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)

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)

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)

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)

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.

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.

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)

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 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)

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)

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)

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)

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)

What is a fact ? Are there such things ?

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)

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)

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 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)

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)

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)

I shall attempt in what follows to show how mereology, taken together with certain topological notions, can yield the basis for future investigations in formal ontology. I shall attempt to show also how the mereological framework here advanced can allow the direct and natural formulation of a series of theses – for example pertaining to the concept of boundary – which can be formulated only indirectly (if at all) in set-theoretic terms.

A ‘duality’ is a formal mapping between the spaces of solutions of two empirically equivalent theories. In recent times, dualities have been found to be pervasive in string theory and quantum field theory. Naïvely interpreted, duality-related theories appear to make very different ontological claims about the world—differing in e.g. space-time structure, fundamental ontology, and mereological structure. In light of this, duality-related theories raise questions familiar from discussions of underdetermination in the philosophy of science: in the presence of dual (...) theories, what is one to say about the ontology of the world? In this paper, we undertake a comprehensive and non-technical survey of the landscape of possible ontological interpretations of duality-related theories. We provide a significantly enriched and clarified taxonomy of options—several of which are novel to the literature. (shrink)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a (...) process that is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

What is the ontology of collective action? I have in mind three connected questions. 1. Do the truth conditions of action sentences about groups require there to be group agents over and above individual agents? 2. Is there a difference, in this connection, between action sentences about informal groups that use plural noun phrases, such as ‘We pushed the car’ and ‘The women left the party early’, and action sentences about formal or institutional groups that use singular noun (...) phrases, such as ‘The United States declared war on Japan on December 8th, 1941’ and ‘The Supreme Court ruled that segregation is unconstitutional in 1954 in Brown vs. Board of Education’? 3. Under what conditions does it make sense to speak of a group doing something together, and what, if anything, is a collective action? In this paper, I argue that a) understanding action sentences about groups does not commit us to the existence of group agents per se, but only to the existence of individual agents; b) there is no difference in this regard between sentences which attribute actions to informal groups on the one hand and institutional groups on the other; c) collective action can be both intentional and unintentional; d) any random group of agents each of whom does something is also a group which does something together; e) while there is a sense in which groups per se perform no primitive collective actions, and therefore no actions at all, f) there is a sensible extension of talk of actions to groups, though it should be treated strictly speaking, like talk of group agents, as a façon de parler, for g) the only agents per se are individuals and the only actions are theirs. -/-. (shrink)

This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and (...) information scientists. (shrink)

Although the relationship of part to whole is one of the most fundamental there is, this is the first full-length study of this key concept. Showing that mereology, or the formal theory of part and whole, is essential to ontology, Simons surveys and critiques previous theories--especially the standard extensional view--and proposes a new account that encompasses both temporal and modal considerations. Simons's revised theory not only allows him to offer fresh solutions to long-standing problems, but also has far-reaching (...) consequences for our understanding of a host of classical philosophical concepts. (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)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the (...) patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological (...) theorizing in abstract fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the (...) light of the interconnections between them. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (...) (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

The best arguments for possible worlds as states of affairs furnish us with equally good arguments for impossible worlds of the same sort. I argue for a theory of impossible worlds on which the impossible worlds correspond to maximal inconsistent classes of propositions. Three objections are rejected. In the final part of the paper, I present a menu of impossible worlds and explore some of their interesting formal properties.

As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...) benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future. (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)

One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a semantics (...) for the theory and a provably sound axiomatization. (shrink)

The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in (...) many influential ontologies, illustrating our results by reference to examples drawn from the domain of the life sciences. (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)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results (...) of protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy for (...) the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)