September 4, 2017
1. Barry Smith (ed.), Structure and Gestalt: Philosophy and Literature in Austria-Hungary and Her Successor States, Amsterdam: John Benjamins, 1981, x + 348pp.
P. M. Simons, Conceptus, 17 (1983), 131–134.
J. Shearmur, Free Life, 3/2 (1983), 16–17.
W. Stock, Philosophischer Literaturanzeiger, 37 (1984), 93–96.
R. Cardinal, Explorations in Knowledge, 2 (1985), 68–69.
2. Barry Smith (ed.), Parts and Moments. Studies in Logic and Formal Ontology, Munich: Philosophia, 1982, reprinted 2001, 564pp.
V. Muñoz Delgado, Estudios Filosoficos, (1982) 38, 611–613.
I. Niiniluoto, Zentralblatt für Mathematik, (1983) 489, 15–16.
D. P. Henry, History and Philosophy of Logic, (1983) 4, 228–229.
F. G. Asenjo, Rivista Latinoamericana de Filosofía, (1983) 9, 174–177.
U. Charpa, “Neues zur Lehre von den Ganzen und Teilen”, Philosophische Rundschau, 1/2 (1984), 52–59.
J.M. Salanskis, “Parties, Moments et Modalités”, Critique, 443 (1984), 290–296.
R. Sokolowski, Review of Metaphysics, 38 (1984), 140–142.
B. Schuwey, Philosophy and Phenomenological Research, 45 (1985), 474–476.
G. Berger, Noûs, (1986) 20, 115–121.
J. Wolenski, “Czeski i momenty”, Studia Filozoficzne, 1–2/242–243 (1986), 191–195.
D. Münch, Philosophischer Literaturanzeiger, 39 (1986), 272–276.
R. Casati, “Laboratorio husserliano”, Fenomenologia e scienze dell’uomo, 2/1 (1986), 283–287.
R. Tragesser, Husserl Studies, 5 (1988), 169–173.
N. Hentschel, Zeitschrift für Ganzheitsforschung, 32 (1988), 137–139.
G. Schenk, Wissenschaftliche Zeitschrift der Universität Halle, 39 (1990), 116–118.
3. Wolfgang Grassl and Barry Smith (eds.), Austrian Economics: Historical and Philosophical Background, New York: New York University Press, London/Sydney: Croom Helm, 1986, x + 250pp. Reprint, London: Routledge, 2010.
A. W. Dnes, Scottish Journal of Political Economy, 33 (1986), 391–395.
B. J. Loasby, Economic Journal, 96 (1986), 1165–1166.
R. Ebeling, “The Roots of Austrian Economics”, Market Process, 5 (1987), 20–22, repr. in S. C. Littlechild, ed., Austrian Economics, vol. 1, Aldershot/Brookfield VT: Edward Elgar, 38–40.
J. Walker, Journal of Economic Studies, 14 (1987), 67–68.
J. A. Tucker, Austrian Economics Newsletter, (Fall 1988), 10–11.
4. Barry Smith (ed.), Foundations of Gestalt Theory, Munich and Vienna: Philosophia, 1988, 495pp.
J. Schulte, Lingua e Stile, 23 (1988).
V. Fano, “Gestalt e genesi precategoriale”, Annali, 9 (1988), 165–181.
J. L. Gardies, Revue philosophique de la France et de l’Etranger, 179 (1989), 119.
V. MuZoz-Delgado, Estudios, 46 (1990), 134–135.
C. G. Allesch, Conceptus 24 (1990), 106–107.
C. Porebski, Philosophischer Literaturanzeiger, 43 (1990), 176–178.
D. Münch, History and Philosophy of Logic, 11 (1990), 238–240.
C. G. Allesch, Zeitschrift für klinische Psychopathologie und Psychotherapie, 37 (1989), 476–477.
J. M. Salanskis, “Le concept de Gestalt et la situation contemporaine de la philosophie des sciences”, Les Etudes philosophiques, 4 (1990), 519–536.
J. Wolenski, Ruch Filozoficzny, 17 (1990), 162–164.
E. and J. Dölling, Deutsche Literaturzeitung, 112 (1991), 189–192.
5. J. C. Nyíri and Barry Smith (eds.), Practical Knowledge: Outlines of a Theory of Traditions and Skills, London/Sydney/New York: Croom Helm, 1988, ix + 213pp.
T. Whittock, British Journal of Aesthetics, 29 (1989), 191–192.
F. Adams, Canadian Philosophical Reviews, 9, (1989), 283–285.
J. M. Heaton, Journal of the British Society for Phenomenology, 21 (1990), 299–300.
R. T. Allen, Tradition and Discovery, 17 (1990/91), 36–38.
6. Adolf Reinach, Sämtliche Werke. Kritische Ausgabe mit Kommentar, Band I: Die Werke, Teil I: Kritische Neuausgabe (1905–1914), Teil II: Nachgelassene Texte (1906–1917); Band II: Kommentar und Textkritik, Munich/Hamden/Vienna: Philosophia, 1989, critical edition with commentary by Karl Schuhmann and Barry Smith, 2 vols., xx + 848pp.
U. H. D., Bibliographie de la Philosophie, 36 (1989), 147.
M. Crespo, Diálogo Filosófico, 6 (1990), 274.
J. Seifert, Prima Philosophia, 3 (1990), 408–415.
B. Waldenfels, Philosophische Rundschau, 37 (1990), 348.
J. Machnacz, Zycie katolickie, (1990), 147–150.
V. Munoz Delgado, Estudios, 46 (1990), 161–162.
J. Seifert, Philosophischer Literaturanzeiger, 44 (1991), 24–29.
N. Duxbury, “Apriori Philosophy and Legal Ontology”, Archiv für Rechts- und Sozialphilosophie, 77 (1991), 262–266.
P. Gorner, Journal of the British Society for Phenomenology, 25(3), (1994), 309-311.
7. Hans Burkhardt and Barry Smith (eds.), Handbook of Metaphysics and Ontology, 2 vols., Munich/Philadelphia/Vienna: Philosophia, 1991, reprinted 2001, xxv + 1,005pp.
J. M. Perreault, Choice, (April 1992), 38–39.
A. C. Grayling, Times Literary Supplement, (17 April 1992), 26.
S. Scharnagl, Bayernkurier, (24 October 1992).
Guillermo Hurtado, Tópicos, vol. II, núm. 3, (1992).
O. R. Scholz, Frankfurter Allgemeine Zeitung, (15 September 1992).
Roberto Poli, History and Philosophy of Logic, 24 (1992), 258–260.
James DuBois, Review of Metaphysics, 47 (1993), 391–392.
Roberto Poli, Axiomathes, 1 (1993), 140–142.
John Haldane, Philosophical Quarterly, 43 (1993), 130.
Michele Marsonet, Epistemologia, 16 (1993), 345–347.
M. Moors, Tijdschrift voor Filosofie, 56 (1994), 161–162.
Fran Mau, Philosophischer Literaturanzeiger, 47 (1994), 54–56.
Timothy Joseph Day, Minds and Machines, 5 (1995), 131–134.
Stanley Paulson, Philosophical Books, 44: 2 (2003), 135–153.
8. Barry Smith (ed.), Philosophy and Political Change in Eastern Europe (The Monist Library of Philosophy), La Salle: The Hegeler Institute, 1993, vi + 192pp.
D. Cross, Small Press, (Winter 1994/95).
A. R. Brunello, Choice, (December 1994).
Nebojsa Kujundzic, Dialogue, 36 (1997), 648–650.
T. Sunic, CLIO, 24 (1995), 440–443.
9. Barry Smith, Austrian Philosophy: The Legacy of Franz Brentano, La Salle and Chicago: Open Court, 1994, xiii + 381pp. Paperback edition: 1996.
Terry Skeats, Library Journal, 119 (1 September 1994), 185.
J. Barker, Choice, 32 (March 1995), 1136.
Ulf Höfer, Nachrichten. Forschungsstelle und Dokumentationszentrum für Österreichische Philosophie, 6 (1995), 55–58.
Kurt R. Fischer, Vienna Circle Institute Yearbook, 3 (1995), 303–304.
S. Gandon, “La philosophie autrichienne”, Critique, 51 (October 1995), 794–796.
David Gordon, “Why the Austrian School is Austrian”, The Mises Review, 1:4 (1995), 18–21.
Winfried Löffler, Kontroversen in der Philosophie, 8 (1995), 99–107.
Susan Krantz, Brentano Studien, 6 (1995/96), 325-327.
Richard Beach, Canadian Philosophical Reviews, 16 (1996), 62–64.
Werner Diederich and Eva Picardi, Erkenntnis, 45 (1996), 123–127.
Francis Dunlop, Journal of the British Society for Phenomenology, 27 (1996), 330–332.
Sonja Rinofner-Kreidl, Grazer Philosophische Studien, 52 (1996/97), 191–220.
Robin D. Rollinger, Journal of the History of Philosophy, 35 (1997), 314–315.
Kelley, L. Ross, The Proceedings of the Friesian School, 4 (1998).
Pierre Keller, Modern Austrian Literature, 29 (1996), 180–184.
Gisela Kubon-Gilke, Gestalt Theory (1996), 157–158.
Johannes Brandl, Philosophy and Phenomenological Research, 57 (1997), 697–702.
Manuel Durand-Barthez, Revue de Metaphysique et de Morale (1999), 3, 427-428.
10. Barry Smith (ed.), European Philosophy and the American Academy (The Monist Library of Philosophy), La Salle: The Hegeler Institute, 1994, viii + 226pp.
Barry Gross, Academic Questions, 8 (1995), 88–93.
David C. Jacobs, Teaching Philosophy, 19 (1996), 306–310.
11. Barry Smith and David W. Smith (eds.), The Cambridge Companion to Husserl, Cambridge and New York: Cambridge University Press, 1995, x + 519pp. Reprinted 1996.
Michel Bordeau, “Les nouveaux habits du Professeur Husserl”, Critique, 593 (1996), 893–907.
Brice R. Wachterhauser, Ethics 107 (October 1996), 198.
J. A. Bell, Choice 33 (February 1996), 961.
P. Buckley, Tijdschrift voor Filosofie, 58 (1996), 768–769.
Paul S. MacDonald, Philosophical Writings, 2 (1996), 109-110.
R. P. Buckley, Canadian Philosophical Reviews, 16 (1996), 294–296.
Michael Inwood, International Philosophical Quarterly 36/4 (1996), 490–493.
Paul Gorner, The Philosophical Quarterly, 48 (1998), 419–422.
Wojciech Zelaniec, Brentano Studien, 6 (1997), 334–339.
M. J. Larrabee, Philosophical Review, 106 (1997), 283–286.
Guillermo E. Rosado Haddock, “Edmund Husserl: A Philosopher for all Seasons?” Modern Logic, 7 (1997), 380–395.
Jonathan Barnes, “Just a Swipe at Edmund”, Dialectica, 53: 2 (1999), 151–154.
12. Balázs Mezei and Barry Smith, The Four Phases of Philosophy (Studien zur österreichischen Philosophie), Amsterdam / Atlanta: Rodopi (with appendix: “The Four Phases of Philosophy” by Franz Brentano, translated from the German by Balász Mezei and Barry Smith), 1999, iv + 122pp.
Wolfgang Huemer, Philosophy in Review (Comptes rendus philosophiques), 20 (2000), 206–209.
13. Barry Smith (ed.), Liberal Education in a Knowledge Society, Chicago and La Salle, IL: Open Court, 2002, x + 294 pp.
Ed Brandon, Metapsychology, Jan 19, 2004
14. Barry Smith (ed.), John Searle, Cambridge and New York: Cambridge University Press, 2003, 312 pp.
Rodych, Victor. Philosophy in Review (Comptes rendus philosophiques), 24(5), (2004), 365-367.
Richard De Blacquière-Clarkson, Philosophical Writings, 26 (2004), 75-77.
Briggs, Richard S. Heythrop Journal: A Bimonthly Review of Philosophy and Theology, 46(2), (2005), 270-272.
P. Madigan “John Searle”, Heythrop Journal: Quarterly Review of Philosophy and Theology 47 (2), 2006, 335-337.
15. Aurel Kolnai, On Disgust, Barry Smith and Carolyn Korsmeyer (eds.), Chicago: Open Court, 2003, viii + 120 pp.
Abstract: Kolnai made a breakthrough in the phenomenology of aversion when he showed the "double intentionality" of emotions like fear, focusing on both the object of fear and the subjects' concern for his own well-being, this being one of the ways in which fear differs from disgust. In a surprising yet persuasive move, Kolnai argues that disgust is never related to inorganic or non-biological matter, and that its arousal by moral objects has an underlying similarity with its arousal by organic material: a particular combination of life and death. Kolnai gives an analytic list of various kinds of disgusting objects (which should not be read just before lunch) and shows how disgust relates to the five senses.
Francis Raven, Journal of Aesthetics and Art Criticism, 2004, 62 (4): 408-409.
16. Barry Smith, David Mark and Isaac Ehrlich (eds.), The Mystery of Capital and the Construction of Social Reality, Chicago: Open Court, 2008, xxiv + 360 pp.
Wolfgang Grassl, Journal of Markets and Morality, 11(2), 2008, 343-345.
Maksymilian Del Mar, Dialectica, 63(3), 2009, 365-368
17. Katherine Munn and Barry Smith (eds.), Applied Ontology: An Introduction (free download as e-book), Frankfurt/Lancaster: ontos/Walter de Gruyter, 2008, 342 pp.
Peter Simons, “Ontology Meets Ontologies: Philosophers as Healers”, Metascience, 18(3), 2009, 469-473.
Joshua Gordon, Education for Information, 27(4), 2009, 231-234.
Sanfilippo E. M., Rivista Italiana di Filosofia Analitica Junior, 2:2 (2011), 137-40.
18. Ludger Jansen and Barry Smith (eds.), Biomedizinische Ontologie. Wissen strukturieren für den Informatik-Einsatz (UTB Forum), Zurich: vdf, 2008, 252 pp. As e-book (revised): Zürich: vdf, 2011.
19. Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015, xxiv + 220pp.
Abstract: In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to new disciplinary fields such as biomedical informatics. Applied ontology offers a strategy for organizing scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO) now used by over 100 ontology projects throughout the world, and offers examples of domain ontologies that utilize BFO. The book also describes the Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.
Martin Frické, Journal of the Association for Information Science and Technology, 68, 3, March 2017, 801–804.
1. Roberto Casati, Barry Smith and Graham White (eds.), Philosophy and the Cognitive Sciences, Vienna: Hölder-Pichler-Tempsky 1994, viii + 682pp.
2. Berit Brogaard and Barry Smith (eds.), Rationality and Irrationality, Vienna: öbv&hpt, 2001, 411 pp.
3. Christopher Welty and Barry Smith (eds.), Formal Ontology in Information Systems, New York: ACM Press, 2001, xvi + 348 pp.
4. Pierre Grenon, Christopher Menzel and Barry Smith (eds.), Proceedings of the KI2003 Workshop on Reference Ontologies and Application Ontologies, Hamburg, Germany, September 16, 2003. CEUR Workshop Proceedings 94.
5. Mitsuhiro Okada and Barry Smith, Interdisciplinary Ontology. Proceedings of the First Interdisciplinary Ontology Meeting (Tokyo, Japan, February 26-27, 2008), Tokyo: Keio University Press, 2008.
6. Mitsuhiro Okada and Barry Smith (eds.), Interdisciplinary Ontology. Proceedings of the Second Interdisciplinary Ontology Meeting (Tokyo, Japan, February 28-March 1, 2009), Tokyo: Keio University Press, 2009, iv + 166 pp.
7. Barry Smith (ed.) ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology (Buffalo, NY, July 24-26, 2009). Buffalo: National Center for Ontological Research, 2009.
8. Barry Smith, Riichiro Mizoguchi and Sumio Nakagawa (eds.), Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting (Tokyo, Japan, February 27-28, 2010), Tokyo: Keio University Press, 2010.
9. Mitsuhiro Okada and Barry Smith (eds.), Interdisciplinary Ontology. Proceedings of the Fifth Interdisciplinary Ontology Meeting (Tokyo, Japan, February 23-24, 2012), Tokyo: Keio University Press, 2012, iv + 159 pp.
1. Barry Smith and Richard Scheuermann (eds.), Ontologies for Clinical and Translational Research (Special issue of the Journal of Biomedical Informatics), Amsterdam: Elsevier, 2011, 176 pp.
Abstract: A collection of original papers focusing on the ways in which biomedical ontologies are being used in attempts to break down the barriers between the many different sorts of information relevant to the understanding and treatment of disease, ranging from information deriving from experimental biology and model organism research to clinical trial data and information of the sort contained in electronic health records. The contributions represent both the state of the art and works in progress, and they reveal how far we still have to go if we are to reach the level of domain coverage and semantic consistency sought by those engaged in information-driven clinical and translational research.
