Psychological evidence suggests that laypeople understand the world around them in terms of intuitive ontologies which describe broad categories of objects in the world, such as ‘person’, ‘artefact’ and ‘animal’. However, because intuitive ontologies are the result of natural selection, they only need to be adaptive; this does not guarantee that the knowledge they provide is a genuine reflection of causal mechanisms in the world. As a result, science has parted ways with intuitive ontologies. Nevertheless, since the (...) brain is evolved to understand objects in the world according to these categories, we can expect that they continue to play a role in scientific understanding. Taking the case of human evolution, we explore relationships between intuitive ontological and scientific understanding. We show that intuitive ontologies not only shape intuitions on human evolution, but also guide the direction and topics of interest in its research programmes. Elucidating the relationships between intuitive ontologies and science may help us gain a clearer insight into scientific understanding. (shrink)

This position paper presents an introduction to the special issue of Applied Ontology on “Beautiful Ontologies”. It discusses the relevance of considering the notion of beauty when building and eva...

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)

This paper studies European chemists’ shifting ontologies of materials by comparing the ways in which they classified materials. The focus is on plant materials, their different identities, and the changing ways chemists sorted out and ordered plant materials in the eighteenth and early nineteenth centuries. The main goals of the paper are to follow the development of plant materials from ordinary, everyday materials and commodities in the early eighteenth century to purified carbon compounds and organic substances familiar only to (...) experts in the 1830s, and to reconstruct chemists’ ways of classifying these objects in different practical and intellectual contexts.The study of changes in European chemists’ ways of classifying plant materials over more than a century brings to the foreground a trajectory of ontological shifts that is ‘punctuated’ in the 1750s, the 1790s, and the 1830s. Early eighteenth-century plant materials, which were commodities of the apothecary trade and other arts and crafts, were elevated epistemically as compound components or ‘proximate principles’ of plants in the 1750s, reduced to organic compounds in the 1790s, and replaced by carbon compounds in the 1830s. The last, third transformation of the epistemic constitution of materials and the mode of their classification was accompanied by a deep transformation of the material culture of plant chemistry. After the late 1830s, many of the eighteenth-century vegetable commodities disappeared from chemists’ agenda or were split into different substances individuated and identified in new ways. Coal tar products, and new organic artefacts containing chlorine or bromine, entered the chemical laboratory in the 1820s and became fused with the purified rest of the previous plant and animal substances. The material objects of the new culture of organic chemistry became detached from the materials applied in the extant arts and crafts. It was only in the late 1850s, with the rise of the synthetic dye industry, that a great number of these laboratory substances became involved in industrial production.Keywords: Commodities and scientific objects; Historical ontology; Classification; Plant chemistry; Organic chemistry. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

In this paper, we describe the use of legal ontologies as a basis to improve IT support for professional judges. As opposed to most legal ontologies designed so far, which are mostly based on dogmatic and normative knowledge, we emphasize the importance of professional knowledge and experience as an important pillar for constructing the ontology. We describe an intelligent FAQ system for junior judges that intensively use the ontology.

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use (...) of the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

Patterns and pattern ontologies are a powerful way for pragmatists to address metaphysical issues by rejecting a false dichotomy between pluralism and realism. However, there is a common misconception about patterns that I call the philosophically perverse patterns (PPP) problem. Here, critics of patterns invent perverse examples that meet the metaphysical criteria to count as patterns. I defuse this concern by showing how PPP misunderstands what the pragmatist metaphysics of patterns is supposed to accomplish: the bare definition should not (...) rule out, or in, substantive examples of patterns that instead should involve methodological considerations. I use this response to the PPP problem to show how the metaphysical definition of 'pattern' allows the pragmatist to capture the rich intricacies of ontologies in the sciences and yields two illustrative norms by which methodology can be guided in developing or refining ontologies: cohesion and coherence. (shrink)

We will survey a range of ontologies relevant to space and ground system domains. The ontologies form part of the Common Core Ontology ecosystem (CCO) developed under the IARPA KDD initiative. We focus specifically on the Space Domain Ontologies, a suite of ontologies to support space situational awareness, including the Spacecraft Mission Ontology, Spacecraft Ontology, Space Event Ontology and Space Object Ontology.

Several authors have suggested that a more parsimonious and conceptually elegant treatment of everyday mereological and topological reasoning can be obtained by adopting a spatial ontology in which regions, not points, are the primitive entities. This paper challenges this suggestion for mereotopological reasoning in two-dimensional space. Our strategy is to define a mereotopological language together with a familiar, point-based interpretation. It is proposed that, to be practically useful, any alternative region-based spatial ontology must support the same sentences in our language (...) as this familiar interpretation. This proposal has the merit of transforming a vague, open-ended question about ontologies for practical mereotopological reasoning into a precise question in model theory. We show that (a version of) the familiar interpretation is countable and atomic, and therefore prime. We conclude that useful alternative ontologies of the plane are, if anything, less parsimonious than the one which they are supposed to replace. (shrink)

