The conventional approach to developing expert systems views the domain of application as being “formally defined”. This view often leads to practical problems when expert systems are built using this approach. This paper examines the implications and problems of the formal approach to expert system design and proposes an alternative approach based on the concept of semi-formal domains. This approach, which draws on the work of socio-technical information systems, provides guidelines which can be used for the (...) design of successful expert systems. (shrink)

Disputes over causes play a central role in legal argumentation and liability attribution. Legal approaches to causation often struggle to capture cause-in-fact in complex situations, e.g. overdetermination, preemption, omission. In this paper, we first assess three current theories of causation to illustrate their strengths and weaknesses in capturing cause-in-fact. Secondly, we introduce a semi-formal framework for modelling causal arguments through strict and defeasible rules. Thirdly, the framework is applied to the Althen vaccine injury case. And lastly, we discuss (...) the need for new criteria based on a common causal argumentation framework and propose ideas on how to integrate the current theories of causation to assess the strength of causal arguments, while also acknowledging the tension between evidence-based and policy-based causal analysis in law. (shrink)

Disputes over causes play a central role in legal argumentation and liability attribution. Legal approaches to causation often struggle to capture cause-in-fact in complex situations, e.g. overdetermination, preemption, omission. In this paper, we first assess three current theories of causation to illustrate their strengths and weaknesses in capturing cause-in-fact. Secondly, we introduce a semi-formal framework for modelling causal arguments through strict and defeasible rules. Thirdly, the framework is applied to the Althen vaccine injury case. And lastly, we discuss (...) the need for new criteria based on a common causal argumentation framework and propose ideas on how to integrate the current theories of causation to assess the strength of causal arguments, while also acknowledging the tension between evidence-based and policy-based causal analysis in law. (shrink)

Disputes over causes play a central role in legal argumentation and liability attribution. Legal approaches to causation often struggle to capture cause-in-fact in complex situations, e.g. overdetermination, preemption, omission. In this paper, we first assess three current theories of causation to illustrate their strengths and weaknesses in capturing cause-in-fact. Secondly, we introduce a semi-formal framework for modelling causal arguments through strict and defeasible rules. Thirdly, the framework is applied to the Althen vaccine injury case. And lastly, we discuss (...) the need for new criteria based on a common causal argumentation framework and propose ideas on how to integrate the current theories of causation to assess the strength of causal arguments, while also acknowledging the tension between evidence-based and policy-based causal analysis in law. (shrink)

Context: Von Foerster’s concept of eigenbehavior can be recognized against the broader context of enactivism as it has been advocated by Varela, Thompson and Rosch, by Noë and recently by Hutto and Myin, among others. This flourishing constellation of ideas is on its way to becoming the new paradigm of cognitive science. However, in my reading, enactivism, putting stress on the constitutive role of action when it comes to mind and perception, faces a serious philosophical challenge when attempting to account (...) for the way we actually perceive our environments, most importantly for the fact that we perceive things or objects. Von Foester’s eigenbehavior is understood here as a concept supposed to take on this challenge. Problem: In this article I tackle the following issues: Enactivism must be able to account for the apparent stability of the perceived world: this is not a realm of a never-ending flux of stimuli; it is a realm of stable things. Enactivism is committed to the anti-Cartesian endeavor seeking to bridge the gap between the inner and the outer; between the subjective and the objective. Now, these two points constrain each other so that one cannot address simply by regarding the apparent stability of things as a projection that springs out of the internal machinery binding inputs with outputs. This is because the very idea of such an internal machinery opposes, i.e., it employs the Cartesian dichotomy. So, enactivism is in need of an account of that would not oppose its anti-Cartesian commitment. Method: I introduce the ontology of location and niche theory, as it has been brought forth by Varzi, Casati, and Smith, and develop it so that it can be used in the philosophy of mind. This is a conceptual, semi-formal philosophical analysis. Results: I shall come up with the idea of object conceived of a product of action, and - drawing on von Foerster’s central idea - as a product of coordination of perceptions. Yet, it is not coordination of stimuli but coordination of cognitive connections. The notion of connection is thus articulated in the article and cast as the central concept in my proposal. Implications: We are able to account for both and (2. The apparent stability of the perceived world is due to the setting up and maintaining of connections between the perceiver and the things perceived, resulting in the establishment of what I call a cognitive niche. Constructivist content: Constructivism, broadly construed, takes, in my reading, a negative stance in the first place. Namely, it opposes what I call the metaphysics of the ready-made world. So, it holds that there is no ready-made reality; however it remains open when it comes to positive claims: a mind-independent reality does not exist at all or it does exist but it is not ready-made and as such it must be brought to completion, so to speak, or enacted, as Varela et al. would say, by a cognitive subject. In this article, I follow the latter and address one specific issue: how the enacted world gains its relatively stable architecture. (shrink)