2. Stefano Borgo, Riichiro Mizoguchi and Barry Smith (eds.) The Ontology of Functions (Special issue of Applied Ontology), Amsterdam: IOS Press, 6 (2), 2011, 64 pp.
Abstract: This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.
3. Andreas Tolk and Barry Smith (eds.), Command and Control Ontology (Special issue of the International Journal of Intelligent Defence Support Systems), 4 (3), 2011, 98 pp.
Abstract: Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available for integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these.
1. Barry Smith, “The Ontogenesis of Mathematical Objects”, Journal of the British Society for Phenomenology, 6 (1975), 91–101.
Abstract: Mathematical objects are divided into (1) those which are autonomous, i.e., not dependent for their existence upon mathematicians’ conscious acts, and (2) intentional objects, which are so dependent. Platonist philosophy of mathematics argues that all objects belong to group (1), Brouwer’s intuitionism argues that all belong to group (2). Here we attempt to develop a dualist ontology of mathematics (implicit in the work of, e.g., Hilbert), exploiting the theories of Meinong, Husserl and Ingarden on the relations between autonomous and intentional objects. In particular we develop a phenomenology of mathematical works, which has the stratified intentional structure discovered by Ingarden in his study of the literary work.
2. Barry Smith, “Frege and Husserl: The Ontology of Reference”, Journal of the British Society for Phenomenology, 9 (1978), 111–125.
Abstract: Analytic philosophers apply the term ‘object’ both to concreta and to abstracta of certain kinds. The theory of objects which this implies is shown to rest on a dichotomy between object-entities on the one hand and meaning-entities on the other, and it is suggested that the most adequate account of the latter is provided by Husserl’s theory of noemata. A two-story ontology of objects and meanings (concepts, classes) is defended, and Löwenheim’s work on class-representatives is cited as an indication of how the need for higher types may be obviated, even in mathematical contexts. The paper concludes with a sketch of the taxonomy of the object realm which results from the above.
3. Barry Smith, “An Essay in Formal Ontology”, Grazer Philosophische Studien, 6 (1978), 39–62.
Abstract: This paper is both a working introduction to the realist ontological theory put forward by the Polish phenomenologist Roman Ingarden and also a development of Ingarden’s views in the light of current tendencies in analytic philosophical logic. The central theme of the paper is the ontological analysis of states of affairs, and in particular of negative states of affairs, a topic which is of some specific interest in forming a connecting link between the Brentano-Meinong-Husserl tradition to which Ingarden belonged, and the (Frege)-Russell-Wittgenstein tradition which gave rise to modern philosophical logic.
4. Barry Smith, “Law and Eschatology in Wittgenstein’s Early Thought”, Inquiry, 21 (1978), 425–441.
Abstract: The paper investigates the role played by ethical deliberation and ethical judgment in Wittgenstein’s early thought in the light of twentieth-century German legal philosophy. In particular the theories of the phenomenologists Adolf Reinach, Wilhelm Schapp and Gerhart Husserl are singled out, as resting on ontologies which are structurally similar to that of the Tractatus. In each case it is actual and possible Sachverhalte which constitute the prime ontological category. The study of the relationship between the states of affairs depicted, e.g., in the sentences of a legal trial and prior fact-complexes to which these may correspond suggests one possible connecting link between the logical and ontological sections of the Tractatus and the ethical reflections appearing at the end. It is argued that the latter can best be understood in terms of the idea of a “last judgment” (with its associated ethical rewards and punishments) which would relate to the world as a whole as a penal trial relates to individual complexes of facts.
5. Barry Smith, “Ingarden vs. Meinong on the Logic of Fiction”, Philosophy and Phenomenological Research, 16 (1980), 93–105.
Abstract: For Meinong, familiarly, fictional entities are not created, but rather merely discovered (or picked out) from the inexhaustible realm of Aussersein (beyond being and non-being). The phenomenologist Roman Ingarden, in contrast, offers in his Literary Work of Art of 1931 a constructive ontology of fiction, which views fictional objects as entities which are created by the acts of an author (as laws, for example, are created by acts of parliament). We outline the logic of fiction which is implied by Ingarden’s approach, showing how it distinguishes the properties possessed by fictional objects (for instance of having been created by such and such an author in such and such a work) from characteristics (for instance of smoking a pipe, of living in Baker Street) which are merely associated with such objects.
Polish translation as: “Ingarden versus Meinong o logice fikcji”, in Z. Muszynski (ed.), Z badan nad prawda i poznaniem, Lublin: Wydawnictwo UMC-S (1998), 283–296.
6. Barry Smith, “Logic, Form and Matter”, Proceedings of the Aristotelian Society, Supplementary Volume 55 (1981), 47–63.
Abstract: It is argued on the basis of ideas derived from Wittgenstein’s Tractatus and Husserl’s Logical Investigations that the formal comprehends more than the logical. More specifically: that there exist certain formal-ontological constants (part, whole, overlapping, etc.) which do not fall within the province of logic. A two-dimensional directly depicting language is developed for the representation of the constants of formal ontology, and means are provided for the extension of this language to enable the representation of certain materially necessary relations. The paper concludes with a discussion of the relationship between formal logic, formal ontology and mathematics.
7. Barry Smith, “Osztrák és magyar filozófia: Wittgenstein és Pauler logikájáról”, Magyar Filozófiai Szemle (1981), 139–144.
8. Barry Smith and Kevin Mulligan, “Framework for Formal Ontology”, Topoi, 3 (1983), 73–85.
Abstract: We draw on the 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.
9. Barry Smith, “Weininger und Wittgenstein”, in B. F. McGuinness and A. Gargani (eds.), Wittgenstein and Contemporary Philosophy (Teoria, 5), Pisa: ETS (1984), 156–165.
Abstract: The paper 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 lines. The conclusion is drawn, however, that, while in the Notebooks many of Weininger’s views are still accepted, by the time of the Tractatus Wittgenstein has moved to a position in which a thinker like Weininger must be conceived as propounding so much more “ethical nonsense.” Wittgenstein adopts in the Tractatus a wholly new conception of the ethical, a form of logical individualism or quietism.
Romanian translation in Revista de filosofie, 49, (2002), 233-246.
10. Barry Smith, “Acta cum fundamentis in re”, Dialectica, 38 (1984), 157–178.
Abstract: The paper defends a theory of mind according to which certain sorts of acts are ‘real material relations’ and compares this theory to causal theories of reference and perception. All mental acts are dependent for their existence upon the subject (person, organism) whose acts they are. Relational acts are dependent also on intended objects in the world. The relational theory thus implies a rejection of the Cartesian thesis to the effect that we could in principle have exactly the same thoughts even though the objects of these thoughts did not exist. It implies thereby also a rejection of Husserlian phenomenology. Husserl’s earlier work on the formal ontology of part, whole and dependence nevertheless provides a framework which can allow a precise formulation of the relational theory.
11. Barry Smith, “Ten Conditions on a Theory of Speech Acts”, Theoretical Linguistics, 11 (1984), 311–330.
Abstract: It is now generally recognized that figures such as Reid, Peirce, and Reinach formulated theories of speech acts avant la lettre of Austin and Searle, in Reid and Reinach’s cases under the heading ‘theory of social acts’. Here we address the question as to what conditions would have to be satisfied for such theories to count as ‘theories of speech acts’ in the now familiar sense.
12. Kevin Mulligan, Peter M. Simons and Barry Smith, “Truth-Makers”, Philosophy and Phenomenological Research, 44 (1984), 287–321.
Abstract: A realist theory of truth for a class of sentences holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. The authors uphold the mutual independence of logical and ontological complexity. The theory is compared with that of Wittgenstein’s Tractatus, and the authors outline formal principles of truthmaking taking account of both kinds of complexity and suggesting how to overcome Wittgenstein’s problem of negation.
Reprinted in Jean-Maurice Monnoyer, Metaphysics and Truthmakers, Frankfurt/Lancaster/New Brunswik: Ontos, 9-50.
Reprinted in E. J. Lowe and A. Rami (eds.), Truth and Truth-Making, Chesham: Acumen (2009), 59-86.
German translation as: “Wahrmacher”, in L. Bruno Puntel (ed.), Der Wahrheitsbegriff. Neue Explikationsversuche (a collection of readings on modern theories of truth), Darmstadt: Wissenschaftliche Buchgesellschaft (1987), 210–255.
French translation as “Vérifacteurs”, Études de philosophie, no. 9-10, 2008-2011 (published August 2011), translated by B. Langlet and J.-F. Rosecchi, 104-138.
13. Barry Smith, “De la modification du sentiment: l’esthétique de l’Ecole de Graz”, Revue d’Esthétique, 9 (1985), 19–37.
14. Barry Smith, “Ontologische Aspekte der Husserlschen Phänomenologie”, Husserl Studies, 3 (1986), 115–130.
Abstract: A study of the background of Husserl’s early thinking in the perceptual psychology of Carl Stumpf and of the implications of Stumpfian ideas for an understanding of Husserl’s phenomenology. Other topics treated include the ontology of part, whole and dependence; gestalt theory; and Husserl’s notion of the synthetic a priori.
15. Barry Smith, “The Substitution Theory of Art”, Grazer Philosophische Studien, 25/26 (1986), 533–557.
Abstract: 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.
Italian translation as: “La teoria sostituzionale dell’arte”, in E. Pulcini (ed.), Teorie delle passioni (Supplementi di Topoi), 3 (1989), 186–209.
16. Kevin Mulligan and Barry Smith, “A Relational Theory of the Act”, Topoi, 5/2 (1986), 115–130.
Abstract: The paper defends a view of perceptual acts as real relations of a subject to an object. To make this view coherent, a theory of different types of relations is developed, resting on ideas on formal ontology put forward by Husserl in his Logical Investigations and on the theory of relations sketched in Smith’s “Acta cum fundamentis in re”. The theory is applied to the notion of a Cambridge change, which proves to have an unforeseen relevance to our understanding of perception.
17. Kevin Mulligan and Barry Smith, “Husserl’s Logical Investigations”, Grazer Philosophische Studien, 27 (1986), 199–207.
Abstract: The magisterial analyses of logic and meaning advanced in Husserl's Logical Investigations of 1900/01 have for a number of reasons been neglected by analytical philosophers in subsequent decades. This state of affairs has to do, in part, with the history of the editions and translations of Husserl's writings. Findlay's readable but imperfect translation appeared seventy years after the work itself was first published, and the editors and translators and expositors of Husserl's works have reflected the prevailing philosophical atmosphere on the Continent by concentration their energies on Husserl's later writings. Now, however, over eighty years after the appearance of Husserl 's one true masterpiece, a critical edition of the work is at last available in completed form. We here analyze the structure and content of this new edition, published as part of the Husserliana series by the Husserl Archive in Louvain.
18. Kevin Mulligan and Barry Smith, “A Husserlian Theory of Indexicality”, in Grazer Philosophische Studien, 28 (1986), 133–163.
Abstract: It is well known that Husserl’s Logical Investigations contain the beginnings of an account of the meanings of indexical expressions, expressions whose meanings depend essentially on some sort of explicit or implicit pointing or indication [Anzeigen], and therefore on some contribution by the surroundings of speaker and hearer. Husserl in fact speaks explicitly of ‘occasional expressions’, that is of expressions like ‘this’ and ‘that’ whose meanings depend on features of the occasion of use, but it is possible to gauge the full implications of his explicit remarks on the problem of indexical or occasional meanings only if these are read in conjunction with what he says elsewhere in the Investigations, especially on the subject of perceptual judgments and proper names. Moreover, Husserl’s deliberations on indication, perception and naming, as also what he has to say on demonstrative pronouns, spatial and temporal adverbs and tenses, must themselves be understood – like everything else in this work – as applications of a very general theory of meaning and of structure or dependence. In what follows we shall set out Husserl’s account of indexicality and develop it in various ways. Unlike Husserl himself – who retrospectively described his own account as an ‘act of violence’ – we are strongly of the opinion that this effort is worthwhile.
19. Barry Smith, “The Substance of Brentano’s Ontology”, Topoi, 6/1 (1987), 39–49.
Abstract: This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In an appendix, however, Brentano puts forward an even more radical suggestion, inspired by the physics of Kelvin. According to this final view, space itself is an accident of a deeper substance: the present time.
20. Barry Smith, “The Ontology of Epistemology”, Reports on Philosophy, 11 (1987), 57–66.
Abstract: Ingarden’s puzzle is: how can we come to know what is essentially involved in an act of knowing? As starting point he takes what he holds to be a particular good candidate example of such an act, namely an act of perceiving an apple. Here we have act and object standing in a certain first-level relation to each other. We now in a second level act of reflection, make this first-level relation into an object, and strive to apprehend this object as an instantiation of the essence knowledge. But how, on this basis, could we ever establish that we had indeed grasped this essence, and that this is indeed the appropriate essence? Surely, through some third-level act of reflection on this second-level act. We expound from an ontological point of view Ingarden's idea as to how this regress can be avoided.
Polish translation as: “Ontologia epistemologii”, in W. Strozewski and A. Wegrzecki (eds.), W Kregu Filozofii Romana Ingardena, Warsaw/Cracow: PWN, 1995, 111–119.
21. Barry Smith, “Zalai Béla és a tiszta lét Metafizikája”, Magyar Filozófiai Szemle (1987/3), 584–593.
Abstract: Between 1910 und 1915 the Hungarian philosoper Der ungarische Philosoph Béla Zalai (1882-1915) developed his “comparative metaphysics of systems”, which had a significant influence on both the young Georg Lukács and also on Karl Mannheim. Through an analysis of Zalai’s approach to metaphysics, we show how he served to mediate between the realist Austrian philosophy of Meinong and of the early Husserl on the one side, and the German (idealistic, Kantian) philosophy then dominant in Hungary.
German version: “Bela Zalai und die Metaphysik des reinen Seins”, Brentano Studien, 5 (1994), 59–68.
22. Karl Schuhmann and Barry Smith, “Questions: An Essay in Daubertian Phenomenology”, Philosophy and Phenomenological Research, 47 (1987), 353–384.
Abstract: This is a historical study of the logical, psychological and linguistic dimensions of the act of questioning, with special reference to the work of the Munich school of phenomenology and of E. Husserl. The essay is a contribution to recent work on anticipations by the Munich school of the theory of speech acts.
23. Barry Smith, “The Soul and Its Parts: A Study in Aristotle and Brentano”, Brentano–Studien, 1 (1988), 75–88.
Abstract: The piece of wax takes on the form of the seal; but this occurs in a way that is largely indifferent to the particular constitution of the seal. Similarly, Aristotle says, ‘the sense is affected by what is coloured or flavoured or sounding, but it is indifferent as to what in each case the substance is’. We show that Brentano takes this Aristotelian account of the relation between sense and its objects as the basis for his theory of mind in the Psychology from an Empirical Standpoint.
24. Barry Smith, “The Primacy of Place: An Investigation in Brentanian Ontology”, Topoi, 8 (1989), 43–51.
Abstract: In his later writings Brentano defended a peculiar doctrine to the effect that the substances of the material world are three-dimensional places. The paper presents the psychological origins of this view and shows how the issue as to the nature of substance can throw light not only on Brentanian and Aristotelian ontology but also on a spectrum of views ranging from Quine, Kotarbinski and Lesniewski to Twardowski and Meinong.
25. Barry Smith, “Logic and the Sachverhalt”, The Monist, 72 (1989), 52–69.
Abstract: Logic is often conceived as a science of propositions, or of relations between propositions. There is an alternative view, however, defended by Meinong, Pfänder, Reinach and others, which sees logic as a science of “Sachverhalte” or states of affairs. A consideration of this view, which was defended especially by thinkers within the tradition of Brentano, throws new light on the problems of intentionality and of mental content. It throws light also on the development of logic in Poland. Here the influence of Brentano’s student Kasimir Twardowski is especially important, and the paper concludes with a new interpretation of Tarski’s work on truth against the background of Twardowski’s thinking.
Revised version in: L. Albertazzi, M. Libardi and R. Poli (eds.), The School of Franz Brentano, Dordrecht/Boston/Lancaster: Kluwer (1996), 323–341.
Italian translation as: “Dalla psicologia del giudizio all’ontologia dello stato di cose” in Discipline Filosofiche, 7: 2 (1997), 7–28.
26. Barry Smith, “On the Origins of Analytic Philosophy”, Grazer Philosophische Studien, 35 (1989), 153–173.
Abstract: 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 newly fashionable habit of referring to analytic philosophy as ‘Anglo-American’ leads to a ‘grave historical distortion’. If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy ‘could at least as well be called "Anglo-Austrian"’ (p. 7). We here show the implications of this assertion for a more adequate understanding of the relations between analytic and Continental philosophy.
27. Barry Smith, “Aristotle, Menger, Mises: An Essay in the Metaphysics of Economics”, History of Political Economy, Annual Supplement to vol. 22 (1990), published simultaneously as B. Caldwell (ed.), Carl Menger and His Economic Legacy, Durham and London: Duke University Press, 1990), 263–288.