Psychological evidence suggests that laypeople understand the world around them in terms of intuitive ontologies which describe broad categories of objects in the world, such as ‘person’, ‘artefact’ and ‘animal’. However, because intuitive ontologies are the result of natural selection, they only need to be adaptive; this does not guarantee that the knowledge they provide is a genuine reflection of causal mechanisms in the world. As a result, science has parted ways with intuitive ontologies. Nevertheless, since the (...) brain is evolved to understand objects in the world according to these categories, we can expect that they continue to play a role in scientific understanding. Taking the case of human evolution, we explore relationships between intuitive ontological and scientific understanding. We show that intuitive ontologies not only shape intuitions on human evolution, but also guide the direction and topics of interest in its research programmes. Elucidating the relationships between intuitive ontologies and science may help us gain a clearer insight into scientific understanding. (shrink)

The potential of large language models (LLM) has captured the imagination of the public and researchers alike. In contrast to previous generations of machine learning models, LLMs are general-purpose tools, which can communicate with humans. In particular, they are able to define terms and answer factual questions based on some internally represented knowledge. Thus, LLMs support functionalities that are closely related to ontologies. In this perspective article, I will discuss the consequences of the advent of LLMs for the field (...) of applied ontology. (shrink)

Abstract The explosion of interest in large language models (LLMs) has been accompanied by concerns over the extent to which generated outputs can be trusted, owing to the prevalence of bias, hallucinations, and so forth. Accordingly, there is a growing interest in the use of ontologies and knowledge graphs to make LLMs more trustworthy. This rests on the long history of ontologies and knowledge graphs in constructing human-comprehensible justification for model outputs as well as traceability concerning the impact (...) of evidence on other evidence. Understanding the nature of arguments and argumentation is critical to each, especially when LLM output conflicts with what is expected by users. The central contribution of this article is to extend the Arguments Ontology (ARGO) - an ontology specific to the domain of argumentation and evidence broadly construed - into the space of LLM fact-checking in the interest of promoting justification and traceability research through the use of ARGO-based ‘blueprints’. (shrink)

Recent work in the ontology of music suggests that we will avoid confusion if we distinguish between two kinds of question that are typically posed in music ontology. Thus, a distinction has been made between fundamental ontology and higher-order ontology. The former addresses questions about the basic metaphysical options from which ontologists choose. For instance, are musical works types, indicated types, classes of particulars, or some other kind of entity? Higher-order ontology addresses the question of what lies ‘at the centre’ (...) of a specific form of music, such as rock or jazz—or perhaps classical music. The argument of this essay is, first, that a close examination of the best efforts in two of these territories shows that they have the effect of pressing the music in each sphere into implausible Procrustean beds. Second, it is argued that the general question that higher-order ontologies pose, that is, ‘What work-kind is it that lies at the centre of a given kind of music, F?’ is a question based on a mistaken but seductive assumption, namely that the concept of the work of F has actual application. In fact, these concepts—upon which higher-order ontology depends—are mere artefacts of philosophy. The question is also addressed why the assumption is so seductive. Finally, the question finally is posed about what, if anything, is implied from the foregoing about the traditional ontology of classical music. (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED (...) CT community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...) medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an (...) effort called Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research (...) projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Alzheimer’s disease is emerging into public view in unprecedented ways. Foremost among these is the embodied form of elderly men and women appearing in commercial imagery for patient advocacy groups or pharmaceutical advertisements, but scientific imagery also seeps into the visual media cultures that surround us. The recent reconfiguration of Alzheimer’s disease is due to expanding ageing populations, an aggressive biopharmaceutical industry becoming a fast-growing material-semiotic realm that is providing powerful images of both gendered and racialized embodiment. Such a visual, (...) and yet highly material, realm is in need of feminist interventions, engaging with the images and ideas that circulate around ageing, medicine, human and non-human embodiment. From a non-representationalist and posthumanist perspective identified as feminist visual studies of technoscience, the authors seek to further the discussion in the direction of understanding the ‘scattered ontologies’ of Alzheimer’s — in laboratory practice, the realm of medical media and in commercial appeals to coherent individuality and human cognition — as gendered domains of figural reality and performative matter. (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)

The distinction between reference ontologies and application ontologies crept rather unobtrusively into the recent literature on knowledge engineering. A lot of the discourse surrounding this distinction – notably, the one framing the workshop generating this collection of papers – suggests the two types of ontologies are in some sort of opposition to one another. Thus, Borge et al. [3] characterize reference ontologies (more recently, foundational ontologies) as rich, axiomatic theories whose focus is to clarify the (...) intended meanings of terms used in specific domains. Application ontologies, by contrast, provide a minimal terminological structure to fit the needs of a specific community. Reflecting their minimal nature, Masolo et al. [7] refer to such ontologies as “lightweight” ontologies. An application ontology can be lightweight in a second respect as well, namely, that it may not necessarily take the form of fully-fledged axiomatic theory. Rather, it might only be a taxonomy of the relevant domain, a division of the domain into a salient collection of classes, perhaps ordered by the subclass relation. Importantly, though, for an application ontology to “fit the needs of a specific community” needn’t require representational accuracy. In the “worst” case (from a reference ontology perspective), to fit the needs of a community is just to represent uncritically what people in that community think about the ontology’s domain. (shrink)