Introduction: I lay out the broad contours of my thesis: a defence of mathematical nominalism, and nominalism more generally. I discuss the possibility of metaphysics, and the relationship of nominalism to naturalism and pragmatism. Chapter 2: I delineate an account of abstractness. I then provide counter-arguments to claims that mathematical objects make a di erence to the concrete world, and claim that mathematical objects are abstract in the sense delineated. Chapter 3: I argue that the epistemological problem with abstract objects (...) is not best understood as an incompatibility with a causal theory of knowledge, or as an inability to explain the reliability of our mathematical beliefs, but resides in the epistemic luck that would infect any belief about abstract objects. To this end, I develop an account of epistemic luck that can account for cases of belief in necessary truths and apply it to the mathematical case. Chapter 4: I consider objections, based on metaphysical considerations and linguistic data, to the view that the existential quantifier expresses existence. I argue that these considerations can be accommodated by an existentially committing quantifier when the pragmatics of quantified sentences are properly understood. I develop a semi-formal framework within which we can define a notion of nominalistic adequacy. I show how our notion of nominalistic adequacy can show why it is legitimate for the nominalist to make use of platonistic “assumptions” in inference-making. Chapter 5: I turn to the application of mathematics in science, including explanatory applications, and its relation to a number of indispensability arguments. I consider also issues of realism and anti-realism, and their relation to these arguments. I argue that abstraction away from pragmatic considerations has acted to skew the debate, and has obscured possibilities for a nominalistic understanding of mathematical practices. I end by explaining the notion of a pragmatic meta-vocabulary, and argue that this notion can be used to carve out a new way of locating our ontological commitments. Chapter 6: I show how the apparatus developed in earlier chapters can be utilised to roll out the nominalist project to other domains of discourse. In particular, I consider propositions and types. I claim that a unified account of nominalism across these domains is available. Conclusion: I recapitulate the claims of my thesis. I suggest that the goal of mathematical enquiry is not descriptive knowledge, but understanding. (shrink)

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. (shrink)

James Franklin has argued that the formal, mathematical sciences of complexity — network theory, information theory, game theory, control theory, etc. — have a methodology that is different from the methodology of the natural sciences, and which can result in a knowledge of physical systems that has the epistemic character of deductive mathematical knowledge. I evaluate Franklin’s arguments in light of realistic examples of mathematical modelling and conclude that, in general, the formal sciences are no more able to (...) guarantee certainty than the natural sciences. Yet the formal sciences are characterized by a ‘domain-independence’ that is philosophically interesting, and I argue that it is this property that Franklin actually employs to distinguish the formal from the natural sciences. I use Einstein’s ‘principle’/‘constructive’ theory distinction to contrast the domain-independence of physical theories with the domain-independence of formal mathematical theories, and show how both kinds of domain-independence function to generate the domain-independence that is observed in the complex systems sciences. © 1999 Elsevier Science Ltd. All rights reserved. (shrink)

Replies to Kevin de Laplante’s ‘Certainty and Domain-Independence in the Sciences of Complexity’ (de Laplante, 1999), defending the thesis of J. Franklin, ‘The formal sciences discover the philosophers’ stone’, Studies in History and Philosophy of Science, 25 (1994), 513-33, that the sciences of complexity can combine certain knowledge with direct applicability to reality.

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Domain extension in mathematics occurs whenever a given mathematical domain is augmented so as to include new elements. Manders argues that the advantages of important cases of domain extension are captured by the model-theoretic notions of existential closure and model completion. In the specific case of domain extension via ideal elements, I argue, Manders’s proposed explanation does not suffice. I then develop and formalize a different approach to domain extension based on Dedekind’s Habilitationsrede, to which Manders’s account is compared. I (...) conclude with an examination of three possible stances towards extensions via ideal elements. (shrink)

Assuming the indefinite extensibility of any domain of quantification leads to reasoning with extensible domain semantics. It is showed that some theorems (e.g. Thomson's) in conventional semantics logic are not theorems in a logic provided with this new semantics.

