•  21
    OHMI: The Ontology of Host-Microbiome Interactions
    with Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Alexander V. Alekseyenko, and Jihad S. Obeid
    Journal of Biomedical Semantics 10 (1): 1-14. 2019.
    Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of H…Read more
  •  6
    Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych
    with Janna Hastings, Gwen Frishkoff, Mark Jensen, Russell Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica Turner, Maryann Martone, and Przemysław Nowakowski
    Avant: Trends in Interdisciplinary Studies 7 (3): 101-117. 2016.
  •  10
    Phenomenological Tendencies in British Moral Theory
    with Dallas Willard
    In Lester Embree (ed.), Encyclopedia of Phenomenology, Kluwer Academic Publishers. pp. 81-85. 1995.
    There is an inherent phenomenological tendency in British moral theory, especially from John Locke onward. The purpose of his Essay was, he said, to consider the discerning faculties of a man, as they are employed about the objects which they have to do with. This is language that might serve well in a general description of the work of Husserl and other phenomenologists
  •  14
    Warum hat sich die deutsche Philosophie so sehr und so langanhaltend an Autoritäten und Texte gebunden gefühlt, fast als ob man – wie die alten Iatrophilologen – Wissen aus bloßen Worten herauspressen wollte? Warum haben sich in Deutschland so häufig philosophische Sprachstile entwickelt, die ein Hindernis fur das Verständnis der entsprechenden Texte sind?
  •  13
    Witasek
    In Monika Betzler & Julian Nida-Rümelin (eds.), Ästhetik und Kunstphilosophie von der Antike bis zur Gegenwart in Einzeldarstellungen, Alfred Kröner Verlag. pp. 821-824. 1998.
    Stephan Witasek was a student and follow of Meinong, who applied Meinong's ideas on the ontology of the non-existent to the working out of a theory of aesthetic phenomena in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows how our feelings undergo certain sorts of structural modifications when they are directed towards what does not exist. He draws a distinction between genuine mental phenomena and what he calls ‘phantasy-material’, asserting that ‘the job of the aesthetic object, w…Read more
  •  25
    In his Untimely Meditations on the Relations between Self and Non-Self, Paolo Bozzi considers two popular approaches to answering the question of how it is possible, given the nature of our experience, that we can delimit what we take to be ourselves from what we take to be outside of ourselves. He considers two popular approaches to answering this question—one rooted in the discussion of personal identity in Hume’s Treatise on Human Nature, the other rooted in the origins of constructivism in p…Read more
  •  92
    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 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 over…Read more
  •  83
    We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that the pump exists because something was needed that…Read more
  •  96
    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 arr…Read more
  •  123
    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 ontology descending from BFO…Read more
  •  130
    In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will imp…Read more
  •  76
    W dziełach Arystotelesa, lub z medievals, jak również w pismach późniejszych zdroworozsądkowe filozofów, takich jak Thomas Reid czy GE Moore’a, możemy znaleźć rodzinę różnych prób uporania się ze strukturami rozsądku i wspólnego -sense świat, który jest nam dany w normalnym, doświadczenie pre-teoretycznym. Będziemy argumentować, co wynika, że ​​teoria takich struktur stanowi ważny i dotychczas niedoceniany związek między wczesnym psychologii Gestalt z jednej strony, oraz współczesnych osiągnięć …Read more
  •  52
    A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work is …Read more
  •  67
    How Many Kafka's Are There?
    with Sonia Kamińska
    Polish Journal of Aesthetics 53 (2): 9-13. 2019.
    The aim of this volume is to present Kafka not as a writer, or not only as a writer, but as a philosopher. However, even after narrowing the scope of our interest down, there will still be several Kafka’s left on the table. Themes treated in the volume include: the so-called Brentano School in Prague, Kafka’s affiliation to the Louvre Circle, Kafka and existentialist philosophy, Kafka’s Jewish heritage, his love of Nietzsche and Meister Eckhart and—last but not least, since he was such an except…Read more
  •  89
    Geographical Categories: An Ontological Retrospective
    with David M. Mark
    International Journal of Geographical Information Science 15 (7). 2001.
    Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review the paper and at…Read more
  •  63
    Preliminary version of “Towards a History of Speech Act Theory”, in A. Burkhardt (ed.), Speech Acts, Meanings and Intentions. Critical Approaches to the Philosophy of John R. Searle, Berlin/New York: de Gruyter, 1990, 29–61.
  •  26
    Die ganze Welt ist eine Bühne: Zur Ökologie und Ontologie menschlicher und tierischer Lebenswelt
    Interdisziplinäre Phänomenologie / Interdisciplinary Phenomenology (Kyoto) 1 31-44. 2004.