Abstract: 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. I argue tha the historical situation in which Menger found himself points to the inevitability of the Aristotelian reading and that this reading fits also very naturally to the text of Menger's works. At the same time I will explain why the diversity of interpretations is not, however, entirely surprising. Menger broke new ground in economic theory in part by fashioning new linguistic instruments not easily open to unambiguous interpretation.
Reprinted in: E. Younkins (ed.), Philosophers of Capitalism: Menger, Mises, Rand, and Beyond, New York: Lexington Books, 2005, 199-222.
28. Karl Schuhmann and Barry Smith, “Elements of Speech Act Theory in the Work of Thomas Reid”, History of Philosophy Quarterly, 7 (1990), 47–66.
Abstract: Historical research has recently made it clear that, prior to Austin and Searle, the phenomenologist Adolf Reinach (1884-1917) developed a full-fledged theory of speech acts under the heading of what he called "social acts". He we consider a second instance of a speech act theory avant la lettre, which is to be found in the common sense philosophy of Thomas Reid (1710-1796). Reid’s s work, in contrast to that of Reinach, lacks both a unified approach and the detailed analyses of pertinent examples. But his writings leave no doubt that he is acutely aware of the very problems concerning language structure and use out of which contemporary speech act theory has evolved and that he goes a good way towards solving these problems in the spirit of the modern theory.
29. Barry Smith, “Textual Deference”, American Philosophical Quarterly, 28 (1991), 1–13.
Abstract: Works of philosophy written in English have spawned a massive secondary literature dealing with ideas, problems or arguments. 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, but also in relation to more recent German-language philosophy. Yet 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 peculiar asymmetry by examining those factors which might be conducive to the growth of a commentary literature in a given culture.
Danish translation as: “Textlig Œrbødighed”, Kritik, 116 (1995), 89–99.
Russian translation as: “???????? ????????”, Logos 5 (2000), 124–139.
30. Barry Smith, “German Philosophy: Language and Style”, Topoi, 10 (1991), 155–161.
Abstract: The paper addresses the apparent asymmetry as between German and English philosophical texts, turning on the fact that translations from the former into the latter language are typically much more easily obtained than in the reverse direction. A range of factors are shown to be involved, both stylistic and sociological. Most important, however, is a difference in the conception of what philosophy is in the two cultures.
31. Barry Smith, “La verità trionfa: Da T. G. Masaryk a Jan Patocka”, Discipline Filosofiche, 2 (1991), 207–227.
Abstract: Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.
German version as: “Von T. G. Masaryk bis Jan Patocka. Eine philosophische Skizze”, in J. Zumr and T. Binder (eds.), T. G. Masaryk und die Brentano-Schule, Graz/Prague: Czech Academy of Sciences (1993), 94–110.
32. Karl Schuhmann and Barry Smith, “Neo-Kantianism and Phenomenology: The Case of Emil Lask and Johannes Daubert”, Kant-Studien, 82 (1991), 303–318.
Abstract: Johannes Daubert he was an acknowledged leader, and in some respects the founder, of the early phenomenological movement, and was considered – as much by its members as by Husserl himself – the most brilliant member of the group. In Daubert’s unpublished writings we find a series of reflections on Lask, and on Neo-Kantianism, which form the subject-matter of this paper. They range over topics such as the ontology of the ‘Sachverhalt’ or state of affairs, truthvalues (Wahrheitswerte) and the value of truth, negative judgments and the copula, and the relation between perception and judgment.
33. Barry Smith, “Zum Wesen des Common Sense: Aristoteles und die naive Physik”, Zeitschrift für philosophische Forschung, 46 (1992), 508–525.
Abstract: The paper relates classical treatments of physics and metaphysics to contemporary work on common sense in the field of artificial intelligence (J. Hobbs, P. Hayes, et al.). It defends the universality (and truth) of certain basic principles of common-sense physics and shows why these basic principles must leave certain issues undetermined.
Revised version as: “Räumliche Entitäten: Örter, Löcher, Grenzen“, in L. Jansen and B. Smith (eds.), Die biomedizinische Ontologie. Philosophie – Lebenswissenschaften – Informationstechnik (UTB Forum), Zurich: vdf, 2008, 113-126.
34. Barry Smith, “The Soul and Its Parts, II: Varieties of Inexistence”, Brentano-Studien, 4 (1992/93), 35–51.
Abstract: From the point of view of Brentano’s philosophy, contemporary philosophy of mind presupposes an over-crude theory of the internal structures of mental acts and states and of the corresponding types of parts, unity and dependence. We here describe Brentano’s own account of the part-whole structures obtaining in the mental sphere, and show how it opens up new possibilities for mereological investigation. One feature of Brentano’s view is that the objects of experience are themselves parts of mind, so that there is a sense in which for him (as e.g. for Leibniz) ontology is a proper part of rational or descriptive psychology.
Romanian translation in: Revista de Filosofie, 49(3-4), (2002), 233-246.
35. Barry Smith, “Putting the World Back into Semantics”, Grazer Philosophische Studien, 44 (1993), 91–109.
Abstract: To what in reality do true logically simple sentences with empirical content correspond? Two extreme positions can be distinguished in this regard: ‘Great Fact’ theories, such as are defended by Davidson; and trope-theories, which see such sentences being made true simply by those events or states to which the relevant main verbs correspond. A position midway between these two extremes is defended, one according to which sentences of the given sort are made true by what are called ‘dependence structures’, or in other words by certain complex concrete portions of reality between the parts of which relations of dependence are defined. Principles governing such dependence-structures are laid down, principles of an ontologically motivated sort which serve as basis for a “topological semantics” conceived as an alternative to standard set-theoretic approaches to semantics of the Tarskian sort. These principles are then used to resolve certain puzzles generated by the (semantically motivated) theory of events put forward by Davidson.
Reprinted in Peer F. Bundgaard and Frederik Stjernfelt (eds.), Semiotics (Critical Concepts in Linguistics Series), London: Routledge (2010).
Russian translation in: Ophyr, n.d.
36. Barry Smith, “An Essay on Material Necessity”, P. Hanson and B. Hunter (eds.), Return of the A Priori (Canadian Journal of Philosophy, Supplementary Volume 18), (1993), 301–322.
Abstract: 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.
37. Karl Schuhmann and Barry Smith, “Two Idealisms: Lask and Husserl”, Kant-Studien, 83 (1993), 448–466.
Abstract: Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else.
Polish translation as: “Dwa oblicza idealizmu: Lask a Husserl”, in A. J. Norasa and D. Kuboka (eds.), Miedzy kantyzmem a neokantyzmem, Katowice: Wydawnictwo Uniwersyteto Slaskiego (2002), 130–156.
38. Barry Smith and Roberto Casati, “Naive Physics: An Essay in Ontology”, Philosophical Psychology, 7/2 (1994), 225–244.
Abstract: 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 from a knowledge of these historical roots of their discipline, which are shown to imply above all a critique of the set-theory-based models of reality typically presupposed by contemporary work in common-sense ontology.
French version: “La physique naïve: un essai d’ontologie”, Intellectica, 17 (1993), 173–197.
39. Barry Smith, “Zur Kognition räumlicher Grenzen: Eine mereotopologische Untersuchung”, Kognitionswissenschaft, 4 (1995), 177–184.
Abstract: The perception of spatial bodies is at least in part a perception of bodily boundaries or surfaces. The usual mathematical conception of boundaries as abstract constructions is, however, of little use for cognitive science purposes. The essay therefore seeks a more adequate conception of the ontology of boundaries building on ideas in Aristotle and Brentano on what we may call the coincidence of boundaries. It presents a formal theory of boundaries and of the continua to which they belong, of a sort which allows a resolution of certain Zeno-style paradoxes. The theory proves to be applicable not only in the cognitive science field but also in regard to problems relating to the ontology of geographical and geopolitical boundaries.
40. Barry Smith, “Formal Ontology, Common Sense, and Cognitive Science”, International Journal of Human-Computer Studies, 43 (1995), 641–667.
Abstract: Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences.
Condensed version in: AI*IA Notizie. Periodico dell’Associazione Italiana per l’Intelligenze Artificiale, 7 (1994), 11–18.
Italian translation as: “L’ontologia del senso commune”, in E. Agazzi (ed.), Valore e Limiti del Senso Comune, Milan: FrancoAngeli (2004), 261–284.
41. Barry Smith, “More Things in Heaven and Earth”, Grazer Philosophische Studien, 50 (1995), 187–201.
Abstract: Philosophers in the field of analytic metaphysics have begun gradually to come to terms with the fact that there are entities in a range of categories not dreamt of in the set-theory and predicate-logic-based ontologies of their forefathers. Examples of such “entia minora” would include: boundaries, places, events, states holes, shadows, individual colour- and tone-instances (tropes), together with combinations of these and associated simple and complex universal species or essences, states of affairs, judgment-contents, and myriad abstract structures of the sorts which are studied by the mathematical sciences. How, as hunter-gatherer ontologists, are we to bring order into this vast array? How are we to gauge the ontological merits of given candidate entities, and how are we to understand their relation to entities of more humdrum sorts? Meinong, it turns out, offers a very simple answer to all of these questions.
42. Barry Smith, “The Structures of the Commonsense World”, Acta Philosophica Fennica, 58 (1995), 290–317.
Abstract: The paper seeks to show how the world of everyday human cognition might be treated as an object of ontological investigation in its own right. The paper is influenced by work on affordances and prototypicality of psychologists such as Gibson and Rosch, by work on cognitive universals of the anthropologist Robin Horton, and by work of Patrick Hayes and others on ‘naive’ or ‘qualitative physics’. It defends a thesis to the effect that there is, at the heart of common sense, a theoretical core of true propositions pertaining to mesoscopic objects, and that the latter are to be understood as relating mereologically to the objects studied by physical science.
Preprinted in: S. Poggi (ed.), Gestalt Psychology. Its Origins, Foundations and Influence, Florence: Olschky (1994), 209–232.
Italian translation as: “Le strutture del mondo del senso commune”, in Iride (Florence), 9 (1992), 22–44. Partially reprinted as “Ontologia ecologia” in M. Ferraris (ed.), Ontologia, Naples: Guida (2003), 146–151.
German translation as: “Die Struktur der Common-Sense Welt”, Logos, N. F. 1 (1994), 422–449.
43. Barry Smith, “Mereotopology: A Theory of Parts and Boundaries”, Data and Knowledge Engineering, 20 (1996), 287–303.
Abstract: The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One central goal of the paper is to provide a rigorous formulation of Brentano’s thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering.
44. Barry Smith, “On Substances, Accidents and Universals: In Defence of a Constituent Ontology”, Philosophical Papers, 26 (1997), 105–127.
Abstract: The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake.
45. Barry Smith, “Ontologie des Mesokosmos: Soziale Objekte und Umwelten”, Zeitschrift für philosophische Forschung, 52 (1998), 521–540.
Abstract: Erst in neuester Zeit haben sich analytische Philosophen vorbehaltlos dem Bereich der Metaphysik gewidmet. Unter den interessantesten Ergebnissen dieser ,analytischen Metaphysik' ist John Searles neues Buch zur Ontologie der sozialen Gegenstände (Die Konstruktion der gesellschaftlichen Wirklichkeit. Zur Ontologie sozialer Tatsachen, Hamburg: Rowohlt, 1997). Was sind Staaten, Gemeinschaften, Gesetze? Nach Searle sind diese Gegenstände Korrelate einer ,kollektiven Intentionalität'. Searle vertritt m.a.W. eine kognitive Theorie von sozialen Gegenständen. Ein Problem bei einer solchen Theorie ist, daß wir Analogien zu bestimmten sozialen Gebilden auch bei Tieren begegnen, die den begrifflichen Apparat einer kollektiven Intentionalität nicht besitzen. Um dieses Problem zu umgehen, liegt es nahe, die biologischen Lehren von tierischen Umwelten, die etwa durch von Uexküll entwickelt wurden, auszunutzen. Von Uexkülls Umweltlehre ist jedoch eine Art organische Monadologie: jedes Tier, jeder Mensch, ist in seiner eigenen spezifischen Umwelt beheimatet, und es wird also schwer verständlich, wie das Verhalten zwischen Tieren überhaupt möglich ist. Der vorliegende Beitrag bietet eine Lösung dieses Problems, durch die wir auch eine verbesserte Auffassung der Ontologie sozialer Gegenstände überhaupt gewinnen. Als Grundlage dieser Auffassung dient die realistische Theorie menschlicher Umwelten, die in der ökologischen Psychologie J. J. Gibsons und Roger Barkers entwickelt wurde.
46. Barry Smith, “Boundaries: A Brentanian Theory”, Brentano-Studien 8 (1998/99), 107–114.
Abstract: We outline Brentano’s theory of boundaries, for instance between two neighboring subregions within a larger region of space. Does every such pair of regions contain points in common where they meet? Or is the boundary at which they meet somehow pointless? On Brentano’s view, two subregions such do not overlap; rather, along the line where they meet there are two sets of points which are not identical but rather spatially coincident. We outline Brentano’s theory of coincidence, and show how he uses it to resolve a number of Zeno-like paradoxes.
Revised version as: “Zeno’s Paradox for Colors”, in Robert Dostal, Lester Embree, Joseph J. Kockelmans, J. N. Mohanty, and Olav K. Wiegand (eds.), Phenomenology of German Idealism, Hermeneutics, and Logic, Dordrecht: Kluwer (2000), 201–207.
47. Barry Smith, “Truthmaker Realism”, Australasian Journal of Philosophy, 77 (3) (1999), 274–291.
Abstract: We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments.
48. Barry Smith and Achille Varzi, “The Niche”, Nous, 33:2 (1999), 198–222.
Abstract: The categories of object and attribute, substance and accident, continuant and occurrent, have long enjoyed a dominant position in the history of metaphysics. The concept of niche (environment, setting, habitat), on the other hand, has been almost entirely neglected, in spite of the wide application of this and similar concepts in a variety of disciplines, from evolutionary biology to context based semantics. The paper presents a theory of the niche, a theory of objects in their settings. It defends a view of niches as special sorts of parts of reality and builds upon existing work exploiting the resources of mereology (or the theory of part and whole) as an instrument of realist ontology. The theory will be illustrated above all by means of simple biological examples, but the concept of niche should be understood as being, like concepts such as part, boundary and location, a formal concept, one that is applicable in principle to a wide range of different domains.
Extended abstract published as: “Mereology, Topology, Ecology: A Formal Theory of Organism-Niche Relations”, in J. Cachro and K. Kijania-Placek (eds.), 11th International Congress of Logic, Methodology and Philosophy of Science. Volume of Abstracts, Cracow: Jagiellonian University (1999), p. 351.
Polish translation as: “Nisza,” Filozofia Nauki, 8: 3/4 (2000), 5–30.
49. Barry Smith and David Mark, “Ontology with Human Subjects Testing: An Empirical Investigation of Geographic Categories”, American Journal of Economics and Sociology, 58: 2 (April 1999), 245–272.
Abstract: Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories.
50. Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.
Abstract: We argue that the basic typology of spatial boundaries involves an opposition between bona fide (or physical) boundaries on the one hand, and fiat boundaries on the other, the latter being exemplified especially by boundaries induced through human demarcation, for example in the geographic realm. The classical metaphysical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology.
Revised version of Barry Smith and Achille Varzi, “The Formal Ontology of Boundaries”, Electronic Journal of Analytic Philosophy, 5: 5 (1997).
Russian translation in: Ophyr, n.d.
51. Barry Smith, “Les objets sociaux,” Philosophiques, 26/2 (1999), 315–347.
Abstract: One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psychological environments of cognitive subjects and the different sorts of external (physical, geographical, social) environments which they inhabit. The present essay addresses this environmental version of the problem of intentionality. It draws not only on the work of Husserl and Scheler but also on the Gestalt psychological writings of Kurt Koffka and Kurt Lewin. It considers the influential subjective idealist theory of animal environments put forward by J. von Uexküll and contrasts this with a realist theory of organism-environment interaction based on the work of the ecological psychologists J. J. Gibson and Roger Barker. This realist theory is then exploited as a basis for an ontology of social objects of a range of different sorts.
52. Werner Ceusters, Ignace Desimpel, Barry Smith and Stefan Schulz, “Using Cross-Lingual Information to Cope with Underspecification in Formal Ontologies”, Studies in Health Technology and Informatics, 95 (2003), 391–396.
Abstract: Description logics and other formal devices are frequently used as means for preventing or detecting mistakes in ontologies. Some of these devices are also capable of inferring the existence of inter-concept relationships that have not been explicitly entered into an ontology. A prerequisite, however, is that this information can be derived from those formal definitions of concepts and relationships which are included within the ontology. In this paper, we present a novel algorithm that is able to suggest relationships among existing concepts in a formal ontology that are not derivable from such formal definitions. The algorithm exploits cross-lingual information that is implicitly present in the collection of terms used in various languages to denote the concepts and relationships at issue. By using a specific experimental design, we are able to quantify the impact of cross-lingual information in coping with underspecification in formal ontologies.