Any discussion of the concept of “formal science” must acknowledge that the term is used in different ways, for different purposes, by different people. For some, the formal sciences are defined by the exclusive use of deductive methods for discovering, or reasoning about, the properties of formal, abstract systems. On this view, the formal sciences are synonymous with mathematics, formal logic, and certain branches of linguistics and computer science that emphasize the study of formal (...) languages. For others, “formal science” means something like “exact science”, or “formalized science”. On this view, any scientific discipline that places heavy emphasis on mathematical or logical formalization of key theoretical concepts and theories, could be described as a formal science. This latter conception of formal science is much more liberal than the former, and would include all of physics, much of chemistry, and some parts of biology, ecology, psychology and economics, as well as newer computationoriented disciplines like artificial life and artificial intelligence that do not fit easily within the traditional classification of the sciences. (shrink)

This paper develops the first parts of a logical framework for the empirical sciences, by means of a redefinition of theory structuralism as originally developed by Joseph Sneed, Wolfgang Stegmüller, and others, in the context of a ‘rigid’ logic as based on a fixed (therefore rigid) ontology. The paper defends a formal conception of the empirical sciences that has an irreducible ontological basis and is unable, in general, to provide purely structural characterizations of the domain of a theory. The (...) extreme rationalist utopia of a characterization of the real world ‘up to isomorphism’, therefore, is rejected. (shrink)

This article proposes a method for the semi-automatic extraction of resemblance metaphor terms from a manually annotated corpus of marine biology texts in English and Spanish. The corpus was first searched for target domain terms as well as for lexical markers indicative of metaphors. The combination of these search strategies for metaphor extraction resulted in a set of English-Spanish term pairs. After analysing and comparing these metaphor candidates, a quantitative analysis provided comparative statistical data regarding marine biology metaphor. Finally, (...) the metaphorical nature of marine biology terms was verified in three ways. The first verification strategy entailed an adapted version of the Metaphor Identification Procedure (CitationPragglejaz Group, 2007). The second involved the analysis of contextual data extracted from the corpus, and the third involved the analysis of visual images from an online marine biology database and from the Google search engine. (shrink)

Semi-contraction is a withdrawal operation defined by Fermé in "On the logic of theory change: Contraction without recovery." In this paper we propose: (1) an axiomatic characterization of semi-contraction; (2) an alternative construction for semi-contraction based on semi-saturatable sets, inspired by Levi's saturatable sets; (3) a special kind of semi-contraction that satisfies the Lindström and Rabinowicz interpolation thesis.

The aim of this work is to analyse the concept of semi-sentence from a linguistic, formal and computational point of view. A semi-sentence can be characterised as a sentence which, from a grammatical perspective, is neither absolutely correct nor incorrect . This study focuses on: - a characterisation of the semi-sentences in the setting of the grammar of a language. This study will help to analyse in depth the concept of grammaticality [3]; - the correlate of (...) semi-sentences in formal languages, i.e., semi-strings, which arise from applying productions that deviate from that which is strictly permitted by the rules of grammar [6]; - a Prolog program for handling semi-grammaticality in a computational manner [2]. (shrink)

These notes discuss formalizing contexts as first class objects. The basic relationships are: ist(c,p) meaning that the proposition p is true in the context c, and value(c,p) designating the value of the term e in the context c Besides these, there are lifting formulas that relate the propositions and terms in subcontexts to possibly more general propositions and terms in the outer context. Subcontextx are often specialised with regard to time, place and terminology. Introducing contexts as formal objects will (...) permit axiomatizations in limited contexts to be expanded to transcend the original limitations. This seems necessary to provide AI programs using logic with certain capabilities that human fact representation and human reasoning possess. Fully implementing transcendence seems to require further extensions to mathematical logic, ie. beyond the nonmonotonic inference methods first invented in AI and now studied as a new domain of logic. (shrink)

We study semi-isolation as a binary relation on the locus of a complete type and prove that—under some additional assumptions—it induces the strict order property.