There is a growing interest in how people conceptualise the legal domain for the purpose of legal knowledge systems. In this paper we discuss four such conceptualisations (referred to as ontologies): McCarty's language for legal discourse, Stamper's norma formalism, Valente's functional ontology of law, and the ontology of Van Kralingen and Visser. We present criteria for a comparison of the ontologies and discuss the strengths and weaknesses of the ontologies in relation to these criteria. Moreover, we critically (...) review the criteria. (shrink)

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous and other subjugated communities require an ontological pluralism that recognizes the plurality of both representational tools and ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. We conclude (...) by arguing that this dynamic provides important lessons for reorienting agendas in social ontology through Southern Ontologies. (shrink)

The theme of this year’s Spindel Conference was Social Ontologies of Race. This editorial introduction serves as both a general introduction to the topic of racial ontology and an introduction to this volume’s contributions. I will first explain some central ideas for discussions of ontology in general. I will then make some basic taxonomic distinctions common to discussions of racial ontology and suggest some clarifications. I will then go on to discuss the five contributions to this volume.

The use of ontologies to model human behaviours that affect health is challenging since this process involves data from multiple inter-related domains that unfold and evolve over time. However, while current ontology development methodologies are generic enough to model any domain of interest, they do not provide design guidelines for modelling time-related aspects. This paper proposes a methodology for ontology development that entails the requirements for behaviours modelling based on passive temporal data. Its main focus is on temporal representations (...) of classes and their holistic relations since no other methodology approaches ontology design from its temporal perspective. We exemplify these ideas by modelling the sleep behaviour domain, its relations to other behavioural aspects, and its effects on health. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption (...) of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

Recent years have witnessed growing concerns about how we should conduct conservation activities in a world of human-altered biophysical conditions. The ‘novel ecosystems’ perspective has emerged as a way to meet this challenge. Yet its focus on accepting ‘new natures’ as the ‘new normal’ has drawn much criticism from those wedded to conventional forms of conservation, such as ‘ecological restoration’. This paper: 1) provides a much needed review of this dispute; 2) formulates and deploys an original analytical framework, which draws (...) on Thomas Kuhn's ‘theoretical history’ of science and Charles Taylor's moral philosophy to extricate the entangled moral and material ontologies of nature which conflate facts with values in the world-building activities of disputants; and 3) identifies and examines the processes underlying these world-building activities. The paper closes by offering an initial suggestion on how to explore options for resolving this highly contentious debate. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research (...) projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

This book is intended as a philosophical introduction to geo-ontologies, in response to their increasing diffusion within the contemporary debate, where philosophy plays a fundamental, though still unexplored, role. Accordingly, the first part offers a short overview of the ontological background of geo-ontologies, which comprehends computer science, philosophy and geography. The second part is devoted to describe the ontology of geography, to define notions such as geographical entities and boundaries, and to trace some philosophical tools useful for spatial (...) representation. The third part investigates the emerging of geo-ontologies from the spatial turn and is concerned with a taxonomy for geo-ontologies grounded on some fundamental geographical distinctions. Finally, the last part presents the emergence of Digital Humanities and the consequent proliferation of geographical projects focused on the ancient world, in particular Greek and Roman. (shrink)

Several metaphysical debates have typically been modeled as oppositions between a relationist approach and a substantivalist approach. Such debates include the Bundle Theory and the Substratum Theory about ordinary material objects, the Bundle (Humean) Theory and the Substance (Cartesian) Theory of the Self, and Relationism and Substantivalism about time. In all three debates, the substantivalist side typically insists that in order to provide a good treatment of the subject-matter of the theory (time, Self, material objects), it is necessary to postulate (...) the existence of a certain kind of substance, while the other side, the relationist one, characteristically feels that this is an unnecessary expense and that one can get the job done in an ontologically cheaper way just with inter-related properties or events. In this paper I shall defend the view that there is much less of a disagreement between relational ontologies and substantival ontologies than it is usually thought. I believe that, when carefully examined, the two sides of the debate are not that different from each other, in all three cases of pairs of views mentioned above. As we will see, both the relational side and the substantival side work in the same way, suffer from and answer the same objections, and are structurally extremely similar. It will be an important question – one that I shall discuss in detail, and that is indeed the main point of interest for me in this paper – whether this means that the two sides of the debate are somehow 'equivalent' or not, and what 'equivalent' could mean. (shrink)

In this paper back-and-forth structures are applied to the semantics of natural language. Back-and-forth structures consist of an event structure and an interval structure communicating via a relational link; transitions in the one structure correspond to transitions in the other. Such entities enable us to view temporal constructions (such as tense, aspect, and temporal connectives) as methods of moving systematically between information sources. We illustrate this with a treatment of the English present perfect, and progressive aspect, that draws on ideas (...) developed in Moens & Steedman (1988), and discuss the role of rich ontologies in formal semantics. (shrink)