• University at Buffalo
    Department of Philosophy
    Biomedical Informatics
    Computer Science and Engineering
    Distinguished Professor, Julian Park Chair
University of Manchester
Department of Philosophy
PhD, 1976
APA Eastern Division
Buffalo, New York, United States of America
  •  460
    Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases
    with Jonathan Simon, James M. Fielding, and Mariana C. Dos Santos
    International Journal of Medical Informatics 75 (3-4): 224-231. 2005.
    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)…Read more
  •  453
    Ontology-based knowledge representation of experiment metadata in biological data mining
    with Scheuermann Richard, Kong Megan, Dahlke Carl, Cai Jennifer, Lee Jamie, Qian Yu, Squires Burke, Dunn Patrick, Wiser Jeff, Hagler Herb, Herb Hagler, and David Karp
    In Jake Chen & Stefano Lonardi (eds.), Biological Data Mining, Chapman Hall / Taylor and Francis. pp. 529-559. 2009.
    According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay awar…Read more
  •  445
    The metaphysics of real estate
    Topoi 20 (2): 161-172. 2001.
    The thesis that an analysis of property rights is essential to an adequate analysis of the state is a mainstay of political philosophy. The contours of the type of government a society has are shaped by the system regulating the property rights prevailing in that society. Views of this sort are widespread. They range from Locke to Nozick and encompass pretty much everything else in between. Defenders of this sort of view accord to property rights supreme importance. A state that does not suffici…Read more
  •  445
    On the Origins of Analytic Philosophy (review)
    Grazer Philosophische Studien 35 (1): 153-173. 1989.
    Analytic philosophers have until recently been reluctant to pursue historical investigations into the Central European roots of their own philosophical tradition. The most recent book by Michael Dummett, however, entitled Origins of Analytic Philosophy, shows how fruitful such investigations can be, not only as a means of coming to see familiar philosophical problems in a new light, but also as a means of clarifying what, precisely, ‘analytic philosophy’ might mean. As Dummett points out, the ne…Read more
  •  442
    Logic and formal ontology
    In J. N. Mohanty & W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, University Press of America. pp. 29-67. 1989.
    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 …Read more
  •  440
    Disputes over territory are a major contributing factor to the disruption of international relations. We believe that a cumulative, integrated, and continuously updated resource providing information about such disputes in an easily accessible form would be of benefit to intelligence analysts, military strategists, political scientists, and also to historians and others concerned with international disputes. We propose an ontology-based strategy for creating such a resource. The resource will co…Read more
  •  438
    In defense of extreme (fallibilistic) apriorism
    Journal of Libertarian Studies 12 (1). 1996.
    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 quest…Read more
  •  435
    The essay provides an account of the development of Reinach’s philosophy of “Sachverhalte” (states of affairs) and on problems in the philosophy of law, leading up to his discovery of the theory of speech acts in 1913. Reinach’s relations to Edmund Husserl and to the Munich phenomenologists are also dealt with.
  •  433
    Basic Formal Ontology for bioinformatics
    with Anand Kumar and Thomas Bittner
    IFOMIS Reports. 2005.
    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…Read more
  •  429
    Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology
    with John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay Cowell, Sebastian Duesing, and Regina Hurley
    Open Science Foundation Preprints. 2020.
    Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological conte…Read more
  •  429
    Gestalt psychology
    In Edward Craig (ed.), Routledge Encyclopedia of Philosophy, Routledge. pp. 51-54. 1998.
    The term ‘Gestalt’ was introduced into psychology by the Austrian philosopher Christian von Ehrenfels in an essay entitled “On ‘Gestalt-Qualities’” published in 1890. ‘Gestalt,’ in colloquial German, means roughly: ‘shape’ or ‘structure’ or ‘configuration’, and Ehrenfels demonstrates in his essay that there are certain inherently structural features of experience which need to be acknowledged in addition to simple tones, colours and other mental ‘atoms’ or ‘elements’. His essay thus initiated a …Read more
  •  426
    The Neurological Disease Ontology
    with Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Alan Ruttenberg, Kinga Szigeti, and Alexander D. Diehl
    Journal of Biomedical Semantics 4 (42): 42. 2013.
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by…Read more
  •  424
    This paper is concerned with certain ontological issues in the foundations of geographic representation. It sets out what these basic issues are, describes the tools needed to deal with them, and draws some implications for a general theory of spatial representation. Our approach has ramifications in the domains of mereology, topology, and the theory of location, and the question of the interaction of these three domains within a unified spatial representation theory is addressed. In the final p…Read more
  •  422
    The structures of the common-sense world
    Acta Philosophica Fennica 58. 1995.