Inspired by a framework of multi lingual sequent calculus, we introduce a formal logical system called locally continuous sequent calculus to represent _L_-domains. By considering the logic states defined on locally continuous sequent calculi, we show that the collection of all logic states of a locally continuous sequent calculus with respect to set inclusion forms an _L_-domain, and every _L_-domain can be obtained in this way. Moreover, we define conjunctive consequence relations as morphisms between our sequent calculi, and (...) prove that the category of locally continuous sequent calculi and conjunctive consequence relations is equivalent to that of _L_-domains and Scott-continuous functions. This result extends Abramsky’s “Domain theory in logical form” to a continuous setting. (shrink)

Exact sciences are described as sciences whose theories are formalized. These are contrasted to inexact sciences, whose theories are not formalized. Formalization is described as a broader category than mathematization, involving any form/content distinction allowing forms, e.g., as represented in theoretical models, to be studied independently of the empirical content of a subject-matter domain. Exactness is a practice depending on the use of theories to control subject-matter domains and to align theoretical with empirical models and not merely a state (...) of a science. Inexact biological sciences tolerate a degree of “mismatch” between theoretical and empirical models and concepts. Three illustrations from biological sciences are discussed in which formalization is achieved by various means: Mendelism, Weismannism, and Darwinism. Frege’s idea of a “conceptual notation” is used to further characterize the notion of a form/content distinction. (shrink)

What counts as human rationality: reasoning processes that embody content-independent formal theories, such as propositional logic, or reasoning processes that are well designed for solving important adaptive problems? Most theories of human reasoning have been based on content-independent formal rationality, whereas adaptive reasoning, ecological or evolutionary, has been little explored. We elaborate and test an evolutionary approach, Cosmides' social contract theory, using the Wason selection task. In the first part, we disentangle the theoretical concept of a “social contract” (...) from that of a “cheater-detection algorithm”. We demonstrate that the fact that a rule is perceived as a social contract — or a conditional permission or obligation, as Cheng and Holyoak proposed — is not sufficient to elicit Cosmides' striking results, which we replicated. The crucial issue is not semantic, but pragmatic: whether a person is cued into the perspective of a party who can be cheated. In the second part, we distinguish between social contracts with bilateral and unilateral cheating options. Perspective change in contracts with bilateral cheating options turns P & not-Q responses into not-P & Q responses. The results strongly support social contract theory, contradict availability theory, and cannot be accounted for by pragmatic reasoning schema theory, which lacks the pragmatic concepts of perspectives and cheating detection. (shrink)

This paper discusses the stability and Hopf bifurcation analysis of the diffusive Kaldor–Kalecki model with a delay included in both gross product and capital stock functions. The reaction-diffusion domain is considered, and the Galerkin analytical method is used to derive the system of ordinary differential equations. The methodology used to determine the Hopf bifurcation points is discussed in detail. Furthermore, full diagrams of the Hopf bifurcation regions considered in the stability analysis are shown, and some numerical simulations of the limit (...) cycle are used to confirm the theoretical outcomes. The delay investment parameter and diffusion coefficient can have great impacts on the Hopf bifurcations and stability of the business cycle model. The investment parameters for the gross product and capital stock as well as the adjustment coefficient of the production market are also studied. These parameters can cause instability in, and the stabilization of, the business cycle model. In addition, we point out that, as the delay investment parameter increases, the Hopf bifurcation points for the diffusion coefficient values decrease considerably. When the delay investment parameter has a very small value, the solution of the business cycle model tends to become steady. (shrink)

This work has been selected by scholars as being culturally important and is part of the knowledge base of civilization as we know it. This work is in the public domain in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. Scholars believe, and we concur, that this work is important enough to be (...) preserved, reproduced, and made generally available to the public. To ensure a quality reading experience, this work has been proofread and republished using a format that seamlessly blends the original graphical elements with text in an easy-to-read typeface. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

Ontology and theology cannot be combined if ontology excludes non physical causes. This paper examines some possibilities for ontology to be combined with theology in so far as non physical causes are permitted. The paper builds on metaphysical findings that shows that separate ontological domains can interact causally indirectly via interfaces. As interfaces are not universes a first universe is allowed to be caused by an interface without violating the principle of causal closure of any universe. Formal theology (...) can therefore be based on the assumption that the (first) universe is caused by God if God is defined as the first cause. Given this, formal theology and science can have the same ontological base. (shrink)

