• 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
  •  357
    GOL: A general ontological language
    with Wolfgang Degen, Barbara Heller, and Heinrich Herre
    In Chris Welty & Barry Smith (eds.), Formal Ontology in Information Systems (FOIS), Acm Press. pp. 34-46. 2001.
    Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory h…Read more
  •  357
    Towards new information resources for public health: From WordNet to MedicalWordNet
    with Christane Fellbaum and Udo Hahn
    Journal of Biomedical Informatics 39 (3): 321-332. 2006.
    In the last two decades, WORDNET has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MEDICAL WORDNET. This resource is not to be conceived merely as a lexical extension of the original WORDNET to medical terminology; indeed, there is already a considerable degree of overlap between WORDNET and the vocabulary of medicine. Instead…Read more
  •  356
    A multi-INT semantic reasoning framework for intelligence analysis support
    with Janssen Terry, Basik Herbert, and Dean Mike
    In L. Obrst, Terry Janssen & W. Ceusters (eds.), Ontologies and Semantic Technologies for the Intelligence Community, Ios Press. pp. 57-69. 2010.
    Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.
  •  354
    La physique naïve: un essai d'ontologie
    Intellectica 17 (2): 173--197. 1993.
    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 Kohler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit f…Read more
  •  354
    The niche
    Noûs 33 (2): 214-238. 1999.
    The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biolo…Read more
  •  353
    Explications vérifactionnistes
    Philosophiques 38 (1): 177-194. 2011.
    Le présent article est une tentative nouvelle d’articuler le rôle d’une théorie des vérifacteurs. Nous soutenons que la théorie de la vérifaction constitue une pierre angulaire dans une bonne méthodologie en métaphysique, mais que l’amalgame entre la théorie de la vérifaction et la théorie de la vérité a été responsable de certains excès associés aux approches vérifactionnistes dans la littérature récente. Nous montrons que la théorie de la vérifaction conserve son attrait comme instrument d’inv…Read more
  •  352
    A semantic approach for knowledge capture of microRNA-target gene interactions
    with Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Xiaowei Wang, and Zixing Liu
    Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, sema…Read more
  •  351
    Brentano and Kafka
    Axiomathes 8 (1): 83-104. 1997.
    There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summari…Read more
  •  350
    Weininger und Wittgenstein
    Teoria 2. 1984.
    The paper [which is in German] seeks to show how Weininger’s interpretations of Kant and Schopenhauer help us to understand some of the peculiar reflections on the will, on happiness and unhappiness, and on the problems of life, which are to be found in Wittgenstein's Notebooks. It seeks to explain, above all, why Wittgenstein should wish to reject the basic ethical axiom of “love thy neighbor.” There follows a sketch of one possible Kantian interpretation of the Tractatus along Weiningerian lin…Read more
  •  349
    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
  •  348
    Bridging the gap between medical and bioinformatics: An ontological case study in colon carcinoma
    with Anand Kumar, Yum Lina Yip, and Pierre Grenon
    Computers in Biology and Medicine 36 (7): 694--711. 2006.
    Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in t…Read more
  •  347
    The functions of definitions in ontologies
    with Selja Seppälä and Alan Ruttenberg, ,
    To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.
  •  346
    Toward a Realistic Science of Environments
    Ecological Psychology 21 (2): 121-130. 2009.
    The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces,…Read more
  •  345
    Living high and letting die
    Philosophy 76 (3): 435-442. 2001.
    Imagine that your body has become attached, without your permission, to that of a sick violinist. The violinist is a human being. He will die if you detach him. Such detachment seems, nonetheless, to be morally permissible. Thomson argues that an unwantedly pregnant woman is in an analogous situation. Her argument is considered by many to have established the moral permissibility of abortion even under the assumption that the foetus is a human being. Another popular argument is that presented by…Read more
  •  344
    Austrian Origins of Logical Positivism
    In Barry Gower (ed.), Logical Positivism in Perspective, Croom Helm. pp. 35-68. 1988.
    Recent work on Austrian philosophy has revealed, hitherto, unsuspected links between Vienna circle positivism on the one hand, and the thought of Franz Brentano and his circle on the other. the paper explores these links, casting light also on the Polish analytic movement, on the development of gestalt psychology, and on the work of Schlick and Neurath.
