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)

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)

Some formal ontological relations are identified, in the context of an account of ontological categorization. It is argued that neither formal ontological relations nor ontological categories should themselves be regarded as elements of being, but that this does not undermine the claim of formal ontology to be a purely objective science. It is also argued that some formal ontological relations, like some ontological categories, are more basic than others. A four‐category ontology is proposed, in which two (...) basic categories of universals and two basic categories of particulars are distinguished in terms of certain formal ontological relations characteristically obtaining between entities belonging to the different categories. (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)

Formal ontology as a main branch of metaphysics investigates categories of being. In the formal ontological approach to metaphysics, these ontological categories are analysed by ontological forms. This analysis, which we illustrate by some category systems, provides a tool to assess the clarity, exactness and intelligibility of different category systems or formal ontologies. We discuss critically different accounts of ontological form in the literature. Of ontological form, we propose a character- neutral relational account. In this metatheory, (...) ontological forms of entities are their standings in internal relations whose holding is neutral on the character of their relata. These relations are “formal ontological relations”. Entities belong to ontological categories because they stand in the same formal ontological relations. We hold a nominalist relationalism about ontological categories and forms. We conclude by showing that our metatheory is useful for understanding categorial fundamentality/non- fundamentality, different formal ontologies, and for unifying metaphysical questions. (shrink)

Formal ontology combines two ideas, one originating with Husserl, the other with Frege: that of ontology of the formal aspects of all objects, irrespective of their particular nature, and ontology pursued by employing the tools of modern formal disciplines, notably logic and semantics. These two traditions have converged in recent years and this is the first collection to encompass them as a whole in a single volume. It assembles essays from authors around the world already widely known (...) for their work in formal ontology, and illustrates that through the application of formal methods the ancient discipline of ontology may be put on a firm methodological basis. The essays not only illuminate the nature of ontology and its relation to other areas, in language, logic and everyday life, but also demonstrate that common issues from the analytical and phenomenological traditions may be discussed without ideological barriers. Audience: advanced students of and specialists in philosophy, linguistics, cognitive science, computer science, database engineering. (shrink)

Axiomatic Formal Ontology is a fairly comprehensive systematic treatise on general metaphysics. The axiomatic method is applied throughout the book. Its main theme is the construction of a general non-set-theoretical theory of intensional entities. Other important matters discussed are the metaphysics of modality, the nature of actual existence, mereology and the taxonomy of entities.

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)

This volume collects the papers presented at the 9th edition of the Formal Ontology in Information Systems conference, FOIS 2016, held July 6–9, 2016, in Annecy, France. As in the previous editions, FOIS 2016 included keynote addresses, full paper presentations, an Ontology Competition, an Early Career Symposium in its scientific program and was preceded by the Interdisciplinary Summer School on Ontological Analysis, now at its third edition and held June 27–July 1 in Bolzano-Bozen, Italy.

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)

The problem of concept representation is relevant for many sub-fields of cognitive research, including psychology and philosophy, as well as artificial intelligence. In particular, in recent years it has received a great deal of attention within the field of knowledge representation, due to its relevance for both knowledge engineering as well as ontology-based technologies. However, the notion of a concept itself turns out to be highly disputed and problematic. In our opinion, one of the causes of this state of affairs (...) is that the notion of a concept is, to some extent, heterogeneous, and encompasses different cognitive phenomena. This results in a strain between conflicting requirements, such as compositionality, on the one hand and the need to represent prototypical information on the other. In some ways artificial intelligence research shows traces of this situation. In this paper, we propose an analysis of this current state of affairs. Since it is our opinion that a mature methodology with which to approach knowledge representation and knowledge engineering should also take advantage of the empirical results of cognitive psychology concerning human abilities, we outline some proposals for concept representation in formal ontologies, which take into account suggestions from psychological research. Our basic assumption is that knowledge representation systems whose design takes into account evidence from experimental psychology may therefore give better results in many applications. (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)

Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.