53. Barry Smith and John Searle, “The Construction of Social Reality: An Exchange”, American Journal of Economics and Sociology, 62: 2 (2003), 285-309.
Abstract: Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a banks computers, however, the formula fails, because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account.
Reprinted in Laurence S. Moss and David Koepsell (eds.), John Searle's Ideas about Social Reality: Extensions, Criticisms, and Reconstructions, Oxford: Wiley-Blackwell (2003).
French translation as: “L’ontologie de la realité sociale”, in P. Livet and R. Ogien (eds.), L’Enquête ontologique, du mode de l'existence des objets sociaux, Paris: Editions EHESS (2000), 185–208.
54. Barry Smith, “Philosophie, Politik und wissenschaftliche Weltauffassung: Zur Frage der Philosophie in Österreich und Deutschland”, Grazer Philosophische Studien 58/59 (2000), 241–262.
Abstract: One of the most remarkable philosophical phenomena of the last 20 years is the rise of so-called ‘Continental Philosophy’ (C.P.), a creation above all of the North American university. Lectures under the heading of ‘Continental Philosophy’ are offered every year in Anglo-Saxon universities to many thousands of philosophy students, a practice which appears questionable not least for the reason that the lectures in question deal not with philosophy in Continental Europe as a whole, but rather only with a certain narrow segment of Franco-German philosophy, in which Heidegger seems to serve as the sole fixed point. Around him are assembled a progression of Paris-based thinkers expounding progressively more nonsensical claims concerning the ‘end’ of philosophy (or of the ‘modern’, of ‘the author’, of ‘man’, of ‘identity’, and so forth). In all of this the later Husserl is sometimes taken into account as C.P.-precursor, his teacher Franz Brentano however not at all. Other prominent German philosophers of the 20th century such as Ernst Cassirer or Nicolai Hartmann are likewise totally ignored, and so also are French philosophers in the tradition of Poincaré, Bergson or Gilson, as well as Polish, Scandinavian or Czech philosophers. The essay offers an explanation of these peculiar facts, which has to do with the different roles of politics and science in the different parts of Europe.
Abstract: Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality.
56. Barry Smith and Berit Brogaard, “Living High and Letting Die”, Philosophy, 76 (2001), 435–442 (published under the pseudonym Nicola Bourbaki).
Abstract: You wake up one morning in a hospital operating theater and learn that a glitch in the hospital’s computer has brought it about that a tiny radio has been attached to your stomach. The radio is transmitting to an unconscious violinist who has been found to have a rare and fatal kidney ailment in virtue of which his brain is no longer able to send signals to his kidneys. If you remove the radio, the violinist will die. But never mind, it is only for nine months. By then he will have recovered from his ailment, and the radio can safely be removed. Are you morally obliged to agree to this situation?
57. Barry Smith and David M. Mark, “Geographical Categories: An Ontological Investigation”, International Journal of Geographical Information Science, 15: 7 (2001), 591–612.
Abstract: This paper reports the results of a series of experiments designed to establish how non-expert subjects conceptualize geospatial phenomena. Subjects were asked to give examples of geographical categories in response to a series of differently phrased elicitations. The results yield an ontology of geographical categories—a catalogue of the prime geospatial concepts and categories shared in common by human subjects independently of their exposure to scientific geography. When combined with nouns such as feature and object, the adjective geographic elicited almost exclusively elements of the physical environment of geographical scale or size, such as mountain, lake and river. The phrase things that could be portrayed on a map, on the other hand, produced many geographical scale artefacts (roads, cities, etc.) and fiat objects (states, countries, etc.), as well as some physical feature types. These data reveal considerable mismatch as between the meanings assigned to the terms ‘geography’ and ‘geographic’ by scientific geographers and by ordinary subjects, so that scientific geographers are not in fact studying geographical phenomena as such phenomena are conceptualized by naive subjects. The data suggest, rather, a special role in determining the subject-matter of scientific geography for the concept of what can be portrayed on a map. This work has implications for work on usability and interoperability in geographical information science, and it throws light also on subtle and hitherto unexplored ways in which ontological terms such as ‘object’, ‘entity’ and ‘feature’ interact with geographical concepts.
Reprinted in: Peter Fisher (ed.), Classics from the International Journal of Geographical Information Science, London: Taylor and Francis, 2006, 481–506.
58. Barry Smith, “Fiat Objects”, Topoi, 20: 2 (September 2001), 131–148.
Abstract: Extended entities have boundaries of two different sorts: those that do, and those that do not correspond to physical discontinuities. Call the first sort (coastlines, the surface of your nose) bona fide boundaries; and the second (the boundary of Montana, the boundary separating your upper from your lower torso) fiat boundaries. Fiat boundaries are found especially in the geographic realm, but are involved wherever language carves out portions of reality in ways which do not reflect physical discontinuities. These ideas are applied to the treatment of cognitive categorization, of the semantics of vagueness, of Quine’s indeterminacy thesis, and of standard ontological problems such as Tibbles’ tail.
Italian translation as: “Oggetti Fiat”, Rivista di Estetica, 20/2 (2002), 58–87.
59. Barry Smith and Leonardo Zaibert, “The Metaphysics of Real Estate”, Topoi, 20: 2 (September 2001), 161–172.
Abstract: The parceling of land into real estate is more than a simple geometrical affair. Real estate is a historical product of interaction between human beings, political, legal and economic institutions, and the physical environment. And while many authors, from Jeremy Bentham to Hernando de Soto, have drawn attention to the ontological (metaphysical) aspect of property in general, no comprehensive analysis of landed property has been attempted. The paper presents such an analysis and shows how landed property differs from other types of property in a way which implies a special role for political and economic philosophy of property rights in land.
60. Barry Smith, “Husserlian Ecology” (in Japanese), Human Ontology (Kyoto), 7 (2001), 9–24.
Abstract: While Husserl sought to find room in his later writings for the surrounding world of human practical experience, and while similar efforts were made also by later phenomenologists such as Heidegger, and Sartre, and Merleau-Ponty, in none of these authors do we find sustained attempts to grapple with the interactions between the world of human thought, feeling and action on the one hand and the surrounding environment as this is described by physics and biology on the other. Some attempts were made in this regard by Gestalt psychologists such as Wertheimer, Köhler, Koffka, and Lewin, and Koffka and Lewin in their turn influenced two American psychologists J. J. Gibson and Roger Barker, both of whom (independently) conceived their work under the banner of ‘ecological psychology.’ It is against this background that the term 'Husserlian ecology' is to be understood in what follows.
Japanese translation, 25-41.
61. Barry Smith, “Truthmaker Realism: Response to Gregory”, Australasian Journal of Philosophy, 80 (2) (2002), 231–234.
Abstract: Standard definitions of the truthmaker relation in terms of necessitation fail. This is because there exist malignant necessitators (every contingent object is a malignant necessitator for every necessary truth). In my "Truthmaker Realism" (Australasian Journal of Philosophy, 77, 1999) I show that these standard definitions can be repaired by adding a second factor, in some ways the dual of necessitation, which I call ‘projection’. Projection imposes on the relation between truths and truthmakers the additional requirement of relevance or aboutness. In his "Smith on Truthmakers" (Australasian Journal of Philosophy, 79, 2001), Dominic Gregory attempts to show that this attempt to prune the abundance of malignant necessitators fails. His argument reveals the existence of some unclarities in the prose commentary to the formal theory of my original paper. Here, however, I show that it does not undermine this formal theory itself.
62. Barry Smith and Achille Varzi, “Surrounding Space: The Ontology of Organism-Environment Relations”, Theory in Biosciences, 121 (2002), 139–162.
Abstract: The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types—for example in genotypes, phenotypes and environment types—and in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes.
63. Barry Smith and Berit Brogaard, “Quantum Mereotopology”, Annals of Mathematics and Artificial Intelligence, 35/1–2 (2002), 153–175.
Abstract: Mereotopology is an extension of mereology (the formal theory of part-whole relations) which includes also relations of boundary, countinuity and contact. Mereotopology faces problems when its methods are applied to objects which lose and gain parts yet preserve their identities over time. We offer a new solution to these problems, based on a theory of partitions of reality of finite grain. This theory is extended to a theory of coarse- and fine-grained histories (or finite sequences of partitions evolving over time), drawing on machinery developed within the framework of the so-called ‘consistent histories’ interpretation of quantum mechanics.
Shorter version in: Spatial and Temporal Granularity. Papers from the AAAI Workshop (AAAI Technical Report WS-00-08), Menlo Park: AAAI Press (2000), 25–31.
64. Barry Smith and Berit Brogaard, “A Unified Theory of Truth and Reference”, Logique et Analyse, No. 169-170 (2000, published 2003), 49–93.
Abstract: 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 supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis.
French translation: “Une théorie unifiée de la vérité et de la référence” in J. M. Monnoyer (ed.), La Structure du Monde: Objets, Propriétés, États du choses, Paris: Vrin (2004), 141–184.
65. Barry Smith and David M. Mark, “Do Mountains Exist? Towards an Ontology of Landforms”, Environment and Planning B (Planning and Design), 30(3) (2003), 411–427.
Abstract: Do mountains exist? The answer to this question is surely: yes. In fact, ‘mountain’ is the example of a kind of geographic feature or thing most commonly cited by English speakers (Mark, et al., 1999; Smith and Mark 2001), and this result may hold across many languages and cultures. But whether they are considered as individuals (tokens) or as kinds (types), mountains do not exist in quite the same unequivocal sense as do such prototypical everyday objects as chairs or people.
Abstract: When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the relation between fetus and mother.
German translation as: “Sechzehn Tage: Wann beginnt ein menschliches Leben?”, in G. Imaguire and Christine Schneider (eds.), Untersuchungen zur Ontologie, Munich: Philosophia, 2006, 3–40.
Revised version as “Die Ontologie des Embryos”, in L. Jansen and B. Smith (eds.), Biomedizinische Ontologie. Philosophie – Lebenswissenschaften - Informationstechnik (UTB Forum), Zurich: vdf, 2008, 199-228.
67. Thomas Bittner and Barry Smith “Vague Reference and Approximating Judgements”, Spatial Cognition and Computation, 3: 2 (2003), 137–156.
Abstract: We propose a new account of vagueness and approximation in terms of the theory of granular partitions. We distinguish different kinds of crisp and non-crisp granular partitions and we describe the relations between them, concentrating especially on spatial examples. We describe the practice whereby subjects use regular grid-like reference partitions as a means for tempering the vagueness of their judgments, and we demonstrate how the theory of reference partitions can yield a natural account of this practice, which is referred to in the literature as ‘approximation’.
68. Pierre Grenon and Barry Smith, “SNAP and SPAN: Towards Dynamic Spatial Ontology”, Spatial Cognition and Computation, 4: 1 (March 2004), 69–103.
Abstract: 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.
69. Barry Smith and Anand Kumar, “Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology”, BIOSILICO: Drug Discovery Today, 2 (2004), 246–252.
Abstract: The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the status of a de facto standard in the field of gene and gene product annotations and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. As the GO Consortium has recognized, however, its controlled vocabulary is as currently constituted marked by a number of problematic features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation.
70. Thomas Bittner, Maureen Donnelly and Barry Smith, “Endurants and Perdurants in Directly Depicting Ontologies”, AI Communications, 13: 4 (2004), 247–258.
Abstract: We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities such as organisms, geographic features, or qualities as they exist at some given moment of time. A SPAN ontology comprehends perduring entities such as processes and their parts and aggregates as they unfold themselves through some temporal interval. We give an axiomatic account of the theory of directly depicting ontologies and of the core parts of the metaontological fragment within which they are stembedded.
71. Jean-Luc Verschelde, Mariana Casella Dos Santos, Tom Deray, Barry Smith and Werner Ceusters, “Ontology-Assisted Database Integration to Support Natural Language Processing and Biomedical Data-Mining”, in: R. Hofestädt (ed.), Journal of Integrative Bioinformatics, 1 (2004), 1-10. Repr. in: Yearbook of Bioinformatics (2004), 39–48.
Abstract: Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes and diseases as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language.
72. Barry Smith and Pierre Grenon, “The Cornucopia of Formal-Ontological Relations”, Dialectica 58: 3 (2004), 279–296.
Abstract: We present a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between three and four-dimensionalism.
73. Anand Kumar, Barry Smith and Daniel Novotny, “Biomedical Informatics and Granularity”, Comparative and Functional Genomics, 5 (2004), 501–508. PMC2447428
Abstract: An explicit formal ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
74. Barry Smith and Bert R. E. Klagges, “Philosophie und biomedizinische Forschung”, Allgemeine Zeitschrift für Philosophie, 30: 1 (2005), 5–26.
Abstract: 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.
Revised version in L. Jansen and B. Smith (eds.), Biomedizinische Ontologie. Philosophie – Lebenswissenschaften - Informationstechnik (UTB Forum), Zurich: vdf, 2008, 17-30.
English version as “Bioinformatics and Philosophy”, in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 17-30.
75. Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan Rector and Cornelius Rosse, “Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. PMC1175958
Abstract: To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
76. Werner Ceusters, Barry Smith and Louis Goldberg, “A Terminological and Ontological Analysis of the NCI Thesaurus”, Methods of Information in Medicine, 44 (2005), 498–507.
Abstract: Objective: The National Cancer Institute Thesausus is described by its authors as “a biomedical vocabulary that provides consistent, unambiguous codes and definitions for concepts used in cancer research” and which “exhibits ontology-like properties in its construction and use”. We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. Materials and methods: We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Results: We found many mistakes and inconsistencies with respect to the term-formation principles used, the underlying knowledge representation system, and missing or inappropriately assigned verbal and formal definitions. Conclusion: Version 04.08b of the NCI Thesaurus suffers from the same broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent.
Abstract: Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas. Includes a classification of biomedical entities which revises the classification provided in Rosse, et al.
78. Berit Brogaard and Barry Smith, “On Luck, Responsibility and the Meaning of Life”, Philosophical Papers¸ 34(3), 2005, 443–458.
Abstract: A life we view as an ordered sequence of actions and events of a special kind. We then defend the thesis that a meaningful life is a life upon which some sort of valuable pattern has been imposed—a pattern which relates not merely to what goes on inside the person’s head, but which involves also, in serious ways, the person having an effect upon the world. Meaningfulness is then a special kind of value which a human life can bear. More specifically, it is a kind of intrinsic value – something that we value for its own sake. We then argue that it is crucial that, if such an imposed shape or pattern is to contribute to meaningfulness, then it must be the result of the person’s own efforts and of his or her own decisions.
Abstract: 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.
80. Jonathan Simon, James Fielding and Barry Smith, “Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases”, International Journal of Medical Informatics, 75 (3-4), 2006, 224-231.
Abstract: 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). With this project we aim to move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”.
81. Anand Kumar, Barry Smith, Domenica Pisanelli, Aldo Gangemi and Mario Stefanelli, “Clinical Guidelines as Plans: An Ontological Theory”, Methods of Information in Medicine, 45 (2), 2006, 204-210.
Abstract: Objective: Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. Method: The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of individuals organized into teams. We provide various levels of implementation representing different levels of conformity on the part of health care organizations. Result: Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than are standard guideline-based management systems. They do justice to the fact (1) that responsibilities within a health care organization are widely shared, and (2) that health care professionals may on different occasions be noncompliant with guidelines for a variety of well justified reasons. Conclusion: The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in the complication of its implementation.
82. Anand Kumar, Yum Lina Yip, Barry Smith and Pierre Grenon, “Bridging the Gap between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma”, Computers in Biology and Medicine 2006; 36, (7-8): 694-711.
Abstract: 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 the electronic patient records in such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma.
83. Barry Smith, “From Concepts to Clinical Reality: An Essay on the Benchmarking of Biomedical Terminologies”, Journal of Biomedical Informatics, 2006; 39(3): 288-298.
Abstract: It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support.
Revised version as “New Desiderata for Biomedical Terminologies”, in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 83-109.
84. Christiane Fellbaum, Udo Hahn and Barry Smith, “Towards New Information Resources for Public Health – From WordNet to Medical WordNet”, Journal of Biomedical Informatics, 2006; 39(3): 321-332.
Abstract: 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, we propose a new type of repository, consisting of three large collections of (1) medically relevant word forms, structured along the lines of the existing Princeton WORDNET; (2) medically validated propositions, referred to here as medical facts, which will constitute what we shall call MEDICAL FACTNET; and (3) propositions reflecting laypersons’ medical beliefs, which will constitute what we shall call the MEDICAL BELIEFNET. We introduce a methodology for setting up the MEDICAL WORDNET. We then turn to the discussion of research challenges that have to be met in order to build this new type of information resource.
85. Werner Ceusters and Barry Smith, “Strategies for Referent Tracking in Electronic Health Records”, Journal of Biomedical Informatics, 2006; 39(3): 362-378.
Abstract: The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto.
86. Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Richter JD, Noy NF and Musen MA, “National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge”, Omics: A Journal of Integrative Biology, 10(2), 2006, 185-198.
