Barry Smith

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.

Un mince fil dans la vaste littérature sur Kafka concerne la connaissance qu’avait Kafka de la philosophie, et plus précisément l’utilisation, dans les récits de Kafka, de quelques-unes des idées principales de Franz Brentano. Kafka a suivi des cours de philosophie à l’Université Charles, cours donnés par des étudiants de Brentano, Anton Marty et Christian von Ehrenfels. Il fut aussi, pendant plusieurs années, membre d’un groupe de discussion organisé par des partisans orthodoxes de la philosophie brentanienne à Prague. Le présent essai résume ce que l’on sait des relations entretenues par Kafka avec le mouvement brentanien. Il porte sur les idées brentaniennes qui concernent l’évidence de la perception intérieure, la conscience oblique, l’introspection active, le jugement correct et incorrect et la conscience en tant qu’espèce de tribunal intérieur, dans le but d’éclairer certains aspects centraux de l’œuvre de Kafka, incluant son style. Nous porterons une attention particulière sur Die Verwandlung et Der Prozess , et nous offrirons une interprétation de ce dernier texte selon laquelle le procès de Joseph K. se passe entièrement dans l’esprit de K. lui-même.

Standard theories in mereotopology focus on relations of parthood and connection among spatial or spatio-temporal regions. Objects or processes which might be located in such regions are not normally directly treated in such theories. At best, they are simulated via appeal to distributions of attributes across the regions occupied or by functions from times to regions. The present paper offers a richer framework, in which it is possible to represent directly the relations between entities of various types at different levels, including both objects and the regions they occupy. What results is a layered mereotopology, a theory which can handle multiple layers (analogous to the layers of a lasagna) of spatially or spatiotemporally coincident but mereologically non-overlapping entities.

As an object in which property rights can be invested, land is a peculiar hybrid structure that comprehends both spatial and non-spatial aspects. Even in its purely spatial aspect land is treated differently from culture to culture, thus for example in the degree to which property rights in land are held to relate to vague or precisely delineated parcels and to portions of space above and below the surface of the earth. When we examine the non-spatial aspects of landed property, however, the dimensions of variability across cultures are multiplied tremendously. The goal is to provide a general framework for comparison of different socio-legal ontologies of land. The relevance of this project turns on the fact that without land (or real estate) it is difficult (perhaps impossible) to obtain credit; without credit it is difficult for nations to develop. Thus, if land is treated in a radically different way from one nation to another, this will surely exert an effect upon the development of nations.

The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal accounts of basic notions such as system, process, and function, and while such informality is acceptable in documentation created for human beings, it falls short of what is needed for computer representations. In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions.

As he recalls in his book Naive Physics, Paolo Bozzi’s experiments on naïve or phenomenological physics were partly inspired by Aristotle’s spokesman Simplicio in Galileo’s Dialogue. Aristotle’s ‘naïve’ views of physical reality reflect the ways in which we are disposed perceptually to organize the physical reality we see. In what follows I want to apply this idea to the notion of a group, a term which I shall apply as an umbrella expression embracing ordinary visible collections (of pieces of fruit in the fruit bowl), but also families, populations, kinds, categories, species and genera. I will try to determine to what extent we can understand what groups, in this broad sense, have in common and how they are distinguished from two sorts of entities with which they are standardly confused, namely sets and wholes.

A meaningful life, we shall argue, is a life upon which a certain sort of valuable pattern has been imposed by the person in question - a pattern which involves in serious ways the person having an effect upon the world. Meaningfulness is thus a special kind of value which a human life can bear. Two interrelated difficulties face ths proposal. One concerns responsiblity: how are we to account for the fact that a life that satisfies the above criteria can have more meaning than a life with the same positive outcomes but which lacks responsiblity on the part of the agent? The other turns on these outcomes themselves: how can the meaningfulness engendered by actions you perform now be affected by what those actions go on to produce in the future, perhaps even after your death? We provide a response to both of these difficulties.