This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present - in other words, virtually any area of activity. The conceptualization relies on recent philosophical and psychological research on artefacts, having resulted in a largely consensual theoretical basis. Furthermore, this ontology of artefacts extends the foundational DOLCE ontology and supplements its axiomatization. The conceptual primitives are as follows: artificial entity, (...) intentional production of entities, (state of) capacity, capacity to play a role in actions of a given type, function and functional object. These primitives enable artefacts in general to be characterized as intentionally and successfully produced entities, and isolate an important subclass of “technical” artefacts to which a function is ascribed. Lastly, we emphasize the novelty of this ontology by comparing it with other works with similar objectives. (shrink)

We propose a novel, ontological approach to studying mathematical propositions and proofs. By “ontological approach” we refer to the study of the categories of beings or concepts that, in their practice, mathematicians isolate as fruitful for the advancement of their scientific activity (like discovering and proving theorems, formulating conjectures, and providing explanations). We do so by developing what we call a “formal ontology” of proofs using semantic modeling tools (like RDF and OWL) developed by the computer science community. In (...) this article, (i) we describe this new approach and, (ii) to provide an example, we apply it to the problem of the identity of proofs. We also describe open issues and further applications of this approach (for example, the study of purity of methods). We lay some foundations to investigate rigorously and at large scale intellectual moves and attitudes that underpin the advancement of mathematics through cognitive means (carving out investigationally valuable concepts and techniques) and social means (like communication, collaboration, revision, and criticism of specific categories, inferential patterns, and levels of analysis). Our approach complements other types of analysis of proofs such as reconstruction in a deductive system and examination through a proof-assistant. (shrink)

Formal Ontology in Information Systems is the flagship conference of the International Association for Ontology and its Applications. Its interdisciplinary research focus lies at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science, as well as in the applications of ontological analysis to conceptual modeling, knowledge engineering, knowledge management, information-systems development, library and information science, scientific research, and semantic technologies in general.As in previous years, FOIS 2014 was a nexus of interdisciplinary research and communication. The current (...) proceedings is divided into four main sections, dealing with: foundations; processes, agency and dispositions; methods and tools; and applications. The last of these covers a broad spectrum of areas, including in particular biology and medicine, engineering, and economy. For the first time in its history, the conference hosted a special track: an ontology competition, the aim of which was to encourage authors to make their ontologies publicly available and to allow them to be evaluated according to a set of predetermined criteria. Papers discussing these ontologies can also be found in this volume.The book will be of interest to all those whose work involves the application of ontologies, and who are looking for a current overview of developments in formal ontology. (shrink)

Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain (...) class='Hi'>ontologies in the natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users. (shrink)

Just as ontology developed over the centuries as part of philosophy, so in recent years ontology has become intertwined with the development of the information sciences. Researchers in various fields have come to realize that a solid foundation for their projects calls for an explicit theorization of the types of entities and relations that make up their respective domains of inquiry, and as the need for integrating such projects arises, so does the need to identify common ontological principles over ad (...) hoc, case-based solutions. This volume collects the papers presented at the third international conference devoted to current research in this area, including invited papers by P. Gärdenfors and A. L. Thomasson. (shrink)

The General Formal Ontology (GFO) is a top-level ontology that is being developed at the University of Leipzig since 1999. Besides introducing some of the basic principles of the ontology, we expound axiomatic fragments of its formalization and present ontological models of several use cases. GFO is a top-level ontology that integrates objects and processes into a unified framework, in a way that differs significantly from other ontologies. Another unique selling feature of GFO is its meta-ontological architecture, which (...) includes set theory into ontology and which accounts for its specific role in common representation approaches. The second level of that architecture starts from the distinction of categories and individuals, which forms the backbone of the world’s structure. Furthermore, GFO comprises several kinds of categories, among them universals and concepts, and it considers several ontological regions and levels. In the context of this special issue paper, we study five pre-determined use cases from the perspective of GFO. The results of these analyses yield insights into how the ontology treats several important notions. Very abridged, this covers material objects and their composition; roles and social entities; properties with their relations to objects and processes, and their changing; changes of processes, including a functional perspective; and, eventually, the nature and changing of concepts as well as terminology. A final part summarizes application projects that use GFO in various contexts. (shrink)

I offer a formal ontological theory where the basic building blocks of the world are timeless events. The composition of events results in processes. Spacetime emerges as the system of all events. Things are construed as bundles of processes. I maintain that such a view is in accord with General Relativity and offers interesting prospects for the foundations of classical and quantum gravity.