    While contemporary philosophers have devoted vast amounts of attention to the language we use in describing and finding our way about the world of everyday experience, they have, with few exceptions, refused to see this world itself as a fitting object of theoretical concern. In what follows I shall seek to show how the commonsensical world might be treated ontologically as an object of investigation in its own right. At the same time I shall seek to establish how such a treatment might help us …Read more
  •  420
    Ontologia i analiza logiczna rzeczywistości
    Filozofia Nauki 2 5-22. 1994.
    The author attempts to show how mereology, taken together with certain topological notions, can yield the foundations for future investigations in formal ontology. He also attempts to show how the mereological framework allows for the direct and natural formulation of a series of theses - for example pertaining to the concept of a boundary - which can be only indirectly formulated (if at all) in set-theoretic terms. The far-reaching ain of the present framework is to serve as a basis for a forma…Read more
  •  418
    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
  •  415
    This book is a survey of the most important developments in Austrian philosophy in its classical period from the 1870s to the Anschluss in 1938. Thus it is intended as a contribution to the history of philosophy. But I hope that it will be seen also as a contribution to philosophy in its own right as an attempt to philosophize in the spirit of those, above all Roderick Chisholm, Rudolf Haller, Kevin Mulligan and Peter Simons, who have done so much to demonstrate the continued fertility of the id…Read more
  •  413
    Ontology for the Intelligence Analyst
    CrossTalk 14 (Nov/Dec): 18-25. 2012.
    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 …Read more
  •  411
    Conceptual Spaces for Space Event Characterization via Hard and Soft Data Fusion
    with Jeremy R. Chapman, David Kasmier, David Limbaugh, Stephen R. Gagnon, John Crassidis, James Llinas, and Alexander P. Cox
    AIAA (American Institute of Aeronautics and Astronautics) Scitech 2021 Forum. 2021.
    The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This pre…Read more
  •  411
    Granular Partitions and Vagueness
    In Chris Welty & Barry Smith (eds.), Formal Ontology in Information Systems (FOIS), Acm Press. pp. 309-320. 2003.
    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 extensio…Read more
  •  408
    An Essay on Material Necessity
    Canadian Journal of Philosophy (sup1): 301-322. 1992.
    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…Read more
  •  407
    Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a biomedical ethics ontology
    with David Koepsell, Robert Arp, and Jennifer Fostel
    Journal of Empirical Research on Human Research Ethics 4 (1): 43-58. 2009.
    Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI)…Read more
  •  407
    The Question of Apriorism
    Austrian Economics Newsletter (1/2): 1-5. 1990.
    We defend a view according to which Austrian economics rests on what can most properly be called an Aristotelian methodology. This implies a realist perspective, according to which the world exists independently of our thinking and reasoning activities; an essentialist perspective, according to which the world contains certain simple essences or natures which may come together in law-like ways to form more complex static and dynamic wholes, and an apriorist perspective, according to which given …Read more
  •  402
    Discussion of “Biomedical informatics: We are what we publish”
    with Geissbuhler Antoine, W. E. Hammond, A. Hasman, R. Hussein, R. Koppel, C. A. Kulikowski, V. Maojo, F. Martin-Sanchez, P. W. Moorman, Moura La, F. G. De Quiros, M. J. Schuemle, Barry Smith, and J. Talmon
    Methods of Information in Medicine 52 (6): 547-562. 2013.
    This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.
  •  401
    Acta cum fundamentis in re
    Dialectica 38 (2‐3): 157-178. 1984.
    It will be the thesis of this paper that there are among our mental acts some which fall into the category of real material relations. That is: some acts are necessarily such as to involve a plurality of objects as their relata or fundamenta. Suppose Bruno walks into his study and sees a cat. To describe the seeing, here, as a relation, is to affirm that it serves somehow to tie Bruno to the cat. Bruno's act of seeing, unlike his feeling depressed, his putative thinking-about-Santa-Claus or his …Read more
  •  401
    CARO: The Common Anatomy Reference Ontology
    with Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, and Chris J. Mungall
    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…Read more
  •  400
    Naive physics
    Philosophical Psychology 7 (2). 1994.
    The project of a 'naive physics' has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as K hler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit…Read more
  •  400
    Ontological realism: A methodology for coordinated evolution of scientific ontologies
    with Werner Ceusters
    Applied ontology 5 (3): 139-188. 2010.
    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed fo…Read more
  •  400
    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 correspondin…Read more
  •  399
    Ontology and Geographic Kinds
    with David M. Mark
    In T. Poiker & N. Chrisman (eds.), Proceedings of the 8th International Symposium on Spatial Data Handling, International Geographic Union. pp. 308-320. 1998.
    Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our e…Read more