Barry Smith

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness.

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.

We presuppose a position of scientific realism to the effect (i) that the world exists and (ii) that through the working out of ever more sophisticated theories our scientific picture of reality will approximate ever more closely to the world as it really is. Against this background consider, now, the following question: 1. Do the empirical theories with the help of which we seek to approximate a good or true picture of reality rest on any non-empirical presuppositions? One can answer this question with either a 'yes' or a 'no'. 'No' is the preferred answer of most contemporary methodologists -- Murray Rothbard is one distinguished counterexample to this trend -- who maintain that empirical theories are completely free of non-empirical ('a priori') admixtures and who see science as a matter of the gathering of pure 'data' obtained through simple observation. From such data scientific propositions are then supposed to be somehow capable of being established.

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway.

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.

Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules, the adherence to which presupposes simultaneous immersion in disciplines hitherto seen as being unrelated. The paper presents a demonstration of the fruitfulness of this theory by means of an account of some of the political, cultural and intellectual peculiarities of the Habsburg Monarchy.

In perceptual experience we are directed towards objects in a way which establishes a real relation between a mental act and its target. In reading works of fiction we enjoy experiences which manifest certain internal similarities to such relational acts, but which lack objects. The substitution theory of art attempts to provide a reason why we seek out such experiences and the artifacts which they generate. Briefly, we seek out works of art because we enjoy the physiology and the phenomenology of, for example, the experience of love or mountain climbing, and works of art serve as props for the promotion of substitutes for the corresponding genuine feelings. Art arose, or came to be separated out from other, related phenomena, through the discovery that the experience of substitute emotions can be pleasurable.

This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for formal ontology. We provide examples to support this thesis from the domain of biomedicine.

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts.

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, sequence, expression, boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics.

This paper is a fresh attempt to articulate the role of a theory of truthmakers. We argue that truthmaker theory constitutes a cornerstone of good methodology in metaphysics, but that a conflation of truthmaker theory with the theory of truth has been responsible for certain excesses associated with truthmaker-based approaches in the recent literature. If truthmaker theory is not a component of a theory of truth, then truthmaker maximalism – the view that every truth has a truthmaker – loses its primary motivation. More generally, if the task of truthmaker theory is not to provide a definition or account of truth in truthmaker terms, there is no pressing need for hard, a priori principles stating which truths have truthmakers and which do not.

Attempts to trace a unifying thread of ontological realism extending through 1. my early writings on Frege, Brentano, Husserl, Wittgenstein, Ingarden and (with Kevin Mulligan and Peter Simons) on truthmakers; 2. work on formal theories of the common-sense world, and on mereotopology, fiat objects, geographical categories, and environments (with David Mark, Roberto Casati, Achille Varzi), to 3. current work on applied ontology in biology and medicine, and on the theory of document acts and on the ontology of information artifacts.

Where Humeans rule out the possibility of material or non-logical necessity, and thus of any associated knowledge a priori, the German legal philosopher Adolf Reinach defends the existence of a wide class of material necessities falling within the domain of what can be known a priori, for example in fields such as color and shape, rational psychology, law and economics. Categories such as promise or claim or obligation are, in Reinach’s view, exist as nodes in a system of necessary relations, so that anyone who has experience of relevant instances of these categories is implicitly aware also of a corresponding family of relations to certain other categories – as for example that every promise implies a mutually correlated claim and obligation. Midway between the two extremes of Hume and Reinach stands Searle, who accepts necessary relations of the mentioned sorts, but sees them as human creations, following from ‘constitutive rules’ analogous to the rules of chess. We seek to demonstrate that Searle does not occupy a stable and acceptable half-way house between Hume and Reinach; that he, too, if he is to do justice to the very constitutive rules which form the center of his approach, must on pain of circularity embrace something like the Reinachian position.

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data.

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

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.

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation.

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.

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future.

Provides a survey of the development of speech act theory from Aristotle through Reid and Peirce to Edmund Husserl, Anton Marty, Johannes Daubert, Adolf Reinach, and finally to Austin and Searle. A special role is played by Husserl's theory of objectifying acts (meaning, roughly, acts of naming or stating) and of the efforts by his followers to extend this theory to cover phenomena such as questioning and commanding. These efforts culminated in the work of Adolf Reinach, who developed the first systematic theory of speech acts in connection with his monograph of 1913 on “The A Priori Foundations of the Civil Law”.

Two hundred and sixty-three subjects each gave examples for one of five geographic categories: geographic features, geographic objects, geographic concepts, something geographic, and something that could be portrayed on a map. The frequencies of various responses were significantly different, indicating that the basic ontological terms feature, object, etc., are not interchangeable but carry different meanings when combined with adjectives indicating geographic or mappable. For all of the test phrases involving geographic, responses were predominantly natural features such as mountain, river, lake, ocean, hill. Artificial geographic features such as town and city were listed hardly at all for geographic categories, an outcome that contrasts sharply with the disciplinary self-understanding of academic geography. However, geographic artifacts and fiat objects, such as roads, cities, boundaries, countries, and states, were frequently listed by the subjects responding to the phrase something that could be portrayed on a map. In this paper, we present the results of these experiments in visual form, and provide interpretations and implications for further research.

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in which all clinically salient particulars – from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given – should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way. We discuss the ontological and epistemological aspects of our claim and describe a scenario for implementation within EHR systems.

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.

Those who conceive logic as a science have generally favoured one of two alternative conceptions as to what the subject-matter of this science ought to be. On the one hand is the nowadays somewhat old-fashioned-seeming view of logic as the science of judgment, or of thinking or reasoning activities in general. On the other hand is the view of logic as a science of ideal meanings, 'thoughts', or 'propositions in themselves'. There is, however, a third alternative conception, which enjoyed only a brief flowering in the years leading up to the first World War, but whose lingering presence can be detected in the background of more recent ontologising trends in logic, as for example in the 'situation semantics' of Barwise and Perry. This third conception sees logic as a science of special objects called 'Sachverhalte' or 'states of affairs'. A view of this sort is present in simplified form in the works of Meinong, but it received its definitive formulation in the writings of Adolf Reinach, a student of Husserl who is otherwise noteworthy for having anticipated, in a monograph of 1913, large chunks of what later became known as the theory of speech acts.(1).