I have supposed that we need a formal system to represent and explain humans' conceptions of the world. According to this research, such a formal system is representable based on a Conception Language (CL) that is a terminological knowledge representation formalism. In this research, I will offer a formal ontology for conception representation in terminological systems. Such a CL-based ontology will specify the conceptualization of humans' conceptions as well as of the effects of their conceptions on the (...) world. (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 will greatly benefit software application ontologies. To this end LinKBase®, 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, we aim to (...) move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often (...) go hand-in-hand, and were essentially inseparable in medieval thought. This constitutes the foundation for a bridge, and this article analyzes the causality-based ontology of the late medieval philosopher Dietrich of Freiberg from the viewpoint of today's upper-ontology engineering. In this bridging attempt, it offers a translation into English of the first part of Dietrich's De origine (abbreviated title) that is a compromise between traditional scholarly translations of medieval Latin philosophical texts and contemporary ontology. (shrink)

A generalized Wittgensteinian semantics for propositional languages is presented, based on a lattice of elementary situations. Of these, maximal ones are possible worlds, constituting a logical space; minimal ones are logical atoms, partitioned into its dimensions. A verifier of a proposition is an elementary situation such that if real it makes true. The reference (or objective) of a proposition is a situation, which is the set of all its minimal verifiers. (Maximal ones constitute its locus.) Situations are shown to form (...) a Boolean algebra, and the Boolean set algebra of loci is its representation. Wittgenstein's is a special case, admitting binary dimensions only. (shrink)

There are many ontologies of the world or of specific phenomena such as time, matter, space, and quantum mechanics1. However, ontologies of information are rather rare. One of the reasons behind this is that information is most frequently associated with communication and computing, and not with ‘the furniture of the world’. But what would be the nature of an ontology of information? For it to be of significant import it should be amenable to formalization in a logico-grammatical formalism. (...) A candidate ontology satisfying such a requirement can be found in some of the ideas of K. Turek, presented in this paper. Turek outlines the ontology of information conceived of as a part of nature, and provides the ‘missing link’ to the Z axiomatic set theory, offering a proposal for developing a formal ontology of information both in its philosophical and logicogrammatical representations. (shrink)

The concept of formal ontology was first developed by Husserl. It concerns problems relating to the notions of object, substance, property, part, whole, predication, nominalization, etc. The idea of formal ontology is present in many of Husserl?s works, with minor changes. This paper provides a reconstruction of such an idea. Husserl?s proposal is faced with contemporary logical orthodoxy and it is presented also an interpretative hypothesis, namely that the original difference between the general perspective of usual model theory (...) and formal ontology is grounded in the fact that this latter starts from an intended interpretation and not from the set of all the possible interpretations. (shrink)

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. (shrink)

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)

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)

The discussions which follow rest on a 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. The paper concludes with a brief account of some applications of the theory presented. (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)

