• Ifomis Reports (edited book)
    with Barry Smith
    Ifomis. 2004.
  •  14
    Index
    with Katherine Munn, Barry Smith, Bert Klagges, Boris Hennig, Pierre Grenon, Ludger Jansen, Peter Heuer, Ulf Schwarz, and Ingvar Johansson
    In Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction, Ontos. pp. 329-342. 2008.
  •  27
    Is There a Quantum Geography?
    In Timothy Tambassi (ed.), The Philosophy of GIS, Springer. pp. 209-239. 2019.
    Geographyquantum this paper, I argue that a quantum Quantum theory may be the appropriate tool for describing Phenomena with indeterminate Boundariesindeterminate in the Context of the Classifications and Delineations of geographic Regions. A motivation for this claim stems from the Observations that fundamental aspects of information about the GeographyphysicalWorldphysical that follow from the success of Geographyquantum mechanics also apply to information about certain Classes of geographic P…Read more
  •  58
    One aim of this paper is to improve the logical and ontological rigor of the OBO relation ontology by providing axiomatic specifications for logical properties of relations such as part_of, located...
  •  1780
    This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in …Read more
  •  358
    A Theory of Granular Partitions
    In Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction, Ontos. pp. 125-158. 2008.
    Imagine that you are standing on a bridge above a highway checking off the makes and models of the cars that are passing underneath; or a laboratory technician sorting samples of bacteria into species and subspecies; or you are making a list of the fossils in your museum. In each of these cases, you are employing a certain grid of labeled units, and you are recognizing certain objects as being located in those units. Such a grid of labeled units is an example of what we shall call a granular par…Read more
  •  84
    Information, mereology and vagueness
    Applied ontology 18 (2): 119-167. 2023.
    Classical systems of mereology identify a maximuml set of jointly exhaustive and pairwise disjoint (RCC5) relations. The amount of information that is carried by each member of this set of (crisp) relations is determined by the number of bits of information that are required to distinguish all the members of the set. It is postulated in this paper, that vague mereological relations are limited in the amount of information they can carry. That is, if a crisp mereological relation can carry N bits…Read more
  •  121
    The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
    with Robert Hoehndorf, Colin Batchelor, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris J. Mungall, Jane S. Richardson, Jesse Stombaugh, and Eric Westhof
    Applied ontology 6 (1): 53-89. 2011.
    Biomedical Ontologies integrate diverse biomedical data and enable intelligent data-mining and help translate basic research into useful clinical knowledge. We present the RNA Ontology (RNAO), an o...
  •  135
    Classical (i.e., non-quantum) mechanics is the foundation of many models of dynamical physical phenomena. As such those models inherit the ontological commitments inherent in the underlying physics...
  •  260
    Summation relations and portions of stuff
    Philosophical Studies 143 (2): 167-185. 2009.
    According to the prevalent 'sum view' of stuffs, each portion of stuff is a mereological sum of its subportions. The purpose of this paper is to re-examine the sum view in the light of a modal temporal mereology which distinguishes between different varieties of summation relations. While admitting David Barnett's recent counter-example to the sum view, we show that there is nonetheless an important sense in which all portions of stuff are sums of their subportions. We use our summation relation…Read more
  •  84
    Vague size predicates
    Applied ontology 6 (4): 317-343. 2011.
    Vague predicates such as heap, tall, bald, near to, nicer than, etc., are characterized by their Sorites susceptibility and the existence of borderline cases. In attempting to develop a general theory, diverse vague predicates are often analyzed in rather broad natural language settings. Because this has proven to be rather difficult, the phenomenon of vagueness is studied here in a narrower and strictly formalized setting: Vague size predicates such as “roughly the same size” and “negligible in…Read more
  •  1238
    A Spatio-Temporal Ontology for Geographic Information Integration
    International Journal for Geographical Information Science 23 (6): 765-798. 2009.
    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 pa…Read more
  •  154
    In R. Holte and A. Howe (eds.), Proceedings of the Twenty-Second AAAI Conference on Artificial Intelligence (AAAI-07).
  •  1279
    Basic Formal Ontology for bioinformatics
    with Barry Smith and Anand Kumar
    IFOMIS Reports. 2005.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith…Read more
  •  621
    The theory of granular partitions is designed to capture in a formal framework important aspects of the selective character of common-sense views of reality. It comprehends not merely the ways in which we can view reality by conceiving its objects as gathered together not merely into sets, but also into wholes of various kinds, partitioned into parts at various levels of granularity. We here represent granular partitions as triples consisting of a rooted tree structure as first component, a doma…Read more
  •  636
    Directly depicting granular ontologies
    In Thomas Bittner & Barry Smith (eds.), Directly depicting granular ontologies, . pp. 117--151. 2004.
    Published in extended form as "Endurants and Perdurants in Directly Depicting Ontologies", We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate in such processes. For this purpose we distinguish between ontologies and metaontology. Ontologies are based on very simple directly depicting languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent …Read more
  •  1013
    Normalizing medical ontologies using Basic Formal Ontology
    In K. Versorgung & V. Forschung (eds.), Ubiquitäre Information (Proceedings of GMDS 2004), Videel Ohg. pp. 199-201. 2004.
    Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized…Read more
  •  783
    Vague Reference and Approximating Judgements
    Spatial Cognition and Computation 3 (2). 2003.
    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 …Read more
  •  109
    This paper shows in a case study that for the development, the presentation, and the computer-assisted verification of formal ontologies the usage of higher-order languages and associated proof ass...
  •  703
    Formal ontologies of space and time
    In Thomas Bittner & Barry Smith (eds.), Ifomis Reports, Ifomis. 2004.
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The…Read more
  •  1146
    Granular Partitions and Vagueness
    In Barry Smith & Christopher Welty (eds.), Formal Ontology in Information Systems (FOIS), Acm Press. pp. 309-320. 2001.
    There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extensio…Read more
  •  782
    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 c…Read more
  •  1185
    A Taxonomy of Granular Partitions
    In W. Kuhn M. F. Worboys & S. Timpf (eds.), Spatial Information Theory: Foundations of Geographic Informa­tion Science, Springer. pp. 28-43. 2003.
    In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed partitions along…Read more
  •  1405
    A Theory of Granular Partitions
    In Matt Duckham, Michael F. Goodchild & Michael Worboys (eds.), Foundations of Geographic Information Science, Taylor & Francis. pp. 117-151. 2003.
    We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentional…Read more
  •  716
    We propose a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this semantic view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this theory provides a general fr…Read more