Researchers in areas such as artificial intelligence, formal and computational linguistics, biomedical informatics, conceptual modeling, knowledge engineering and information retrieval have come to realise that a solid foundation for their research calls for serious work in ontology, understood as a general theory of the types of entities and relations that make up their respective domains of inquiry. In all these areas, attention is now being focused on the content of information rather than on just the formats and languages (...) used to represent information. The clearest example of this development is provided by the many initiatives growing up around the project of the Semantic Web. And, as the need for integrating research in these different fields arises, so does the realisation that strong principles for building well-founded ontologies might provide significant advantages over ad hoc, case-based solutions. The tools of formal ontology address precisely these needs, but a real effort is required in order to apply such philosophical tools to the domain of information systems. Reciprocally, research in the information sciences raises specific ontological questions which call for further philosophical investigations. The purpose of FOIS is to provide a forum for genuine interdisciplinary exchange in the spirit of a unified effort towards solving the problems of ontology, with an eye to both theoretical issues and concrete applications. This book contains a wide range of areas, all of which are important to the development of formal ontologies. (shrink)

I distinguish two types of reduction within the context of quantum-classical relations, which I designate “formal” and “empirical”. Formal reduction holds or fails to hold solely by virtue of the mathematical relationship between two theories; it is therefore a two-place, a priori relation between theories. Empirical reduction requires one theory to encompass the range of physical behaviors that are well-modeled in another theory; in a certain sense, it is a three-place, a posteriori relation connecting the theories and the (...) domain of physical reality that both serve to describe. Focusing on the relationship between classical and quantum mechanics, I argue that while certain formal results concerning singular \ limits have been taken to preclude the possibility of reduction between these theories, such results at most provide support for the claim that singular limits block reduction in the formal sense; little if any reason has been given for thinking that they block reduction in the empirical sense. I then briefly outline a strategy for empirical reduction that is suggested by work on decoherence theory, arguing that this sort of account remains a fully viable route to the empirical reduction of classical to quantum mechanics and is unaffected by such singular limits. (shrink)

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”. (shrink)

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 such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of 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 one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes 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. (shrink)

This volume is a collection of original contributions about the core knowledge in fundamental domains. It includes work on naive physics, such as formal specifications of intuitive theories of spatial relations, time causality, substance and physical objects, and on naive psychology.

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and (...) relations employing the BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

FOIS is the flagship conference of the International Association for Ontology and its Applications, a non-profit organization which promotes interdisciplinary research and international collaboration at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science. This book presents the papers delivered at FOIS 2023, the 13th edition of the Formal Ontology in Information Systems conference. The event was held as a sequentially-hybrid event, face-to-face in Sherbrooke, Canada, from 17 to 20 July 2023, and online from 18 to (...) 20 September 2023. In total, 62 articles from 19 different countries were submitted, out of which 25 were accepted for inclusion in the conference and for publication; corresponding to an acceptance rate of 40 percent. The contributions are separated into the book’s three sections: (1) Foundational ontological issues; (2) Methodological issues around the development, alignment, verification and use of ontologies; and (3) Domain ontologies and ontology-based applications. In these sections, ontological aspects from a wide variety of fields are covered, primarily from various engineering domains including cybersecurity, manufacturing, petroleum engineering, and robotics, but also extending to the humanities, social sciences, medicine, and dentistry. A noticeable trend among the contributions in this edition of the conference is the recognition that improving the tools to analyze, align, and improve ontologies is of paramount importance in continuing to advance the field of formal ontology. The book will be of interest to all formal and applied ontology researchers, and to those who use formal ontologies and information systems as part of their work. (shrink)

Each science has its own domain of investigation, but one and the same science can be formalized in different languages with different universes of discourse. The concept of the domain of a science and the concept of the universe of discourse of a formalization of a science are distinct, although they often coincide in extension. In order to analyse the presuppositions and implications of choices of domain and universe, this article discusses the treatment of omega arguments in three very different (...) formalizations of arithmetic. In Peano's formalization the domain is a restricted class of individuals, while the universe of discourse is the unrestricted class of all individuals. In Gödel's formalization the domain is a restricted class of individuals as in Peano's formalization, but the universe of discourse coincides with the domain. In Whitehead-Russell's formalization the domain is a class of logical notions in Tarski's sense, that are necessarily not individuals, whereas the universe of discourse is the unrestricted class of individuals as in Peano's formalization. The present approach emphasizes the viewpoint that the universe of discourse of a given discourse is important in determining which propositions are expressed by which sentences. (shrink)

In this article, we reflect on the use of formal methods in the philosophy of science. These are taken to comprise not just methods from logic broadly conceived, but also from other formal disciplines such as probability theory, game theory, and graph theory. We explain how formal modelling in the philosophy of science can shed light on difficult problems in this domain.