In lieu of an abstract, here is a brief excerpt of the content:FÉLIX MaRTÍNEZ-?????? TOWARDS A FORMAL ONTOLOGY OF FICTIONAL WORLDS In this discussion ' I propose a few concepts for the description and classification of fictional "worlds." The variety of fictional systems of"reality" can be understood, I diink, as an aspect ofthe phenomenon of style in literary imagination.2 But styles of imagination or of vision, and die style of literary works, are more than simply kinds of fictional worlds. (...) To put in some perspective my attempt at classification of literary works according to their systems of reality, I will make first a few remarks on the notion of style. It is a well-known preliminary problem when speaking of style diat this word seems to have more than one meaning in ordinary usage. I think that some ofits current meanings are rich and important, and that literary knowledge would profit if we could reconstruct them in abstract and defined concepts, so that the notions involved were somewhat clarified. I doubt diat diis is possible with current conceptual tools. We can see what is meant, say, when we hear diat a certain person we know "has style"; and we certainly distinguish diis attribute from others such as elegance, good manners, character, taste, originality, mannerisms, or idiosyncracies. Thus, we occasionally perceive in personal behavior a phenomenon called style. A conceptual description or a satisfactory definition of such a given, however, seems very difficult. Speaking of matters of art and literature, "style" has been used, among other things, to designate both the conventional forms of traditional expression (as in "manuals of style") and the anomalous, convention-breaking forms of highly individuated creation (as in die classic conception of Vosslerian-Spitzerian Stylistics, or in Buffon's "Le style c'est l'homme même," as usually understood). Style, dien, as conformity and style as singularity and deviance; style as impersonal decorum and as presence of a unique personal essence in the work. This perplexing ambiguity may be reducible though. Whether conventional and common or personal and innovative, style appears to be a form that characterizes and holds together a creation or a phenomenal entity. Indeed, the fact that 182 Félix Martínez-Bonati183 singular innovations of style often become the common trait of a school or current and sometimes a part of general tradition seems to indicate that neither singularity nor general acceptance are the most basic elements of die notion of style. On first reflection, we may conceive of style as a formal principle that consistently determines the constitution of die pertinent objects. Nonetíieless, constitutive form is too weak a definition for style, since it would also apply to what is called "technique" and even to genre. We must look for a more specific determination. There is anodier ambiguity in everyday uses of die word "style" diat deserves attention. We speak often of "good style" and "bad style." But sometimes we speak as if no style is bad and the thing that matters is to have style at all and as much of it as possible. Thus, we condemn a work because of its having no style or only a weak one. This contradiction probably derives from the confusion of a particular normative, a general normative, and a merely descriptive notion of style. We should keep, if possible, to a merely descriptive notion. Still another uncertainty of usage, in literary matters, relates to the (not universally accepted) restriction of the notion of style to a linguistic one; style, in this restricted usage, is seen as primarily an attribute of diction. The most numerous of literary studies of die style of singular works have been, so far as I can see, descriptions of idiolects. In many cases, the linguistic peculiarity is taken as an index of the world-view or die style of imagination diat is supposed to have produced the work. Alternative to this approach, indeed complementary, is the study of literary style as an attribute of die fictional entities to which literary discourse refers. We find the latter kind of approach mostly in characterizations of genres or of periods ("the naturalist novel," "romance," "classicism," etc.). One may suppose that an exhaustive analysis of the idiolect of a work... (shrink)

What primitive concepts does formal ontology require? Forsaking as too indirect the linguistic way of discerning the categories of being, this paper considers what primitives might be required for representing things in themselves (noumena) and representations of them in a thoroughly crafted large autonomous multi-purpose database. Leaving logical concepts and material ontology aside, the resulting 32 categories in 13 families range from the obvious (identity/difference, existence/non-existence) through the fairly obvious (part/whole, one/many, sequential order) and the surprisingly familiar (illocutionary modes, (...) mass/count, indexical/descriptive) to the controversial (moment/fundament, transparent/opaque) and the arcane (modes of class delimitation, taxonomic rank, aspects of designators). Any such list is speculative and tentative, but the test of this one will be in its implementation, a new departure for philosophical category theories. (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)

Quentin Meillassoux dismisses the question of the right correlation both in his 'After finitude' and in subsequent publications because his work aims to refute correlationism. The central question I want to address in this article is: Does Meillassoux’s position (and the New Realisms more generally) need a correlation to be more than just a formal ontological game? My answer to this question will be a no, but I think that both his and other versions of speculative and new realism (...) need an interconnection between us and the things around us. (shrink)

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...

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

In this contribution I propose a contemporary reading of the ontological dimension of Max Scheler’s early phenomenology of sense perception. My examination will start with a brief informal explanation of this theory, and his scientific and philosophical sources. The second step will be the introduction of some elements of Formal Philosophy : this piece of research will focus on N. B. Cocchiarella’s interpretation of FP and it will allow me to introduce the concept of a Philosophical Formal Ontology (...) in comparison with the computational one. Finally, the third step will be the construction of a semi-formalized model of Scheler’s early phenomenology of sense perception. Here I will use a dynamic-epistemic version of the modal calculus KT5. (shrink)

In this paper I will discuss Barry Smith’s and Kevin Mulligan’s revision of Husserl’s phenomenology, starting from the fact that many Italian scholars seem to follow them in a sense, by dealing with phenomenology as a sort of a priori ontology. Therefore, I will first reconstruct Smith’s and Mulligan’s attempt and its objectives, then I will show how it is rooted in the school of Brentano and, in particular, in Husserl’s phenomenology. Finally, I will provide some arguments against this attempt (...) : first of all that it does not attain a better description of the world, secondly that phenomenology does the job of formal ontology better than the latter. (shrink)