Abstract: The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects.
87. Patricia L. Whetzel, Ryan R. Brinkman, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Mervi Heiskanen, Tina Hernandez-Boussard, Norman Morrison, Helen Parkinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, Daniel Schober, Barry Smith, Robert Stevens, Chris Stoeckert, Chris F. Taylor, Joe White, “Development of FuGO – An Ontology for Functional Genomics Experiments”, Omics: A Journal of Integrative Biology, 10(2), 2006, 199-204. PMC2783628
Abstract: The development of the Functional Genomics Experiment Ontology (FuGO) is a collaborative, international effort which will provide a resource for annotating functional genomics experiments, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain terms that are both universal to functional genomics experiments and those that are domain specific. In this way, the ontology will serve as the ‘semantic glue’ to provide a common understanding of data across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies in order to avoid the need to duplicate these resources, but in such a way as to enable their ease of use in annotation. This project is in the beginning stages of development and the paper will describe the efforts to initiate the project, the scope and organization of the project, the work accomplished to date and the challenges encountered as well as describe future plans.
88. Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith, “Quality Control for Terms and Definitions in Ontologies and Taxonomies”, BMC Bioinformatics, 2006, 7: 212, PMC1482721
Abstract: Ontologies and taxonomies are among the most important computational resources formolecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.
89. Kevin Mulligan, Peter Simons and Barry Smith, “What’s Wrong with Contemporary Philosophy?”, Topoi, 25 (1-2), 2006, 63-67.
Abstract: Abstract Philosophy in the West divides into three parts: Analytic Philosophy (AP), Continental Philosophy (CP), and History of Philosophy (HP). But all three parts are in a bad way. AP is sceptical about the claim that philosophy can be a science, and hence is uninterested in the real world. CP is never pursued in a properly theoretical way, and its practice is tailor-made for particular political and ethical conclusions. HP is mostly developed on a regionalist basis: what is studied is determined by the nation or culture to which a philosopher belongs, rather than by the objective value of that philosopher’s work. Progress in philosophy can only be attained by avoiding these pitfalls.
Finnish translation as “Mikä nykyfilosofiassa on vialla?”, niin & näin, 1 (2014), 69-74 (published with commentary by Tuomas E. Tahko (76-78), Pauliina Remes (80-82) and Susanna Lindberg (85-90).
Portuguese translation as “Ce se întâmpla cu filosofia contemporana?”, Rivista de filosofie, 62 (6), 2015, 759-765.
90. Leo Obrst, Patrick Cassidy, Steve Ray, Barry Smith, Dagobert Soergel, Matthew West and Peter Yim, “The 2006 Upper Ontology Summit Joint Communiqué”, Applied Ontology, 1 (2), 2006, 203-211.
Abstract: On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and expressing a joint intent to build bridges among the existing upper ontologies in ways designed to increase and rationalize their utilization and to enhance their semantic interoperability.
91. Olivier Bodenreider, Barry Smith, Anand Kumar, Anita Burgun, “Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-Based Biomedical Terminologies”, Artificial Intelligence in Medicine, 2007, 39, 183-195. PMC2442845
Abstract: Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed.
92. Werner Ceusters and Barry Smith, “Referent Tracking for Treatment Optimisation in Schizophrenic Patients: A Case Study in Applying Philosophical Ontology to Diagnostic Algorithms”, Journal of Web Semantics, 2006; (4)3, 229-236. PMC203705415
Abstract: The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients in within a framework of guideline-based medicine. We take this algorithm as our starting point in investigating how artifacts of this sort can benefit from the facilities of high-quality ontologies. The IPAP algorithm exists thus far only in a form suitable for use by human beings. We draw on the resources of Basic Formal Ontology (BFO) in order to show how such an algorithm can be enhanced in such a way that it can be used in Semantic Web and related applications. We found that BFO provides a framework that is able to capture in a rigorous way all the types of entities represented in the IPAP schizophrenia algorithm in way which yields a computational tool that can be used by software agents to perform monitoring and control of schizophrenic patients. We discuss the issues involved in building an application ontology for this purpose, issues which are important for any Semantic Web application in the life science and healthcare domains.
93. Werner Ceusters and Barry Smith “Referent Tracking for Digital Rights Management,” International Journal of Metadata, Semantics and Ontologies, 2(1), 2007, 45-53.
Abstract: Digital Rights Management covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets, including management of relationships between rights holders in a digital environment. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of content in its broadest interpretation. Although the system has been very well designed to manage object identifiers, some important questions related to the assignment of identifiers are left open. The paradigm of a referent tracking system (RTS) recently advanced in the healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the DOI models and by showing how they can be corrected using an RTS.
94. Werner Ceusters, Peter Elkin and Barry Smith, “Negative Findings in Electronic Health Records and Biomedical Ontologies: A Realist Approach”, International Journal of Medical Informatics 2007; 76: 326-333. PMC2211452.
Abstract: A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. Methods: We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. Results: We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology in terms of which we were able to accommodate nearly all occurrences of negative findings in the sample studied.
95. Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L. Whetzel, Suzanna Lewis, “The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology, 25 (11), November 2007, 1251-1255. PMC2814061
Abstract: The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved.
96. Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu, “Framework for a Protein Ontology”, BMC Bioinformatics, Nov. 2007, 8(Suppl. 9): S1. PMC2217659
Abstract: 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 describe properties that can be attributed to proteins. For example, protein functions are described by the Gene Ontology (GO) and human diseases by SNOMED CT or ICD10. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed the 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 modifications). PRO will allow the specification of relationships between PRO, GO and other ontologies in the OBO Foundry. Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways (http://pir.georgetown.edu/pro).
97. Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Rolf Apweiler, Michael Ashburner, Catherine A Ball, Pierre-Alain Binz, Alvis Brazma, Ryan Brinkman, Eric W Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Graeme Grimes, Nigel W Hardy, Henning Hermjakob, Randall K Julian, Jr., Matthew Kane, Eugene Kolker, Martin Kuiper, Nicholas Le Novère, Jim Leebens-Mack, Suzanna E Lewis, Ruth McNally, Alexander Mehrle, Norman Morrison, John Quackenbush, Donald G Robertson, Philippe Rocca-Serra, Barry Smith, Jason Snape, Peter Sterk, Stefan Wiemann, “Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project”, Nature Biotechnology, 26 (2008), 889-896. PMC2771753
Abstract: Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists.
98. David P. Hill, Barry Smith, Monica S. McAndrews-Hill, Judith A. Blake, “Gene Ontology Annotations: What they mean and where they come from”, BMC Bioinformatics, 2008; 9(Suppl 5): S2. PMC2367625
Abstract: The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists.
99. David Koepsell, Robert Arp, Jennifer Fostel and Barry Smith, “Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a Biomedical Ethics Ontology”, Journal of Empirical Research on Human Research Ethics, Vol. 4, No. 1, 2009, 43-58. PMC2725426
Abstract: 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); the proposed BMEO would interoperate with OBI, creating a powerful information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation.
100. Thomas Bittner, Maureen Donnelly and Barry Smith, “A Spatio-Temporal Ontology for Geographic Information Integration”, International Journal for Geographical Information Science, 23 (6), 2009, 765-798.
Abstract: This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online.
101. Daniel Schober, Barry Smith, Suzanna E Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F Taylor, Philippe Rocca-Serra and Susanna-Assunta Sansone, “Survey-based naming conventions for use in OBO Foundry ontology development”, BMC Bioinformatics, 2009 (June), 10:125. PMC2684543
Abstract: A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and integration of these ontologies is extremely desirable. However, heterogeneities in naming conventions pose serious obstacles to such integration. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to their general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies.
102. Cecilia Arighi, Hongfang Liu, Darren Natale, Winona Barker, Harold Drabkin, Zhangzhi Hu, Judith Blake, Barry Smith and Cathy Wu, “TGF-beta Signaling Proteins and the Protein Ontology”, BMC Bioinformatics, 10: Art. No. S3 Suppl. 5, May 16 2009. PMC2679403
Abstract: The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or post-translational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of the Protein Ontology.
103. Anna M. Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith and Lindsay G. Cowell, “An improved ontological representation of dendritic cells as a paradigm for all cell types”, BMC Bioinformatics, February 2009, 10:70. PMC2662812
Abstract: The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources.
104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130.
Abstract: 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, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’.
105. Holger Stenzhorn, Stefan Schulz, Martin Boeker and Barry Smith, “Adapting Clinical Ontologies in Real-World Environments”, Journal of Universal Computer Science, 14 (22), 2009, 3767-3780. PMC2853050
Abstract: The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects.
106. Stefan Schulz, Holger Stenzhorn, Martin Boekers and Barry Smith, “Strengths and Limitations of Formal Ontologies in the Biomedical Domain”, Electronic Journal of Communication, Information and Innovation in Health (Special Issue on Ontologies, Semantic Web and Health), 3 (1), 2009, 31-45. PMC2904529
Abstract: We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds of representation in order to provide a more rational basis for using ontologies and related artifacts to advance integration of data and enhance interoperability of associated reasoning systems. We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies as long as the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models.
Portuguese translation as “Vantagens e limitações das ontologias formais na área biomedical”, Reciis: Revista Electronica de Comunicacao Informacao, Inovacao em Saude, March 2009, March 2009, Vol. 3, N 1, 33-48.
107. Gunnar O. Klein and Barry Smith, “Concept Systems and Ontologies: Recommendations for Basic Terminology”, Transactions of the Japanese Society for Artificial Intelligence, 25, 2010, 433-441. PMC3034144.
Abstract: This essay concerns the problems surrounding the use of the term ‘concept’ in current ontology and terminology research. It is based on the constructive dialogue between realist ontology on the one hand and the world of formal standardization of health informatics on the other, but its conclusions are not restricted to the domain of medicine. The term “concept” is one of the most misused in literature and documentation of technical standards in the computer and information technology domains. In this paper we propose to use the term “concept” in the context of producing defined professional terminologies with one specific and consistent meaning, which we then propose for adoption as the agreed meaning of the term in future terminological research, and specifically in the development of formal terminologies to be used in computer systems. We also discuss and propose new definitions of a set of cognate terms. We describe the relations governing the realm of concepts, and compare these to the richer and more complex set of relations obtaining between entities in the real world. On this basis we also summarize an associated terminology for ontologies as representations of the real world and a partial mapping between the world of concepts and the world of reality.
Japanese translation in Journal of the Japanese Society for Artifical Intelligence, 25 (3), 2010, 317-325.
108. David R. Karp, Nishanth Marthandan, Steven G. E. Marsh, Chul Ahn, Frank C. Arnett, Lindsay Cowell, David S. DeLuca, Alexander D. Diehl, Raymond Dunivin, Karen Eilbeck, Michael Feolo, Paula A. Guidry, Wolfgang Helmberg, Suzanna Lewis, Maureen D. Mayes, Chris Mungall, Darren A. Natale, Bjoern Peters, Effie Petersdorf, John D. Reveille, Barry Smith, Glenys Thomson, Matthew J. Waller, Richard H. Scheuermann, “Novel Sequence Feature Variant Type Analysis of the HLA Genetic Association in Systemic Sclerosis”, Human Molecular Genetics, 2010 Feb 15;19(4):707-19. PMC2807365
Abstract: Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis.
Abstract: 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 community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite.
German version as “Biomedizinische Ontologien für die Praxis”, European Journal for Biomedical Informatics, 1 (2009).
110. Jiye Ai, Barry Smith, and David Wong (2010) “Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base”, BMC Bioinformatics, 11:302. PMC2898059
Abstract: 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) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB.
111. Barry Smith and Werner Ceusters, “Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies”, Applied Ontology, 5 (2010), 139–188. PMC3104413
Abstract: 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 for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.
112. Albert Goldfain, Barry Smith and Lindsay G. Cowell, “Towards an Ontological Representation of Resistance: The Case of MRSA”, Journal of Biomedical Informatics, 2011 (Feb.), 44:1, 35-41. PMC2930208.
Abstract: 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.
Abstract: We describe an ontology of philosophy that is designed to help navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is orientated around what philosophical literature is about.
114. Werner Ceusters and Barry Smith, “Foundations for a Realist Ontology of Mental Disease”, Journal of Biomedical Semantics, 2010, 1:10, 1-23. PMC3017014
Abstract: While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology (BFO) and in the application of BFO in the Ontology of General Medical Science (OGMS). We analyzed statements about what counts as a mental disease provided (1) in the research agenda for the DSM-V, and (2) in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future.
115. Werner Ceusters, Maria Capolupo, Georges De Moor, Jos Devlies, Barry Smith, “An Evolutionary Approach to Realism-Based Adverse Event Representations”, Methods of Information in Medicine, 50 (1): 62-73, 2011. PMC2829617
Abstract: Background: Part of the ReMINE project involved the creation of an ontology enabling computer-assisted decision support for optimal adverse event management. Objectives: The ontology had to satisfy the following requirements: (1) to be able to account for the distinct and context-dependent ways in which authoritative sources define the term ‘adverse event’, (2) to allow the identification of relevant RAPS information on the basis of the disease history of a patient as documented in electronic health records, and (3) to be compatible with present and future ontologies developed under the OBO Foundry framework. Methods: We used as feeder ontologies the Basic Formal Ontology, the Foundational Model of Anatomy, the Ontology of General Medical Science, the Information Artifact Ontology and the Ontology of Mental Health. We further used relations defined according to the pattern set forth in the OBO Relation Ontology. In light of the use of the ontology for the representation of adverse events that actually occurred and therefore are registered in a database, we also applied the principles of Referent Tracking. Results: We merged the upper portions of the feeder ontologies and introduced 22 additional representational units of which 13 are generally applicable in biomedicine and 9 in the adverse event context. We provided for each representational unit a textual definition that can be translated into equivalent formal definitions. Conclusion: The resulting ontology satisfies all requirements set forth. Merging the existing ontologies, although all designed under the OBO Foundry principles, brought new insight into what the representational units of such ontologies actually denote.
116. Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang, Cathy H. Wu, “The Protein Ontology: A Structured Representation of Protein Forms and Complexes”, Nucleic Acids Research 2011, 39 (Database Issue), D539-545. PMC3013777
Abstract: 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.
117. Carol J. Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A. Blake, Cathy Wu, “The Representation of Protein Complexes in the Protein Ontology (PRO)”, BMC Bioinformatics, September 2011, 12:371. PMC3189193
Abstract: Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protein-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. Conclusion: PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species.
118. Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story, Barry Smith, and the NCBO team, “The National Center for Biomedical Ontology”, Journal of the American Medical Informatics Association, 19 (2), 2012, 190-195. PMC3277625
Abstract: The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data.
119. Barry Smith, “How to Do Things with Documents”, Rivista di Estetica, 50 (2012), 179-198.
Abstract: This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically on the ontological problems raised by a family of new types of social phenomena – exemplified most dramatically in the domain of finance for example in the form of what are called ‘structured investment vehicles’ – made possible as a result of the employment of computer technology in entity creation. I address also Searle’s most recent work on social ontology, and conclude with an appendix on the theory of documentality advanced by Maurizio Ferraris.
Abstract: A knowledge base to retrieve, integrate and analyze multiple data types collected from saliva samples promises to transform healthcare. Saliva is ideally suited to non-invasive detection and monitoring of disease. However, the absence of a free resource that cross-references disease-based changes in the levels of biomolecules has hamstrung progress in identifying biomarkers of specific illnesses. To address this issue, a team led by Ji-Ye Ai and David Wong at the University of California in Los Angeles are spearheading the creation of the Salivaomics Knowledge Base (SKB), a data management system and web resource to facilitate the discovery of saliva biomarkers using systems biology. The researchers first defined a common and structured vocabulary to describe the diverse data types; now, they are creating a common interface to integrate protein, RNA and metabolite data from multiple independent databases.
120. Ramona L. Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan A. Rensing, Barry Smith, Dennis W. Stevenson, “Ontologies as Integrative Tools for Plant Science”, American Journal of Botany, 99(8): 1–13, 2012. PMC3492881
Abstract: 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.
Abstract: We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework.
Reprinted in D. Oderberg (ed.), Classifying Reality, Oxford: Wiley-Blackwell, 2013, 101-126.
122. Barry Smith, Tatiana Malyuta, David Salmen, William Mandrick, Kesny Parent, Shouvik Bardhan, Jamie Johnson, “Ontology for the Intelligence Analyst”, CrossTalk: The Journal of Defense Software Engineering, November/December 2012, 18-25.
Abstract: 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 a simple case study to show how these benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future.