    Die klassische bikategoriale Ontologie von Substanzen und Akzidentien ist für die Festlegung der Strukturen menschlichen und tierischen Verhaltens nicht hinreichend, da die Umwelten dieses Verhaltens sich nicht in dieses klassische System einfügen. Wir bieten dementsprechend den Grundriß einer Theorie der besonderen Gebilde, die die Alltagswelten menschlicher und tierischer Verhalten konstituieren. Die Ausgangsüberlegung ist die folgende, Wir sind alle (Schau)spieler, und diese brauchen eine Büh…Read more
  •  188
    Interoperability of disparate engineering domain ontologies using Basic Formal Ontology
    with Thomas J. Hagedorn, Sundar Krishnamurty, and Ian R. Grosse
    Journal of Engineering Design 31. 2019.
    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 o…Read more
  •  127
    Since 1950, when Alan Turing proposed what has since come to be called the Turing test, the ability of a machine to pass this test has established itself as the primary hallmark of general AI. To pass the test, a machine would have to be able to engage in dialogue in such a way that a human interrogator could not distinguish its behaviour from that of a human being. AI researchers have attempted to build machines that could meet this requirement, but they have so far failed. To pass the test, a …Read more
  •  91
    Drawing Boundaries
    In Timothy Tambassi (ed.), The Philosophy of GIS, Springer. pp. 137-158. 2019.
    In “On Drawing Lines on a Map” (1995), I suggested that the different ways we have of drawing lines on maps open up a new perspective on ontology, resting on a distinction between two sorts of boundaries: fiat and bona fide. “Fiat” means, roughly: human-demarcation-induced. “Bona fide” means, again roughly: a boundary constituted by some real physical discontinuity. I presented a general typology of boundaries based on this opposition and showed how it generates a corresponding typology of the d…Read more
  •  1
    Proceedings of the KI 2003 Workshop on Reference Ontologies and Application Ontologies (edited book)
    with Pierre Grenon and Christopher Menzel
    CEUR Workshop Proceedings, Vol. 94. 2004.
    Contains the following contributions: Ingvar Johansson: Ontologies and Concepts. Two Proposals Christopher Menzel: Reference Ontologies - Application Ontologies: Either/Or or Both/And? Luc Schneider: Foundational Ontologies and the Realist Bias Guenther Goerz, Kerstin Buecher, Bernd Ludwig, Frank-Peter Schweinberger, and Iman Thabet: Combining a Lexical Taxonomy with Domain Ontology in the Erlangen Dialogue System Vim Vandenberghe, Burkhard Schafer, John Kingston: Ontology Modelling in the Lega…Read more
  •  63
    The Plant Ontology facilitates comparisons of plant development stages across species
    with Ramona Lynn Walls, Laurel Cooper, Justin Lee Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Dennis William Stevenson, and Pankaj Jaiswal
    Frontiers in Plant Science 10. 2019.
    The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover …Read more
  •  316
    An Ontological Approach to Representing the Product Life Cycle
    with J. Neil Otte, Dimitris Kiritsi, Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Ron Rudnicki, and Rahul Rai
    Applied Ontology 14 (2): 1-19. 2019.
    The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to en…Read more
  •  304
    Making AI Meaningful Again
    with Jobst Landgrebe
    Synthese. 2019.
    Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artifi…Read more
  •  735
    A Product Life Cycle Ontology for Additive Manufacturing
    with Munira Mohd Ali, Rahul Rai, and J. Neil Otte
    Computers in Industry 105 191-203. 2019.
    The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates pro…Read more
  •  61
    La vérité et le champ visuel
    In Jean-Michel Roy, Jean Francisco J. Varela & Bernard Pachoud (eds.), Naturaliser la phénoménologie: Husserlianisme et science cognitive, Cnrs Editions. pp. 411-426. 2002.
    La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spat…Read more
  •  46
    Fiat objects
    In Nicola Guarino, Laure Vieu & Simone Pribbenow (eds.), Parts and Wholes: Conceptual Part-Whole Relations and Formal Mereology, 11th European Conference on Artificial Intelligence, Amsterdam, 8 August 1994, Amsterdam:, European Coordinating Committee For Artificial Intelligence. pp. 14-22. 1994.
    Human cognitive acts are directed towards entities of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. A categorial scheme for the objects of human cognition should be (1) critical and realistic. Cognitive subjects are liable to error, even to systematic error of the sort that is manifested by believers in the Pantheon of Olympian gods. Thus not all putative object-directed acts should be recognized as having objects of their own. …Read more
  •  232
    Topological Foundations of Cognitive Science (edited book)
    with Carola Eschenbach and Christopher Habel
    A collection of papers presented at the First International Summer Institute in Cognitive Science, University at Buffalo, July 1994, including the following papers: ** Topological Foundations of Cognitive Science, Barry Smith ** The Bounds of Axiomatisation, Graham White ** Rethinking Boundaries, Wojciech Zelaniec ** Sheaf Mereology and Space Cognition, Jean Petitot ** A Mereotopological Definition of 'Point', Carola Eschenbach ** Discreteness, Finiteness, and the Structure of Topologi…Read more
  •  355
    Ontology-based fusion of sensor data and natural language
    with Erik Thomsen
    Applied Ontology 13 (4): 295-333. 2018.
    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…Read more