The syntactic domain of tense is the clause: tense appears in some form in every clause of a tensed language. Semantic interpretation of tense requires information from context, however. This has been clear at least since Partee's 1984 demonstration of the anaphoric properties of tense. In this talk I will show that the facts about context are quite complex, perhaps more so than has been appreciated. There are three patterns of tense interpretation, depending on the type of discourse context in (...) which a clause appears. I will introduce the notion of discourse mode to account for the different types of context.1 I offer an interpretation of tense in Discourse Representation Theory, a framework which is organized to deal with information from the context. I also show that a syntactically based theory can handle contextually-based tense interpretation. In §1 I set out the basic analysis of tense and show how it applies to sentences in isolation. §2 discusses types of discourse context and patterns of tense interpretation; §3 considers the formal analysis of tense; §4 concludes with a summary and a prediction about temporal interpretation in tenseless languages. (shrink)

The growth of the Semantic Web resulted in the emergence of various kinds of artificial agents navigating the web, sharing resources and communicating among each other in a more and more sophisticated fashion. No one denies the relevance of research concerning the establishment of architectures and models for representing and enabling interaction and communication among agents. In another domain, ontologies have been consecrated as an essential tool to structure information in order to facilitate shareability and re-usability of knowledge resources like (...) the ones found on the Web. It is therefore no surprise that the management of ontologies by interacting and communicating agents is a hot topic for the whole Semantic Web community. In addition, the ontological foundations of agent interaction still remain a very active research area. The present issue of Applied Ontology on Formal Ontologies for Communicating Agents follows a workshop organized in July/August 2006 in the scope of the 11th European Summer School in Logic, Language and Information. After the workshop we issued an open call for contributions that allowed us to select a focused range of works addressing the research topics raised in the original workshop call. We would like to thank Nicola Guarino and Laure Vieu for their help in the organization process, as well as all the reviewers and authors, all workshop participants and other people who contributed in various ways to the success of the workshop and of this issue of Applied Ontology. (shrink)

In fields such as medicine, geography, and mechanics, spatial reasoning involves reasoning about entities that may coincide without overlapping. Some examples are: cavities and invading particles, passageways and valves, geographic regions and tropical storms. The purpose of this paper is to develop a formal theory of spatial relations for domains that include coincident entities. The core of the theory is a clear distinction between mereotopological relations, such as parthood and connection, and relative location relations, such as coincidence. To (...) guide the development of the formal theory, I construct mathematical models in which nontrivial relative location relations are defined. (shrink)

This book describes the mathematical aspects of the semantics of programming languages. The main goals are to provide formal tools to assess the meaning of programming constructs in both a language-independent and a machine-independent way, and to prove properties about programs, such as whether they terminate, or whether their result is a solution of the problem they are supposed to solve. In order to achieve this the authors first present, in an elementary and unified way, the theory of certain (...) topological spaces that have proved of use in the modelling of various families of typed lambda calculi considered as core programming languages and as meta-languages for denotational semantics. This theory is now known as Domain Theory, and was founded as a subject by Scott and Plotkin. One of the main concerns is to establish links between mathematical structures and more syntactic approaches to semantics, often referred to as operational semantics, which is also described. This dual approach has the double advantage of motivating computer scientists to do some mathematics and of interesting mathematicians in unfamiliar application areas from computer science. (shrink)

The archetypal Rumely domain is the ring \widetildeZ of algebraic integers. Its constructible Boolean algebra is atomless. We study here the opposite situation: Rumely domains whose constructible Boolean algebra is atomic. Recursive models (which are rings of algebraic numbers) are proposed; effective model-completeness and decidability of the corresponding theory are proved.

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 2003]. Where information systems ontologists seek to maximize (...) reasoning efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from (...) BFO. The axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

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 to 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. (shrink)

Objectives: Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often (...) misinterpreted to encode all kinds of statements, including those which are not ontological. Method: We distinguish four kinds of statements needed to comprehensively represent domain knowledge: universal statements, terminological statements, statements about particulars and contingent statements. We argue that the task of formal ontologies is solely to represent universal statements, while the non-ontological kinds of statements can nevertheless be connected with ontological representations. To illustrate these four types of representations, we use a running example from parasitology. Results: We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and reasoning applications like clinical decision support systems. (shrink)