123. Laurel Cooper, Ramona L. Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith, Justin Preece, Balaji Athreya, Christopher J. Mungall, Stefan Rensing, Manuel Hiss, Daniel Lang, Ralf Reski, Tanya Z. Berardini, Donghui Li, Eva Huala, Mary Schaeffer, Naama Menda, Elizabeth Arnaud, Rosemary Shrestha, Yukiko Yamazaki, Pankaj Jaiswal, “The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses”, Plant and Cell Physiology, 54 (2) (Database Issue), Feb. 2013, 1-23 (PMC3583023)
Abstract: The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
124. Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Carol J. Bult, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, Olivia Helfer, Hongzhan Huang, Anna Maria Masci, Jia Ren, Natalia V. Roberts, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Meher Shruti Yerramalla, Jian Zhang, Aisha AlJanahi, Irem Celen, Cynthia Gan, Mengxi Lv, Emily Schuster-Lezell, Cathy H. Wu, “Protein Ontology: a controlled structured network of protein entities”, Nucleic Acids Research, 2013, 42(1): D415-21.
Abstract: The Protein Ontology (PRO) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments.
125. Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall, Suzanna E Lewis and the ENVO Consortium, “The Environment Ontology: Contextualizing Biological and Biomedical Entities”, Journal of Biomedical Semantics 2013, 4:43.
Abstract: As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, content, structure, adoption, and governance approach.
126. Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl, “The Neurological Disease Ontology”, Journal of Biomedical Semantics, 2013, 4:42.
Abstract: 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 the Ontology for General Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke.
127. Schiffman E., Ohrbach R., Truelove E., Look J., Anderson G., Goulet J.-P., List T., Svensson P., Gonzalez Y., Lobbezoo F., Michelotti A., Brooks S.L., Ceusters W., Drangsholt M., Ettlin D., Gaul C., Goldberg L., Haythornthwaite J., Hollender L., Jensen R., John M.T., deLaat A., deLeeuw R., Maixner W., van der Meulen M., Murray G.M., Nixdorf D.R., Palla S., Petersson A., Pionchon P., Smith B., Visscher C.M., Zakrzewska J., Dworkin S.F., “Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications: Recommendations of the International RDC/TMD Consortium Network and Orofacial Pain Special Interest Group,” Journal of Oral and Facial Pain and Headache, 28 (2014), 6–27.
Abstract: Aims: The Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients.
128. R. L. Walls, J. Deck, R. Guralnick, S. Baskauf, R. Beaman, S. Blum, S. Bowers, P. L. Buttigieg, N. Davies, D. Endresen, M. A. Gandolfo, R. Hanner, A. Janning, L. Krishtalka, A. Matsunaga, P. Midford, N. Morrison, É. Ó Tuama, M. Schildhauer, B. Smith, B. J. Stucky, A. Thomer, J. Wieczorek, J. Whitacre, and J. Wooley, “Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies”, PLoS One, March 3, 2014, 10.1371/journal.pone.0089606 (PMC3940615)
Abstract: The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
129. David Koepsell and Barry Smith, “Beyond Paper”, The Monist, 97 (2), April 2014, 222–235.
Abstract: 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 the fact that interactive documents seem to blur the distinctions between the static documents (or ‘inscriptions’) which form Ferraris’s starting point, and dynamic software processes. The authors argue further that the Ferraris view as applied to legal documents is flawed because of the fact that courts may treat contractual obligations as enduring even in spite of a complete absence of enduring inscriptions. Finally, the authors note that traces in brains, another important family of inscriptions (as Ferraris conceives them), differ significantly from genuinely documentary inscriptions by their lack of public inspectability.
130. Janna Hastings, Gwen Alexandra Frishkoff, Barry Smith, Mark Jensen, Russell A Poldrack, Jane Lomax, Anita Bandrowski, Fahim T. Imam, Jessica A Turner and Maryann E Martone, “Interdisciplinary perspectives on the development, integration and application of cognitive ontologies”, Frontiers in Neuroinformatics, 8:62, 2014.
Abstract: We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data.
131. Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith, “OAE: The Ontology of Adverse Events”, Journal of Biomedical Semantics, 07/2014, 5:29.
Abstract: 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. The Ontology of Adverse Events (OAE) has been developed to standardize and integrate data relating to AEs and to support computer-assisted reasoning over such data. 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 as those events that are causal consequences of a medical intervention. OAE has been used in the analysis of both vaccine and drug adverse event data, for example, using the influenze vaccine data extracted from the Vaccine Adverse Event Reporting System (VAERS)
132. Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Sallvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky, Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F. Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, István Mikó, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Stefan Richter, Peter N. Robinson, Alan Ruttenberg, Katja S. Schulz, Erik Segerdell, Katja C. Seltmann, Michael J. Sharkey, Aaron D. Smith, Barry Smith, Chelsea D. Specht, R. Burke Squires, Robert W. Thacker, Anne Thessen, Jose Fernandez-Triana, Mauno Vihinen, Peter D. Vize, Lars Vogt, Christine E. Wall, Ramona L. Walls, Monte Westerfeld, Robert A. Wharton, Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula Mabee, “Finding Our Way through Phenotypes”, PLoS Biology, January 2015, 13 (1).
Abstract: Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
133. Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren A Natale, Cathy Wu, Peter D’Eustachio, “Toll-Like Receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the Protein Ontology framework”, PLoS One, April 2015, PONE-D-14-45784R2.
Abstract: The Protein Ontology (PRO) supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Here, we describe extensions of this ontology framework to link complexes to their subcellular locations, molecular functions, and roles in biological processes as defined by the Gene Ontology, using terms from the Relation Ontology. To demonstrate the feasibility of this approach we have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and employ structural and functional relationships inferred from the ontology to suggest plausible resolutions of these discrepancies and gaps.
134. Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn, Jr., James Overton, John Tomaszewski, Metin Gurcan, “Biomedical Imaging Ontologies: A Survey and Proposal for Future Work”, Journal of Pathology Informatics, 2015, 6:37. PMC4485195
Abstract: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as ‘cell’ or ‘image’ or ‘tissue’ or ‘microscope’) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical definitions thereby also supporting reasoning over the tagged data. This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.
135. Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen Borchert, Mnig Tan, Alan Ruttenberg, “OmniSearch: A semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data”, Journal of Biomedical Semantics, 7:24, May 4, 2016.
Abstract: In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://?purl.?obolibrary.?org/?obo/?ncro.?owl.
136. Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug†, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister,Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert Jr., Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng. “The Ontology for Biomedical Investigations”, PLoS ONE, 11(4): e0154556, April 29, 2016.
Abstract: 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 (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The currentrelease of OBI is available at http://purl.obolibrary.org/obo/obi.owl.
137. Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert and Ming Tan, “The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology”, Journal of Biomedical Semantics, 2016, 7:24, 4 May 2016
Abstract: In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://?purl.?obolibrary.?org/?obo/?ncro.?owl.
138. Andrew D. Spear, Werner Ceusters, Barry Smith, “Functions in Basic Formal Ontology”, Applied Ontology, 11 (2), (2016), 103-128.
Abstract: The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application in domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections.
139. Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen Borchert, Ming Tan, “The Development of Non-Coding RNA Ontology”, International Journal of Data Mining and Bioinformatics, 15 (3), June 25, 2016. DOI: 10.1504/IJDMB.2016.077072.
Abstract: Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.
140. Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith and Yongqun He, "The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis", Journal of Biomedical Semantics, 14 September 2016, 7(1):53.
Abstract: Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. The terms in OBCS cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality.
141. Selja Seppälä, Alan Ruttenberg, Yonatan Schreiber, Barry Smith, “Definitions in Ontologies”, Cahiers de Lexicologie, 109, 2 (2016), 175-207.
Abstract: Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.
142. Metin N. Gurcan, John Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith, “Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem”, Journal of Biomedical Informatics, 66 (2017) 129–135.
Abstract: Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts.
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu, “Protein Ontology (PRO): Enhancing and scaling up the representation of protein entities”, Nucleic Acids Research 45 (D1), 2017, D339-D346.
Abstract: The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.
1. Barry Smith, “Historicity, Value and Mathematics”, Analecta Husserliana, 4 (1975), 219–239.
Abstract: At the beginning of the present century, a series of paradoxes were discovered within mathematics which suggested a fundamental unclarity in traditional mathematical methods. These methods rested on the assumption of a realm of mathematical idealities existing independently of our thinking activity, and in order to arrive at a firmly grounded mathematics different attempts were made to formulate a conception of mathematical objects as purely human constructions. It was, however, realised that such formulations necessarily result in a mathematics which lacks the richness and power of the old ‘platonistic’ methods, and the latter are still defended, in various modified forms, as embodying truths about self-existent mathematical entities. Thus there is an idealism-realism dispute in the philosophy of mathematics in some respects parallel to the controversy over the existence of the experiential world to the settlement of which lngarden devoted his life. The present paper is an attempt to apply Ingarden’s methods to the sphere of mathematical existence. This exercise will reveal new modes of being applicable to non-real objects, and we shall put forward arguments to suggest that these modes of being have an importance outside mathematics, especially in the areas of value theory and the ontology of art.
2. Barry Smith, “Matematyka a ontologiczna estetyka Ingardena”, Studia Filozoficzne, 1/122 (1976), 51–56.
Abstract: Outlines a theory of how the existence of mathematical objects can be explained using the aesthetic and ontological conceptual apparatus developed by Roman lngarden in his The Controversy over the Existence of the World and The Literary Work of Art.
3. Karl Schuhmann and Barry Smith, “Against Idealism: Johannes Daubert vs. Husserl’s Ideas I”, Review of Metaphysics, 38 (1985), 763–793.
Abstract: In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.
Reprinted in: Karl Schuhmann, Selected Papers in Phenomenology, C. Leijenhorst and P. Steenbakkers (eds.), Dordrecht, Boston and London: Kluwer (2004), 35–59.
4. Kevin Mulligan and Barry Smith, “Franz Brentano on the Ontology of Mind” (Review article on Brentano’s Deskriptive Psychologie), Philosophy and Phenomenological Research, 45 (1985), 627–644.
Abstract: We provide a detailed exposition of Brentano’s descriptive psychology, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.
5. Wolfgang Grassl and Barry Smith, “The Politics of National Diversity”, The Salisbury Review, 5 (1987), 33–37.
Reprinted in: R. Scruton (ed.), Conservative Thoughts, London: Claridge Press (1988), 101–114.
6. Kevin Mulligan, Peter Simons and Barry Smith, “Drei Briten in Kakanien”, interview by Axel Bühler in Information Philosophie, 3 (1987), 22–33.
7. Johannes Marek and Barry Smith, “Einleitung zu A. Martys ‘Elemente der deskriptiven Psychologie’”, Conceptus, 21 (1987), 33–48, editors’ introduction to extracts from Marty’s lectures (ibid., 49–66).
Abstract: Anton Marty delivered courses on descriptive psychology at regular intervals in the University of Prague. The content of these courses follows closely the ideas of Marty’s teacher Franz Brentano, though with some interesting divergences and extrapolations. The present work is a historical and systematic introduction to an extract from notes taken of Marty’s lecture, with some discussion of the work of Dilthey on similar topics, and of Marty’s influence on Franz Kafka and on the Gestalt psychologist Max Wertheimer.
8. Barry Smith, “On the Austrianness of Austrian Economics”, Critical Review, 4, 1-2 (1990), 212–238.
Abstract: Much recent work on the intellectual background of Austrian economics reveals an unfortunate lack of awareness of the distinct nature of the Austrian contribution to philosophy, from which the Austrian economists drew many of their ideas. The present essay offers a sketch of this contribution, contrasting Austrian philosophy especially with the modes of philosophy dominant in Germany. This makes it possible to throw new light on the relations on Mises, Kant and the Vienna circle, and it allows us also to establish the extent to which Austrian economics might properly be seen as being allied to the German hermeneutic tradition of Dilthey, Gadamer, et al. The essay concludes with a criticism of the hermeneutic relativism recently canvassed by some Austrian economists, concentrating especially on the work of Don Lavoie, whose writing are treated as symptomatic of a wider and somewhat regrettable trend.
9. Barry Smith, “The Question of Apriorism”, Austrian Economics Newsletter, (Fall 1990), 1–5.
Abstract: 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 essences and essential structures are intelligible, in the sense that they ca be grasped non-inductively in our thinking. We show the consequences of this view for an analysis of the thinking of Mises and Hoppe, both of which – we claim – incorporate what we believe to be foreign mixtures of Kantianism in their account of the foundations of Austrian economics.
Reprinted in Rothbard e neo-hayekiani nella Scuola austriaca di economia (Special issue of Nuova Civiltà delle Macchine), Dario Antiseri, Enzo Di Nuoscio, Francesco Di Iorio (eds.), June 2011, 59–68.
Czech translation: “Apriorizmus v ekonómii”
10. Barry Smith, “Puntel on Truth, Or: Old Idealistic Wine in New Semantic Bottles”, Ethik und Sozialwissenschaften. Streitforum für Erwägungskultur, 3 (1992), 166–169.
11. Barry Smith, “No Philosophy. No Transformation. No Theses” [peer commentary on Herta Nagl-Docekal, “The Feminist Transformation of Philosophy”], Ethik und Sozialwissenschaften. Streitforum für Erwägungskultur, 4 (1992), 571–573.
12. Barry Smith, “Report on the International Brentano Conference. Graz, 25–26 May 1990”, in Nachrichten der Forschungsstelle und des Dokumentationszentrums für Österreichische Philosophie, 2 (1990), 9–12.
13. Barry Smith, “First International Summer Institute in Cognitive Science held at UB”, UB International, 3/2 (1994), 4, 7.
14. Barry Smith, “On Feminist Nomadism”, Free Inquiry, 15/2 (1995), 30–31.
15. Ellen Klein and Barry Smith, “Philosophy and Feminist Politics: A Brief Guide”, Free Inquiry, 16/1 (1995/96), 60–61.
16. Barry Smith, “Questionnaire on Cognitive Science”, Kog-Bit. Journal aus dem Graduiertenkolleg Kognitionswissenschaft der Universität Hamburg, 13 (1996), 12.
17. Barry Smith and Peter Baumann, “Von Kant über Pol Pot zu Derrida”, KogBit. Journal aus dem Graduiertenkolleg Kognitionswissenschaft der Universität Hamburg, 14 (1996), 8–11. Revised version as “The Worst Cognitive Performance in History”, Noûsletter, 1997, 13–15.
18. Barry Smith, “Bringing the Humanities Down to Earth”, Academic Questions, 10 (4), 1997, 58-62.
Abstract: The phenomenon known as ‘Pascal’s syndrome’, familiar to those who work with adolescents, affects a significant fraclion of adolescents who, in striving to establish themselves as independent adults, pass lhrough a phase in which they make utterances that amount lo a radical negation of everything their parents think or believe. Such rebellion may express itself in political, religious, economic, or sexual terms. In some cases, however, it leads co what can only be described as an ontological rebellion, expressing itself in utterances such as ‘Reality does not exist,’ or ‘The world is a gigantic conspiracy,’ and so forth. A very small minority of sufferers from such ontological rebellion become philosophers. We address the implications of this phenomenon for the present-day state of the humanities disciplines.
19. Barry Smith, “Applied Ontology: A New Discipline is Born”, Philosophy Today, vol. 12, number 29 (1998), 5–6.
Italian translation as “Ontologo, il mestiere del futoro: È nata l’ontologia applicata”, in: Il Sole 24 Ore (May 24, 1998), p. 35.
20. Barry Smith, “Qu’est-ce qu’une niche? Biologie et Ontologie formelle”, Biofutur. Le Mensuel européen de Biotechnologie, 181 (September 1998), 13.
21. Barry Smith, “Presidential Teaching Tool”, Nousletter (Buffalo), (July 1999), 3–4.
22. Reinhild Steingröver-McRae and Barry Smith, “The Last Days of the Human Race”, Austria Kultur, 9: 5 (September/October 1999), 16–17.
23. Barry Smith, “Revisiting the Derrida Affair,” interview by J. Sims, Sophia, 38: 2 (October 1999).
Abstract: In 1992 the proposal to award an honorary degree to Jacques Derrida exposed Cambridge University to the scrutiny of the academic world as well as to the press. The original proposal led four senior dons in Cambridge to announce a 'non-placet' vote. Barry Smith then authored a letter to The Times published on 9 May, 1992 along with eighteen other signatures from renowned philosophers, calling into doubt Derrida’s qualifications for such an honor. The interview here reproduced describes the background and motivation of the letter, and of Derrida’s response.
24. Barry Smith, “Obiektywnosc percepcji zmyslowej”, Roczniki Filozoficzne 49: 1 (2001), 63–75.
Abstract: There is an old problem in philosophy: the problem of how we pass from the mental theater of our representations to the external realm of concrete physical objects. This problem arises against the background of representationalist theories of the relation between mind and its objects which are marked by the following three features: 1. The perceiving subject is idealized. It is conceived as lying outside any context or environment and in abstraction from any goal-directed behavior. 2. Perception is seen as beginning with raw or bare sensations. Then, by a process of inference, there arise beliefs about external physical objects. 3. Physical objects are assumed to be out there in the world, but to be inaccessible to direct experience. This representationalist theory lives on in the computational theories of the mind and in the doctrines of methodological solipsism embraced by contemporary cognitive scientists. But by making perception dependent on sensation, and by making sensations the direct objects of experience, it has matters exactly upside down. The paper draws on the ecological psychology of J. J. Gibson and Roger Barker in order to provide the metaphysical principles of a more adequate theory.