The paper seeks to indicate ways in which the crude distinction between Anglo-Saxon and Continental philosophy may have to be amended in light of recent developments in Eastern Europe. As is well known, the philosophy of science is to no small part a product of the universities of the Habsburg Empire (in Vienna, Prague, Lemberg/Lwow, etc.). Logic, too, has played a more significant role in Eastern Europe (not least in Poland) than in the philosophical cultures of Germany or France. For these and other reasons, a shift in the center of gravity of Continental philosophy is currently being realized, as younger Eastern European philosophers in newly liberalized institutions begin to return to their roots in their native pre-Communist intellectual traditions.

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning.

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.

Ernst Mach's atomistic theory of sensation faces problems in doing justice to our ability to perceive and remember complex phenomena such as melodies and shapes. Christian von Ehrenfels attempted to solve these problems with his theory of "Gestalt qualities", which he sees as entities depending one-sidedly on the corresponding simple objects of sensation. We explore the theory of dependence relations advanced by Ehrenfels and show how it relates to the views on the objects of perception advanced by Husserl and by the Gestalt psychologists.

There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this theory provides a general framework within which we can understand the relation between vague terms and concepts on the one hand and correlated portions of reality on the other. We also sketch how it might be possible to formulate within this framework a theory of vagueness which dispenses with the notion of truth-value gaps and other artifacts of more familiar approaches.

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking.

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which could afford to be ignored

The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and grouped together into enduring document complexes. We outline some components of a theory of document acts, and show how it can throw light on certain problems in Searle’s ontology of social reality.

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.

It is a truism that the attitude of deference to the text plays a lesser role in Anglo-Saxon philosophy than in other philosophical traditions. Works of philosophy written in English have, it is true, spawned a massive secondary literature dealing with the ideas, problems or arguments they contain. But they have almost never given rise to works of commentary in the strict sense, a genre which is however a dominant literary form not only in the Confucian, Vedantic, Islamic, Jewish and Scholastic traditions of the past, but also in relation to more recent German-language philosophy (thus for example in work on Hegel, Heidegger or Wittgenstein). Moreover Anglo-Saxon philosophers have themselves embraced the commentary form when dealing with Greek or Latin philosophers outside their own tradition. The paper seeks to establish the reasons for this imbalance by examining those factors which might be conducive to the growth of a commentary literature in a given culture.

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data.

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.

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.

There are, familiarly, a range of distinct and competing accounts of the methodological underpinnings of Menger' s work. These include Leibnizian, Kantian, Millian, and even Popperian readings; but they include also readings of an Aristotelian sort, and I have myself made a number of contributions in clarification and defence of the latter. Not only, I have argued, does the historical situation in which Menger found himself point to the inevitability of the Aristotelian reading; this reading fits also very naturally to the text of Menger's works.

Where some have attempted to apply cognitive methods to the study of geography, the present paper is designed to serve as a starting point for applying methods of geographic ontology to the phenomena of cognition. Agglomerations are aggregates of entities that are dispersed through space on geographic scales. Examples include: plagues, biological species, major world religions. The paper applies standard mereotopological theories of spatial regions to agglomerations in this sense. It offers the beginnings of a general theory of the relations between social, cultural, ethnic and religious agglomerations on the one hand and territorially demarcated spatial objects on the other. In this way it serves as the basis for a general ontological theory of types of human groups and also of types of conflict between these groups. At the same time it provides ontological foundations for the epidemiological study of cognitive phenomena, and especially of cognitive phenomena in the sociopolitical realm.

If we are to develop efficient, reliable and secure means for sharing information across healthcare systems and organizations, then a careful analysis of human actions will be needed. To address this need, the HL7 organization has proposed its Reference Information Model (RIM), which is designed to provide a comprehensive representation of the entire domain of healthcare centered around the phenomenon of human action. Taking the Basic Formal Ontology as our starting point, we examine the RIM from an ontological point of view, describing how it fails to provide a representation of the healthcare domain which would enjoy the sort of clarity, coherence, rigor and completeness that is claimed on its behalf.

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria.

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.