  •  344
    Vital Sign Ontology
    with Albert Goldfain, Sivaram Arabandi, Mathias Brochhausen, and William R. Hogan
    We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices.…Read more
  •  341
    Benefits of Realist Ontologies to Systems Engineering
    with Eric Merrell, Robert M. Kelly, David Kasmier, Marc Brittain, Ronald Ankner, Evan Maki, Curtis W. Heisey, and Kevin Bush
    8th International Workshop on Ontologies and Conceptual Modelling (OntoCom). 2021.
    Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) int…Read more
  •  340
    A domain ontology for the non-coding RNA field
    with Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Michael T. Zimmermann, Guoqian Jiang, and Yu Lin
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification o…Read more
  •  339
    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
  •  338
    Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base
    with Jiye Ai and David Wong
    BMC Bioinformatics 11 (1): 302. 2010.
    The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus…Read more
  •  336
    Physics and the phenomenal world
    with Jean Petitot
    In Roberto Poli & Peter Simons (eds.), Formal Ontology, Kluwer. pp. 233-254. 1996.
    The paper challenges the assumption, common amongst philosophers, that the reality described in the fundamental theories of microphysics is all the reality we have. It will be argued that this assumption is in fact incompatible with the nature of such theories. It will be shown further that the macro-world of three-dimensional bodies and of such qualitative structures as colour and sound can be treated scientifically on its own terms, which is to say not only from the perspective of psychology b…Read more
  •  334
    IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain
    with Tatiana Malyuta, Ron Rudnicki, William Mandrick, David Salmen, Peter Morosoff, Danielle K. Duff, James Schoening, and Kesny Parent
    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…Read more
  •  334
    Aristoteles, Kant und die Quantenphysik
    In Ruth Hagengruber (ed.), Philosophie und Wissenschaft, Königshausen Und Neumann. pp. 79-97. 2002.
    Der folgende Vortrag hat zwei Teile. Teil 1 hat mit dem Internet zu tun und mit neuen Entwicklungen im Bereich des so genannten „ontological engineering“. Teil 2 hat zu tun mit der kantischen Philosophie und mit neuen Versuchen, diese Philosophie mit Hilfe der Quantenphysik zu unterstützen. Diese zwei Teile sind nicht vollkommen unabhängig voneinander, aber die Verbindung zwischen den zwei Teilen wird erst im Laufe des Vortrags klar werden.
  •  334
    The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. In what follows we show that the superva…Read more
  •  332
    Framework for a protein ontology
    with Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, and Cathy H. Wu
    BMC Bioinformatics 8 (Suppl 9). 2007.
    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 relations…Read more
  •  331
    The Unified Medical Language System and the Gene Ontology: Some critical reflections
    with Anand Kumar
    In A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence, Springer. pp. 135-148. 2003.
    The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to a…Read more
  •  331
    Functional Anatomy: A Taxonomic Proposal
    with Ingvar Johansson, Katherine Dormandy [nee Munn], Kathleen Elsner, Nikoloz Tsikolia, and DIrk Siebert
    Acta Biotheoretica 53 (3): 153-166. 2005.
    It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.
  •  329
    Objects and their environments: From Aristotle to ecological ontology
    In Andrew U. Frank, Jonathan Raper & Jean-Paul Cheylan (eds.), The Life and Motion of Socio-Economic Units, Taylor & Francis. pp. 79-97. 2001.
    What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas w…Read more
  •  328
    Beyond Paper
    The Monist 97 (2). 2014.
    The authors outline the way in which documents as social objects have evolved from their earliest forms to the electronic documents of the present day. They note that while certain features have remained consistent, processes regarding document authentication are seriously complicated by the easy reproducibility of digital entities. The authors argue that electronic documents also raise significant questions concerning the theory of ‘documentality’ advanced by Maurizio Ferraris, especially given…Read more
  •  328
    Putting Biomedical Ontologies to Work
    with Mathias Brochhausen
    Methods of Information in Medicine 49 (2): 135-40. 2010.
    Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT c…Read more