25. Barry Smith, “From Classical Metaphysics to Medical Informatics”, Humboldt-Kosmos, 79 (July 2002), 31–32.
Italian translation as: “Dalla metafisica classica all’informatica medica” in Maurizio Ferraris (ed.), Ontologia, Naples: Guida (2003), 154–158.
26. Barry Smith, “Groups, Sets, and Wholes”, Revista di estetica, N.S. 24/3 (2003), 129–130.
27. Barry Smith and Werner Ceusters, “Towards Industrial Strength Philosophy: How Analytical Ontology Can Help Medical Informatics”, Interdisciplinary Science Reviews, 28 (2003), 106–111.
Abstract: Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated only once. By serving as a lingua franca for database integration this benchmark taxonomy would ensure that all databases calibrated in its terms would be automatically compatible with each other. We describe one strategy for creating such a lingua franca, in which philosophical ontology plays a central role.
Italian translation as: “Verso una filosofia al servizio dell’industria: l’utilità dell’ontologia analitica per l’informatica medica”, Sistemi Intelligenti, 15: 3 (2003), 407–417.
28. Barry Smith, “The Measure of Civilizations”, Academic Questions, 16: 1 (2002/03), 16–22.
Abstract: Is it possible to compare civilizations one with another? Is it possible, in other words, to construct some neutral and objective framework in terms of which we could establish in what respects one civilization might deserve to be ranked more highly than its competitors? Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reasonably claim that their fellow-believers are characteristically more moral than are many in the West). Criteria such as material well-being will need to play a role, too, as also will happiness or pleasure (and again we note that it is not clear a priori that there is more happiness in the West than there is in other civilizations). But even happiness (pace some proponents of the utilitarian philosophy) comes in different types, and to count in the civilization stakes the happiness involved would presumably need to be of the right kind. We explore what this might mean in terms of the idea of a self-chosen life plan.
29. Barry Smith, “Il senso della vita, oltre ogni nichilismo”, Il Domenicale (3 May 2003), 5.
30. Interview with Barry Smith, COSIT Features, 2003 (on-line interview series on spatial information theory).
31. Barry Smith, “Soldi, elezioni e molecole”, Il Sole 24 Ore (7 December 2003), 37.
32. Barry Smith and Berit Brogaard, “E il 16º giorno nacque un nuovo individuo”, Il Sole 24 Ore (21 December 2003).
33. Barry Smith and Enrico Berti, “Le prime cellule non sono già umane? No, altrimenti saremmo nati due volte”, Il Sole 24 Ore (28 December 2003).
34. Barry Smith, “Die Ontologie als Grundlagenwissenschaft der Informatik”, interview in Information Philosophie, 3 (2003), 120–123.
35. Barry Smith and Dirk Siebert, “Warum benutzen Ärzte keine Computer?”, Deutsches Ärzteblatt/Praxis Computer (January 2004), 18–20.
36. Barry Smith, “Die ganze Welt ist eine Bühne”, Interdisciplinary Phenomenology (Kyoto), 1 (2004), 31–44.
37. Barry Smith, Werner Ceusters and Dirk Siebert, “Was die philosophische Ontologie zur biomedizinischen Informatik beitragen kann”, Information: Wissenschaft und Praxis, 55: 3 (2004), 143–146.
38. Barry Smith, Maurizio Ferraris and Leonardo Zaibert, “La costituzione ontologica”, Il sole 24 Ore (27 June 2004).
39. Barry Smith, “Niente è più sicuro della morte e delle tasse”, Il sole 24 Ore (7 December 2004).
40. James J. Cimino and Barry Smith, “Introduction: International Medical Informatics Association Working Group 6 and the 2005 Rome Conference”, Journal of Biomedical Informatics, 2006; 39(3): 249–251.
41. Barry Smith, “Philosophical Flaws in Standardization”, The Risks of Freedom Briefing, 26 (2006), 3.
42. Thaddeus H. Grasela, Jill Fiedler-Kelly, Brenda Cirincione, Darcy Hitchcock, Kathleen Reitz, Susanne Sardella, and Barry Smith, “Informatics: The Fuel For Pharmacometric Analysis”, AAPS Journal, 2007; March, 9(1), E84–E91. PMC2751306
Abstract: The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision-making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, effectiveness and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready datasets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defining the next generation of pharmacometric informatics.
43. Barry Smith, “The Open Biomedical Ontologies (OBO) Foundry in 2008”, MMHCC (Mouse Models of Human Cancer Consortium) Newsletter, March 2008, 1–2.
44. Robert Arp and Barry Smith, “Ontologies of Cellular Networks”, Science Signalling, Vol. 1, Issue 50 (December 2008), 1-3, DOI: 10.1126/scisignal.150mr2.
Abstract: As part of a series of workshops on different aspects of biomedical ontology sponsored by the National Center for Biomedical Ontology (NCBO), a workshop titled "Ontologies of Cellular Networks" took place in Newark, New Jersey, on 27 to 28 March 2008. This workshop included more than 30 participants from various backgrounds in biomedicine and bioinformatics. The goal of the workshop was to provide an introduction to the basic tools and methods of ontology, as well as to enhance coordination between groups already working on ontologies of cellular networks. The meeting focused on three questions: What is an ontology? What is a pathway? What is a cellular network?
45. Barry Smith, Louis J. Goldberg, Alan Ruttenberg and Michael Glick, “Ontology and the Future of Dental Research Informatics”, The Journal of the American Dental Association, October, 141 (10), 2010, 1173–75.
Abstract: How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR).
46. Barry Smith and Richard H. Scheuermann, “Ontologies for Clinical and Translational Research”, Journal of Biomedical Informatics, 44:1 (2011), 3–7.
47. Barry Smith, Louis J. Goldberg, Alan Ruttenberg and Michael Glick, “Ontology and Research: Authors’ Response”, The Journal of the American Dental Association, 142(3), 2011, 252–54.
48. Fabian Neuhaus, Elizabeth Florescu, Antony Galton, Michael Gruninger, Nicola Guarino, Leo Obrst, Arturo Sánchez-Ruíz, Amanda Vizedom, Peter Yim and Barry Smith, “Creating the Ontologists of the Future”, Applied Ontology 6 (2011), 91–98.
Abstract: The goal of the Ontology Summit 2010 was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue.
49. Barry Smith, “Guest Editorial: caBIG has another fundamental problem: it relies on ‘incoherent’ messaging standard”, The Cancer Letter, 37: 16, April 22, 2011, 1 and 5–6.
50. Stefano Borgo, Riichiro Mizoguchi and Barry Smith, “On the Ontology of Functions”, Applied Ontology, 6 (2011), 99–104.
51. Andreas Tolk and Barry Smith, “Editors’ Introduction to Special Issue on Command and Control Ontology”, International Journal of Intelligent Defence Support Systems, 4 (3), 2011, 209–214.
52. Dipak Kalra, Mark Musen, Barry Smith, Werner Ceusters, “Policy Brief on Semantic Interoperability”, Interoperability Reviews: ARGOS Trans-Atlantic Observatory Policy Briefs, Washington, DC: American Medical Informatics Association, Summer 2011, Vol. 2 No. 1.
53. Georg Fuellen, Melanie Boerries, Hauke Busch, Aubrey de Grey, Udo Hahn, Thomas Hiller, Andreas Hoeflich, Ludger Jansen, Georges E. Janssens, Christoph Kaleta, Anne C. Meinema, Sascha Schäuble, Paul N. Schofield, Barry Smith, Jürgen Sühnel, Julio Vera, Wolfgang Wagner, Eva C. Wonne, Daniel Wuttke, “In-Silico-Approaches and the Role of Ontologies in Aging Research”, Rejuvenation Research, 2013 Dec;16(6):540-6.
Abstract: The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin.
54. Barry Smith, “It Usually Begins with the Gene Ontology”, Methods of Information in Medicine, 2013, 52 (6), 559-60.
Comment on P. L. Elkin, S. H. Brown and G. Wright, “Biomedical Informatics: We Are What We Publish”, Methods of Information in Medicine, 2013, 52 (6), 538-546.
55. Carolyn Korsmeyer and Barry Smith, "Comment: Kolnai's Disgust”, Emotion Review, 6 (3), 2014, 221–222.
Abstract: In his The Meaning of Disgust, Colin McGinn employs elements of the phenomenological theory of disgust advanced by Aurel Kolnai in his “On Disgust” of 1929. Kolnai’s treatment of what he calls “material” disgust and of its primary elicitors—putrefying organic matter, bodily wastes and secretions, sticky contaminants, vermin—anticipates more recent scientific treatments of this emotion as a mode of protective recoil. In her review of McGinn’s book, Nina Strohminger charges McGinn with neglecting such scientific studies. We here attempt to show how Kolnai goes beyond experimental findings in his careful description of the phenomenological differences between disgust and other emotions of forceful disapproval.
56. An interview with the Editor of The Monist, May 31, 2015, OUPblog.
57. “Faculty Interview: Barry Smith”, NousLetter, 21, Summer 2015, 13-17.
58. “The Curious Case of the Complicated Border: The Story of Baarle,” Dutch International Society Magazine, 47 (4), 2016, 11-17.
1. Barry Smith, “Roman Ingarden: Ontological Foundations for Literary Theory”, in J. Odmark (ed.), Language, Literature and Meaning I: Problems of Literary Theory, Amsterdam: Benjamins, 1979, 373–390.
Abstract: The paper seeks to apply the work of the Polish phenomenologist Roman Ingarden to certain problems in literary theory; contrasts the notions of ontological and epistemological incompleteness of the represented objects of a literary work and considers the question of the nature of such objects. The paper concludes by analyzing some of the degrees of freedom possessed by the readings of literary work in relation to the work itself.
2. Barry Smith, “Kafka and Brentano: A Study in Descriptive Psychology”, in Barry Smith (ed.), Structure and Gestalt: Philosophy and Literature in Austria-Hungary and Her Successor States, Amsterdam: John Benjamins, 1981, 113–161.
Abstract: 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 summarizes what is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself.
Revised version as: “Brentano and Kafka”, Axiomathes, 8 (1997), 83–104.
French translation as: “Kafka et Brentano”, Philosophiques, 26/2 (1999), 349–371.
3. Barry Smith, “The Production of Ideas: Notes on Austrian Intellectual History from Bolzano to Wittgenstein”, in Barry Smith (ed.), Structure and Gestalt: Philosophy and Literature in Austria-Hungary and Her Successor States, Amsterdam: John Benjamins, 1981, 211–234.
4. Barry Smith and Kevin Mulligan, “Pieces of a Theory”, in Barry Smith (ed.), Parts and Moments. Studies in Logic and Formal Ontology, Munich: Philosophia, 1982, 15–109.
Abstract: A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.
5. Barry Smith, “Introduction to Adolf Reinach, ‘On the Theory of the Negative Judgment’”, in Barry Smith (ed.), Parts and Moments. Studies in Logic and Formal Ontology, Munich: Philosophia, 1982, 289–313.
Abstract: Reinach’s essay of 1911 establishes an ontological theory of logic, based on the notion of Sachverhalt or state of affairs. He draws on the theory of meaning and reference advanced in Husserl’s Logical Investigations and at the same time anticipates both Wittgenstein’s Tractatus and later speech act theorists’ ideas on performative utterances. The theory is used by Reinach to draw a distinction between two kinds of negative judgment: the simple negative judgment, which is made true by a negative state of affairs; and the polemical negative judgment, which is a performative utterance in which the truth of some earlier judgment – typically a judgment made by some other person – is denied.
6. Barry Smith, “Meinen und Vorstellen in der literarischen Gegenstandskonstitution”, in G. Wolandt (ed.), Kunst und Kunstforschung. Beiträge zur Ästhetik, Bonn: Bouvier, 1983, 49–61.
7. Barry Smith, “Summaries and Note: On the Political Economy of Karl Wittgenstein”, in J. C. Nyíri (ed.), Karl Wittgenstein: Politico-Economic Writings, Amsterdam: John Benjamins, 1984, 197–227.
8. Barry Smith, “Wittgenstein und das ethische Gesetz”, in D. Birnbacher and A. Burkhardt (eds.), Sprachspiel und Methode. Zum Stand der Wittgenstein-Diskussion, Berlin/New York: de Gruyter, 1985, 191–211.
9. Barry Smith, “Preface: Austrian Economics from Menger to Hayek”, in Wolfgang Grassl and Barry Smith (eds.), Austrian Economics: Historical and Philosophical Background, New York: New York University Press, London/Sydney: Croom Helm, 1986, v–viii.
10. Barry Smith, “Austrian Economics and Austrian Philosophy”, in Wolfgang Grassl and Barry Smith (eds.), Austrian Economics: Historical and Philosophical Background, New York: New York University Press, London/Sydney: Croom Helm, 1986, 1–36, reprinted in the series Routledge Revivals, London: Routledge, 2010.
Abstract: Austrian economics starts out from the thesis that the objects of economic science differ from those of the natural sciences because of the centrality of the economic agent. This allows a certain a priori or essentialistic aspect to economic science of a sort which parallels the a priori dimension of psychology defended by Brentano and his student Edmund Husserl. We outline these parallels, and show how the theory of a priori dependence relations outlined in Husserl’s Logical Investigations can throw light on the Austrian account of entrepreneurship.
11. Barry Smith, “The Theory of Value of Christian von Ehrenfels”, in R. Fabian (ed.), Christian von Ehrenfels: Leben und Werk, Amsterdam: Rodopi, 1986, 150–171.
Abstract: Christian von Ehrenfels was a student of both Franz Brentano and Carl Menger and his thinking on value theory was inspired both by Brentano’s descriptive psychology and by the subjective theory of economic value advanced by Menger, the founder of the Austrian school of economics. Value, for Ehrenfels, is a function of desire, and we ascribe value to those things which we either do in fact desire, or would desire if we were not convinced of their existence. He asserts that the needed theoretical understanding of values is to be achieved by generalizing economic laws of valuation to apply to value in general. The law of marginal utility, for example, is a law to the effect that the n+1st sample of a good which I receive is ceteris paribus less valuable than the nth sample (imagine that the samples in question are, for example, a series of identical ham sandwiches). The essay describes how Ehrenfels provides on this basis an account of the different types of values, both intrinsic and non-intrinsic. It outlines also Ehrenfels views on the problem of interpersonal value-comparisons and on the struggle for survival between different values of different types.
12. Kevin Mulligan and Barry Smith, “Mach und Ehrenfels: Über Gestaltqualitäten und das Problem der Abhängigkeit”, in R. Fabian (ed.), Christian von Ehrenfels: Leben und Werk, Amsterdam: Rodopi, 1986, 85–111.
Abstract: 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.
Revised and expanded English version as: “Mach and Ehrenfels: The Foundations of Gestalt Theory”, in Barry Smith (ed.), Foundations of Gestalt Theory, Munich and Vienna: Philosophia, 1988, 124–157.
Romanian translation as: “Mach si Ehrenfels. Fundamentele teoriei gestaltiste”, in Constantin Stoenescu, Ion Tanasescu (eds.), Filosofia Austriaca, Bucharest: Pelican, 2005, 262–294.
13. Barry Smith, “Materials Towards a History of Speech Act Theory”, in A. Eschbach (ed.), Karl Bühler’s Theory of Language, Amsterdam: John Benjamins, 1987, 125–152.
Abstract: 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”.
Revised and expanded version as: “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.
Italian translation as: “Per una storia della teoria degli atti linguistici”, in: Il realismo fenomenologico. Sulla filosofia dei circoli di Monaco e Gottinga, Stefano Besoli e Luca Guidetti (eds.), Macerata: Quodlibet, 2000, 385–418.
Spanish translation as: “Una breve historia de la teoría de los actos de habla”, in Pragmatica: Desarrollos téoricos y debates, translated by Jorge Gómez, Quito: Edicion Abya-Yala, 2002, 13–82.
14. Barry Smith, “Husserl, Language and the Ontology of the Act”, in D. Buzzetti and M. Ferriani (eds.), Speculative Grammar, Universal Grammar, and Philosophical Analysis of Language, Amsterdam: John Benjamins, 1987, 205–227.
Abstract: The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations between mental acts on the one hand and underlying mental states (attitudes, beliefs), on the other, relations between my acts and states, associated uses of language and overt actions on my part and on the part of those other subjects with whom I communicate.
15. Barry Smith, “On the Cognition of States of Affairs”, in K. Mulligan (ed.), Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology, Dordrecht/Boston/Lancaster: Nijhoff, 1987, 189–225.
Abstract: 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.
Italian translation as: “Adolf Reinach e la fondazione della fenomenologia realistica”, Paradigmi, 5 (1987), 229–241 and 6 (1987), 485–507.
16. Karl Schuhmann and Barry Smith, “Adolf Reinach: An Intellectual Biography”, in K. Mulligan (ed.), Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology, Dordrecht/Boston/Lancaster: Nijhoff, 1987, 1–27.
