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 (...) class='Hi'>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)

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.

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)

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.

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)

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)

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 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)

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)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology (...) Auditing (ETA). We describe here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (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)

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)

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 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.

The General Formal Ontology 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)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

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)

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 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)

Genera, typically hand-in-hand with their branching species, are essential elements of vocabulary-based information constructs, in particular scientific taxonomies. Should they also feature in formal ontologies, the highest of such constructs? I argue in this article that the answer is “Yes” and that the question posed in its title also has a Yes-answer: The way medieval ontologists sliced up the world into genera does matter to formal ontology. More specifically, the way Dietrich of Freiberg, a Latin scholastic, conceived (...) and applied strictly generic criteria to slice up the world into its entities can provide some guidelines to the field of formal ontology with respect to not only its contents, but also its scope. In particular, Dietrich's information criterion plays here a central role. (shrink)

The philosophy of science of Patrick Suppes is centered on two important notions that are part of the title of his recent book (Suppes 2002): Representation and Invariance. Representation is important because when we embrace a theory we implicitly choose a way to represent the phenomenon we are studying. Invariance is important because, since invariants are the only things that are constant in a theory, in a way they give the “objective” meaning of that theory. Every scientific theory gives a (...) representation of a class of structures and studies the invariant properties holding in that class of structures. In Suppes’ view, the best way to define this class of structures is via axiomatization. This is because a class of structures is given by a definition, and this same definition establishes which are the properties that a single structure must possess in order to belong to the class. These properties correspond to the axioms of a logical theory. In Suppes’ view, the best way to characterize a scientific structure is by giving a representation theorem for its models and singling out the invariants in the structure. Thus, we can say that the philosophy of science of Patrick Suppes consists in the application of the axiomatic method to scientific disciplines. What I want to argue in this paper is that this application of the axiomatic method is also at the basis of a new approach that is being increasingly applied to the study of computer science and information systems, namely the approach of formal ontologies. The main task of an ontology is that of making explicit the conceptual structure underlying a certain domain. By “making explicit the conceptual structure” we mean singling out the most basic entities populating the domain and writing axioms expressing the main properties of these primitives and the relations holding among them. So, in both cases, the axiomatization is the main tool used to characterize the object of inquiry, being this object scientific theories (in Suppes’ approach), or information systems (for formal ontologies). In the following section I will present the view of Patrick Suppes on the philosophy of science and the axiomatic method, in section 3 I will survey the theoretical issues underlying the work that is being done in formal ontologies and in section 4 I will draw a comparison of these two approaches and explore similarities and differences between them. (shrink)

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that (...) these are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

This paper introduces the special issue on Formal Approaches to the Ontological Argument of the Journal of Applied Logics (College Publications). The issue contains the following articles: Formal Approaches to the Ontological Argument, by Ricardo Sousa Silvestre and Jean-Yves Béziau; A Brief Critical Introduction to the Ontological Argument and its Formalization: Anselm, Gaunilo, Descartes, Leibniz and Kant, by Ricardo Sousa Silvestre; A Mechanically Assisted Examination of Begging the Question in Anselm’s Ontological Argument, by John Rushby; A Tractarian (...) Resolution to the Ontological Argument, by Erik Thomsen; On Kant’s Hidden Ambivalence Toward Existential Generalization in his Critique of the Ontological Argument, by Giovanni Mion; The Totality of Predicates and the Possibility of the Most Real Being, by Srećko Kovač; An Even More Leibnizian Version of Gödel’s Ontological Argument, by Kordula Świętorzecka and Marcin Łyczak; A Case Study On Computational Hermeneutics: E. J. Lowe’s Modal Ontological Argument, by David Fuenmayor. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer (...) science has always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) (...) perspectives within a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

Contemporary logicians have expanded upon the old notions of psychologism in logic and proposed new, weakened versions of it. Those weakened versions postulate that psychologistic logic does not have to inform about the ontology or metaphysics of reasoning. Instead, logic applied in cognitive science could serve as one of many paradigms for making empirical predictions about the observable process of human reasoning. The purpose of this article is to entertain this notion and answer the question: what properties should (...) a logical system formally representing actual human reasoning have? Based on the existing evidence from cognitive science and neuroscience we identified three potential candidates: context-sensitivity (satisfied for example by adaptive logics), content-sensitivity (satisfied by non-Fregean logics) and probabilism (satisfied for example by fuzzy logics). (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...) of situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The purpose of this paper is twofold. First, it aims at introducing the ontological argument through the analysis of five historical developments: Anselm’s argument found in the second chapter of his Proslogion, Gaunilo’s criticism of it, Descartes’ version of the ontological argument found in his Meditations on First Philosophy, Leibniz’s contribution to the debate on the ontological argument and his demonstration of the possibility of God, and Kant’s famous criticisms against the (cartesian) ontological argument. Second, it intends to critically examine (...) the enterprise of formally analyzing philosophical arguments and, as such, contribute in a small degree to the debate on the role of formalization in philosophy. My focus will be mainly on the drawbacks and limitations of such enterprise; as a guideline, I shall refer to a Carnapian, or Carnapian-like theory of argument analysis. (shrink)

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The (...) paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products? (shrink)

The aim of this article is to reconstruct Bocheński’s method of philosophical analysis as well as to clarify the purpose of that method and its basic elements. In the second part of the paper I will compare Bocheński’s method with the methods of modern applied ontology.

Nicola Guarino is widely recognized as one of the founders of applied ontology. His deep interest in the subtlest details of theoretical analysis and his vision of ontology as the Rosetta Stone for semantic interoperability guided the development and understanding of this domain. His motivations in research stem from the conviction that all science must be for the benefit of society at large, and his motto has always been that ontologies are not just for making information systems (...) interoperable, but – more importantly – for ensuring that systems’ users understand each other. He was among the first to recognize that applied ontology must be an interdisciplinary enterprise if it is to capture the intended meaning of the terms used by an information system. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. * The methodology (...) employed for importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, (...) ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

The Unified Foundational Ontology (UFO) was developed over the last two decades by consistently putting together theories from areas such as formal ontology in philosophy, cognitive science, linguistics, and philosophical logics. It comprises a number of micro-theories addressing fundamental conceptual modeling notions, including entity types and relationship types. The aim of this paper is to summarize the current state of UFO, presenting a formalization of the ontology, along with the analysis of a number of cases to (...) illustrate the application of UFO and facilitate its comparison with other foundational ontologies in this special issue. (The cases originate from the First FOUST Workshop – the Foundational Stance, an international forum dedicated to Foundational Ontology research.). (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

The peculiar legacy of Husserl’s mereology, chiefly studied by analytic philosophers interested in ontology, has led to a partial understanding of the III. LU, which is too often reduced to a chapter of “formal ontology”. Yet, the power of this Investigation goes far beyond: it enabled Husserl to deal, in the framework of a unified theory, with a vast range of particular problems. The paper focuses on one of these issues, namely abstraction, so as to expose how (...) Husserl instrumentalizes his formal tools in order to tackle material issues. The existence of an up and down pattern is uncovered: Husserl first reinterprets the psychological problem of abstraction in ontological terms, before coming back to the original problem with new insights. The second, correlative aim of the paper is to emphasize the key role played by Friedrich Schumann, a forgotten yet crucial character for Husserl’s conception of abstraction. (shrink)

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in (...) terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (shrink)