of a logical theory. In Suppes’ view, the best way to characterize a scientific structure is by giving a representation theorem for its models and singling out the invariants in the structure. Thus, we can say that the philosophy of science of Patrick Suppes consists in the application of the axiomatic method to scientific disciplines. What I want to argue in this paper is that this application of the axiomatic method is also at the basis of a new approach that is being increasingly applied to the study of computer science and information systems, namely the approach of formal ontologies. The main task of an ontology is that of making explicit the conceptual structure underlying a certain domain. By “making explicit the conceptual structure” we mean singling out the most basic entities populating the domain and writing axioms expressing the main properties of these primitives and the relations holding among them. So, in both cases, the axiomatization is the main tool used to characterize the object of inquiry, being this object scientific theories (in Suppes’ approach), or information systems (for formal ontologies). In the following section I will present the view of Patrick Suppes on the philosophy of science and the axiomatic method, in section 3 I will survey the theoretical issues underlying the work that is being done in formal ontologies and in section 4 I will draw a comparison of these two approaches and explore similarities and differences between them. (shrink)

Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques (...) such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

This paper introduces the special issue on Formal Approaches to the Ontological Argument of the Journal of Applied Logics (College Publications). The issue contains the following articles: Formal Approaches to the Ontological Argument, by Ricardo Sousa Silvestre and Jean-Yves Béziau; A Brief Critical Introduction to the Ontological Argument and its Formalization: Anselm, Gaunilo, Descartes, Leibniz and Kant, by Ricardo Sousa Silvestre; A Mechanically Assisted Examination of Begging the Question in Anselm’s Ontological Argument, by John Rushby; A Tractarian Resolution (...) to the Ontological Argument, by Erik Thomsen; On Kant’s Hidden Ambivalence Toward Existential Generalization in his Critique of the Ontological Argument, by Giovanni Mion; The Totality of Predicates and the Possibility of the Most Real Being, by Srećko Kovač; An Even More Leibnizian Version of Gödel’s Ontological Argument, by Kordula Świętorzecka and Marcin Łyczak; A Case Study On Computational Hermeneutics: E. J. Lowe’s Modal Ontological Argument, by David Fuenmayor. (shrink)

This work aims to present an overview of the top-level ontology BFO - Basic Formal Ontology - and its applicability for Satellite Systems. As an upper level ontology, the BFO was designed to be extended, providing the basis for the specification of detailed representational artifacts about scientific information domains. These aspects and the challenges of satellite systems complexity and large size compose a suitable scenario for the creation of a specialized dialect to improve efficiency and accuracy (...) when modeling such systems. By analyzing BFO based ontologies in other disciplines and existing satellite models it is possible to describe an application for satellite systems, which can provide a foundation for the creation of a concrete ontology to be applied on satellite modeling. (shrink)

What is a fact ? Are there such things ?

In a first part, I defend that formal semantics can be used as a guide to ontological commitment. Thus, if one endorses an ontological view \(O\) and wants to interpret a formal language \(L\) , a thorough understanding of the relation between semantics and ontology will help us to construct a semantics for \(L\) in such a way that its ontological commitment will be in perfect accordance with \(O\) . Basically, that is what I call constructing (...) class='Hi'>formal semantics from an ontological perspective. In the rest of the paper, I develop rigorously and put into practice such a method, especially concerning the interpretation of second-order quantification. I will define the notion of ontological framework: it is a set-theoretical structure from which one can construct semantics whose ontological commitments correspond exactly to a given ontological view. I will define five ontological frameworks corresponding respectively to: (i) predicate nominalism, (ii) resemblance nominalism, (iii) armstrongian realism, (iv) platonic realism, and (v) tropism. From those different frameworks, I will construct different semantics for first-order and second-order languages. Notably I will present different kinds of nominalist semantics for second-order languages, showing thus that we can perfectly quantify over properties and relations while being ontologically committed only to individuals. I will show in what extent those semantics differ from each other; it will make clear how the disagreements between the ontological views extend from ontology to logic, and thus why endorsing an ontological view should have an impact on the kind of logic one should use. (shrink)

he general theme of this paper is the issue of formalization in philosophy; in a more specific way, it deals with the issue of formalization of arguments in analytic philosophy of religion. One argument in particular – Anselm’s Proslogion II ontological argument – and one specific attempt to formalize it – Robert Adams’ formalization found in his paper “The Logical Structure of Anselm’s Arguments”, published in The Philosophical Review in 1971 – are taken as study cases. The purpose of the (...) paper is to critically analyze Adams’ formalization with the intent to shed some light on the following questions: What are the virtues of formally analyzing arguments and the contributions, if any, of such an enterprise to the debate on Anselm’s argument? Which lessons can Adam’s work teach us about the dangers and limitations of formalization? Do these virtues and dangers teach us something about analysis of arguments in general? (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use (...) of the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

The gulf between philosophical and formal ontology can and should be bridged. In this Editorial, I elaborate briefly on this subject.

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)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is (...) designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

The purpose of this paper is twofold. First, it aims at introducing the ontological argument through the analysis of five historical developments: Anselm’s argument found in the second chapter of his Proslogion, Gaunilo’s criticism of it, Descartes’ version of the ontological argument found in his Meditations on First Philosophy, Leibniz’s contribution to the debate on the ontological argument and his demonstration of the possibility of God, and Kant’s famous criticisms against the (cartesian) ontological argument. Second, it intends to critically examine (...) the enterprise of formally analyzing philosophical arguments and, as such, contribute in a small degree to the debate on the role of formalization in philosophy. My focus will be mainly on the drawbacks and limitations of such enterprise; as a guideline, I shall refer to a Carnapian, or Carnapian-like theory of argument analysis. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The Unified Foundational Ontology (UFO) was developed over the last two decades by consistently putting together theories from areas such as formal ontology in philosophy, cognitive science, linguistics, and philosophical logics. It comprises a number of micro-theories addressing fundamental conceptual modeling notions, including entity types and relationship types. The aim of this paper is to summarize the current state of UFO, presenting a formalization of the ontology, along with the analysis of a number of cases to (...) illustrate the application of UFO and facilitate its comparison with other foundational ontologies in this special issue. (The cases originate from the First FOUST Workshop – the Foundational Stance, an international forum dedicated to Foundational Ontology research.). (shrink)

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The (...) paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products? (shrink)

In the specific case of geography, the real world consists on the one hand of physical geographic features (bona fide objects) and on the other hand of various fiat objects, for example legal and administrative objects, including parcels of real estate, areas of given soil types, census tracts, and so on. It contains in addition the beliefs and actions of human beings directed towards these objects (for example, the actions of those who work in land registries or in census bureaux), (...) and the relations between these beliefs and actions and their targets. The document is a Report of the Specialist Meeting held under the auspices of the Varenius Project. (shrink)

According to standard trope nominalism, there are simple tropes that do not have parts or multiply distinct aspects. Douglas Ehring’s reductio ad absurdum against this standard view concludes that there are no simple tropes. In this paper, we provide a response to Ehring defending the standard view. Ehring’s argument may be refuted by (1) distinguishing the ontological form of tropes from their contribution to the ontological content of the world, and (2) construing tropes as having primitive identity. At the same (...) time, standard trope nominalism is elaborated on by distinguishing between ontological form and content, for which there are also independent reasons. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...) of situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)