Abstract: 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.
17. Barry Smith, “Austrian Origins of Logical Positivism”, in B. Gower (ed.), Logical Positivism in Perspective, London/Sydney: Croom Helm, 1987, Totowa: Barnes and Noble, 1988, 35–68.
Abstract: 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.
Reprinted in: K. Szaniawski (ed.), The Vienna Circle and the Lvov-Warsaw School, Dordrecht/Boston/Lancaster: Kluwer, 1989, 19–53.
18. Barry Smith, “Gestalt Theory: An Essay in Philosophy”, in Barry Smith (ed.), Foundations of Gestalt Theory, Munich and Vienna: Philosophia, 1988, 11–81.
Abstract: The Austrian philosopher Christian von Ehrenfels published his essay "On 'Gestalt Qualities'" in 1890. The essay initiated a current of thought which enjoyed a powerful position in the philosophy and psychology of the first half of this century and has more recently enjoyed a minor resurgence of interest in the area of cognitive science, above all in criticisms of the so-called 'strong programme' in artificial intelligence. The theory of Gestalt is of course associated most specifically with psychologists of the Berlin school such as Max Wertheimer, Wolfgang Kohler and Kurt Koffka. We shall see in what follows, however, that an adequate philosophical understanding of the Gestalt idea and of Ehrenfels' achievement will require a close examination not merely of the work of the Berlin school but also of a much wider tradition in Austrian and German philosophy in general.
19. Barry Smith, “Knowing How vs. Knowing That”, in J. C. Nyíri and Barry Smith (eds.), Practical Knowledge. Outlines of a Theory of Traditions and Skills, London/Sydney/New York: Croom Helm, 1988, 1–16.
Abstract: A sketch of the history of the opposition between propositional and practical knowledge is followed by a brief account of the relevant ideas of Merleau-Ponty, Polanyi, and H. and S. Dreyfus (on expertise and artificial intelligence). The paper concludes with a discussion of the work of Ryle on the notion of a ‘discipline’, drawing implications for a theory of traditions.
20. Barry Smith, “Practices of Art”, in J. C. Nyíri and Barry Smith (eds.), Practical Knowledge. Outlines of a Theory of Traditions and Skills, London/Sydney/New York: Croom Helm, 1988, 172–209.
Abstract: Starting out from the ontology of human work set out by Marx in Das Kapital, the paper seeks to analyse the relations between the artist and his actions and aims, the work of art he produces, and the audience for this work. The paper concludes with a discussion of the problem of creativity in the arts, drawing on ideas of Roman Ingarden and other phenomenologists.
21. Barry Smith, “Logic and Formal Ontology”, in J. N. Mohanty and W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, Lanham: University Press of America, 1989, 29–67.
Abstract: Logic for Husserl is a science of science, a science of what all sciences have in common in their modes of validation. Thus logic deals with universal laws relating to truth, to deduction, to verification and falsification, and with laws relating to theory as such, and to what makes for theoretical unity, both on the side of the propositions of a theory and on the side of the domain of objects to which these propositions refer. This essay presents a systematic overview of Husserl’s views on these matters as put forward in his Logical Investigations. It shows how Husserl’s theory of linguistic meanings as species of mental acts, his formal ontology of part, whole and dependence, his theory of meaning categories, and his theory of categorial intuition combine with his theory of science to form a single whole. Finally, it explores the ways in which Husserl’s ideas on these matters can be put to use in solving problems in the philosophy of language, logic and mathematics in a way which does justice to the role of mental activity in each of these domains while at the same time avoiding the pitfalls of psychologism.
Revised version in: Manuscrito, 23: 2, 2000, 275–323.
Italian translation as: “Logica e ontologia formale nelle Logische Untersuchungen di Edmund Husserl”, Rivista di Filosofia, 83, 1991, 53–70.
22. Barry Smith, “Kasimir Twardowski: An Essay on the Borderlines of Psychology, Ontology and Logic”, K. Szaniawski (ed.), The Vienna Circle and the Philosophy of the Lvov-Warsaw School, Dordrecht/Boston/Lancaster: Kluwer, 1989, 313–373.
Abstract: The influence of Kasimir Twardowski on modern Polish philosophy is all-pervasive. As is well known, almost all important 20th century Polish philosophers went through the hard training of his courses in Lvov. Twardowski instilled in his students an enduring concern for clarity and rigour. He taught them to regard philosophy as a collaborative effort, a matter of disciplined discussion and argument. And he encouraged them to work together with scientists from other disciplines — above all with psychologists, and also with mathematicians — so that the Lvov school of philosophy would gradually evolve into the Warsaw school of logic.
Revised version as: “Kasimir Twardowski: On Content and Object ”, chapter 6 of Barry Smith, Austrian Philosophy: The Legacy of Franz Brentano, La Salle and Chicago: Open Court, 1994, 160-200.
23. Barry Smith, “Constraints on Correspondence” in Traditionen und Perspektiven der analytischen Philosophie. Festschrift für Rudolf Haller, H. Rutte, W. Sauer and W. Gombocz (eds.), Vienna: Hölder/Pichler/Tempsky, 1989, 415–430.
Abstract: My aim is to lay down some constraints on a correspondence theory of truth for empirical sentences of a natural language on the basis of a theory according to which that to which a true empirical sentence of such a language corresponds is a part of the natural world. The problem is to find some means of delineating those portions of the world which serve as correspondents, portions of reality otherwise called ‘truthmakers’.
24. Barry Smith, “Logica Kirchbergensis”, in P. Klein (ed.), Praktische Logik. Traditionen und Tendenzen, Abhandlungen eines Seminars beim 13. Internationalen Wittgenstein-Symposium, Kirchberg am Wechsel 1988 (Veröffentlichungen der Joachim-Jungius Gesellschaft Hamburg, 61), Göttingen: Vandenhoeck & Ruprecht, 1989, 123–145.
Abstract: In der klassischen Logik von Aristoteles bis Wolff findet sich eine durchgängige Parallelität von logischen (einschließlich grammatikalischen und psychologischen) und ontologischen Gebilden. Der Logiker beschäftigt sich mit Subjekt und Prädikat, aber gleichzeitig auch z.B. mit Substanz und Akzidenz als Entitäten in der Welt. Nach Kant begann für die Logik eine Phase, in der diese ontologische oder objektbezogene Seite verloren ging. Gegen Ende des 19. Jahrhunderts beginnt man dann aber wieder über die ontologischen Korrelate des Denkens und des Urteilens zu sprechen. Wir zeigen, dass diese Wiederbelebung der alten Logik mit der Einführung des Terminus ‘Sachverhalt’ in die Sprache der Philosophie verbunden ist.
25. Karl Schuhmann and Barry Smith, “Vorwort”, editors’ forward to vol. I of Adolf Reinach, Sämtliche Werke. Kritische Ausgabe mit Kommentar, Karl Schuhmann and Barry Smith (eds.), Munich/Hamden/Vienna: Philosophia, 1989, XIV–XVIII.
26. Karl Schuhmann and Barry Smith, “Adolf Reinach (1884-1917)”, editors’ introduction to vol. II of Adolf Reinach, Sämtliche Werke. Kritische Ausgabe mit Kommentar, Karl Schuhmann and Barry Smith (eds.), Munich/Hamden/Vienna: Philosophia, 1989, 613–626.
27. Karl Schuhmann and Barry Smith, “Kommentar und Textkritik”, critical apparatus to vol. II of Adolf Reinach, Sämtliche Werke. Kritische Ausgabe mit Kommentar, Karl Schuhmann and Barry Smith (eds.), Munich/Hamden/Vienna: Philosophia, 1989, 627–829.
28. Barry Smith, “The Philosophy of Austrian Economics: Principles and Provocations”, in S. C. Littlechild (ed.), Austrian Economics, vol. I, Aldershot/Brookfield VT: Edward Elgar, 1990, 527–538.
29. Barry Smith, “Brentano and Marty: An Inquiry into Being and Truth”, in K. Mulligan (ed.), Mind, Meaning and Metaphysics: The Philosophy and Theory of Language of Anton Marty, Dordrecht/Boston/Lancaster: Kluwer, 1990, 111–149.
Abstract: A study of the concepts of reality and existence in the work of Franz Brentano and his student Anton Marty. Topics dealt with include: Aristotle’s concept of being in the sense of being true; operationally defined concepts; Brentano’s reism; things and states of affairs.
Revised version as: “Anton Marty: On Being and Truth”, chapter 4 of Barry Smith, Austrian Philosophy: The Legacy of Franz Brentano, La Salle and Chicago: Open Court, 1994.
30. Barry Smith, “On the Phases of Reism”, in J. Wolenski, ed., Kotarbinski: Logic, Semantics and Ontology, Dordrecht/Boston/London: Kluwer, 1990, 137–184.
Reprinted in: Actions, Products, and Things. Brentano and Polish Philosophy, A. Chrudzimski and D. Lukasiewicz (eds.), Frankfurt: ontos, 2006, 115–176.
31. Jean Petitot and Barry Smith, “New Foundations for Qualitative Physics”, in J. E. Tiles, G. T. McKee and C. G. Dean (eds.), Evolving Knowledge in Natural Science and Artificial Intelligence, London: Pitman Publishing, 1990, 231–249.
Abstract: Modern physics is not the science of some ultimate bedrock of reality. Rather (crudely speaking) it is a science which deals with a limited number of ways in which matter manifests itself in qualitative reality. It deals with these manifestations not, however, as denizens of the qualitative world, but in purified form, as quantities or magnitudes. Physics seeks to use mathematical devices to explain the given manifestations by showing how they are subject to formal laws or principles. We describe a variety of such manifestations and show how qualitative reality is preserved, in the physicists’ view of reality, but filtered through structures of a quantitative sort.
32. Barry Smith, “Grundlegung eines fallibilistichen Apriorismus”, in N. Leser, J. Seifert and K. Pflitzner (eds.), Die Gedankenwelt Sir Karl Poppers. Kritischer Rationalismus im Dialog, Heidelberg: Carl Winter Universitätsverlag, 1991, 393–411.
Abstract: We assume 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.
English translation as: “In Defense of Extreme (Fallibilistic) Apriorism”, Journal of Libertarian Studies 12 (1996), 179–192.
33. Barry Smith, “Relevance, Relatedness and Restricted Set Theory”, in G. Schurz and G. J. W. Dorn (eds.), Advances in Scientific Philosophy. Essays in Honour of Paul Weingartner, Amsterdam/Atlanta: Rodopi, 1991, 45–56.
Abstract: What sort of set theory results when restrictions are placed on the sorts of elements which may form a set? Given an arbitrary relevance relation, one can formulate a notion of set which will apply only to totalities of mutually relevant entities. Relevance might signify for example: exists at the same time as, belongs to the same body as, is less than a certain distance from, etc. The resultant theory, which embodies topological constraints, can then be used as the basis for an account of relevance between propositions which is in the tradition of the relevant logics of analytic implication studied by M. Dunn and W. T. Parry.
34. Barry Smith, “Characteristica Universalis”, in K. Mulligan (ed.), Language, Truth and Ontology (Philosophical Studies Series), Dordrecht/Boston/London: Kluwer, 1992, 48–77.
Abstract: Recent work in formal philosophy has concentrated overwhelmingly on the logical problems pertaining to epistemic shortfall - which is to say on the various ways in which partial and sometimes incorrect information may be stored and processed. A directly depicting language, in contrast, would reflect a condition of epistemic perfection. It would enable us to construct representations not of our knowledge but of the structures of reality itself, in much the way that chemical diagrams allow the representation (at a certain level of abstractness) of the structures of molecules of different sorts. A diagram of such a language would be true if that which it sets out to depict exists in reality, i.e. if the structural relations between the names (and other bits and pieces in the diagram) map structural relations among the corresponding objects in the world. Otherwise it would be false. All of this should, of course, be perfectly familiar. (See, for example, Aristotle, Metaphysics, 1027 b 22, 1051 b 32ff.) The present paper seeks to go further than its predecessors, however, in offering a detailed account of the syntax of a working universal characteristic and of the ways in which it might be used.
Danish translation in: Almen Semiotik, 14 (1998), 158–187.
35. Barry Smith, “Austrian Philosophy and Austrian Economics”, in J. Lee Auspitz, et al. (eds.), Praxiologies and the Philosophy of Economics, New Brunswick and London: Transaction Publishers, 1992, 245–272.
36. Barry Smith, “Ontology and the Logistic Analysis of Reality”, in N. Guarino and R. Poli (eds.), Proceedings of the International Workshop on Formal Ontology in Conceptual Analysis and Knowledge Representation, Padova: Institute for Systems Theory and Biomedical Engineering of the Italian National Research Council, 1993, 51–68.
Abstract: I show how mereology, taken together with certain topological notions, can yield the basis for future investigations in formal ontology. I shall attempt to show also how the mereological framework here advanced can allow the direct and natural formulation of a series of theses – for example pertaining to the concept of boundary – which can be formulated only indirectly (if at all) in set-theoretic terms.
Polish translation as: “Ontologia i logiczna analiza rzeczywistosci”, in Filozofia Nauki, 2 (1994), 5–22.
37. Barry Smith, “The New European Philosophy” in Barry Smith (ed.), Philosophy and Political Change in Eastern Europe, La Salle: The Hegeler Institute, 1993, 165–170 and 191–192.
Abstract: 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.
38. Barry Smith, “Husserl’s Theory of Meaning and Reference”, in L. Haaparanta (ed.), Mind, Meaning and Mathematics. Essays on the Philosophy of Husserl and Frege, Dordrecht/Boston/Lancaster: Kluwer, 1994, 163–183.
Abstract: This paper is a contribution to the historical roots of the analytical tradition. As Michael Dummett points out in his Origins of Analytic Philosophy, many tendencies in Central European thought contributed to the early development of analytic philosophy. Dummett himself concentrates on just one aspect of this historical complex, namely on the relationship between the theories of meaning and reference developed by Frege and by Husserl in the years around the turn of the century. It is to this specific issue that the present essay is devoted, though we attempt a more sympathetic reading of Husserl's views on these matters than is to be found in Dummett’s work. Topics covered include Husserl’s theory of intentionality, his view of meanings as types or essences of mental acts, of the relation between meaning and expression, of states of affairs, and of indexicality.
39. Barry Smith, “Filozofia Austriacka” in T. Lubowiecki and A. Rojszczak (eds.), Filozofia Austriacka (Principia VIII–IX), Cracow: Aureus S.C., 1994, 19–50. Polish translation of Chapter 1 of Barry Smith, Austrian Philosophy: The Legacy of Franz Brentano, La Salle and Chicago: Open Court, 1994.
40. Josef Seifert and Barry Smith, “The Truth about Fiction”, in W. Galewicz, E. Ströker and W. Strozewski (eds.), Kunst und Ontologie. Für Roman Ingarden zum 100. Geburtstag, Amsterdam/Atlanta: Rodopi, 1994, 97–118.
41. Barry Smith and David W. Smith, “Introduction” to Barry Smith and David W. Smith (eds.), The Cambridge Companion to Husserl, Cambridge and New York: Cambridge University Press, 1995, 1–44.
42. Barry Smith, “Common Sense”, in Barry Smith and David W. Smith (eds.), The Cambridge Companion to Husserl, Cambridge and New York: Cambridge University Press, 1995, 394–436.
Abstract: Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated.
43. Barry Smith, “The Neurath–Haller Thesis: Austria and the Rise of Scientific Philosophy”, in K. Lehrer and J. C. Marek (eds.), Austrian Philosophy Past and Present (Boston Studies in the Philosophy of Science), Dordrecht/Boston/Lancaster: Kluwer, 1996, 1–20.
Reprinted as: “Austria and the Rise of Scientific Philosophy”, in A. Chrudzimski and W. Huemer (eds.), Phenomenology and Analysis. Essays on Central European Philosophy, Frankfurt and Lancaster: ontos, 2004, 33–56.
French version as: “L’Autriche et la naissance de la philosophie scientifique”, Actes de la Recherche en Sciences Sociales (Paris), 109 (1995), 61–71.
Abstract: The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it is not Austria which is the special case when seen against the background of contemporary mainstream philosophy, but rather Germany and France.
44. Barry Smith, “Foreword” to Wojciech Zelaniec, The Recalcitrant Synthetic A Priori, Lublin: Artom, 1996, 7–8.
45. Barry Smith and Leonardo Zaibert, “Prolegomena to a Metaphysics of Real Estate”, in Roberto Casati (ed.), Shadows and Socio-Economic Units. Foundations of Formal Geography, Department of Geoinformation, Technical University of Vienna, 1996, 151–155.
Abstract: 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.
46. Barry Smith, “Pleasure and Its Modifications: Stephan Witasek and the Aesthetics of the Grazer Schule”, in L. Albertazzi (ed.), The Philosophy of Alexius Meinong (Axiomathes VII, nos. 1–2), 1996, 203–232.