Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Holly Smith has done more than anyone to explore and defend the importance of usability for moral theories. In Making Morality Work, she develops a moral theory that is almost universally usable. But not quite. In this article, I argue that no moral theory is universally usable, in the sense that is most immediately relevant to action, even by agents who know all the normative facts. There is no moral theory knowledge of which suffices to settle deliberation about what (...) to do. However, this is unsurprising if the question of what to do is not a question of fact. One upshot of the discussion is that the search for a universally usable moral theory is misconceived. Another is that, contra Smith (341), agents who are radically uncertain need not lack autonomy. (shrink)

A belief one has is safe if either (i) it could not easily be false or (ii) in any nearby world in which it is false, it is not formed using the method one uses to form one’s actual belief. It seems our mathematical beliefs are safe if mathematical pluralism is true: if, loosely put, almost any consistent mathematical theory is true. It seems, after all, that in any nearby world where one’s mathematical beliefs differ from one’s actual beliefs, one (...) would believe some other true, consistent theory. Focusing on Justin Clarke-Doane’s recent discussion, I argue the thesis that mathematical beliefs are safe given pluralism faces some obstacles. I argue (i) is true of mathematical belief given pluralism only if we deny plausible claims about the interpretation of non-pluralists who many of us could easily be. Unless strong metasemantic theses are true, it is plausible many of us could easily deny or refuse to believe a consistent and true mathematical theory we actually believe. Since philosophical arguments and controversies permeate the methodology of foundational mathematics, I argue we cannot confidently distinguish the methods we use in mathematics between worlds, thus raising doubts about (ii). (shrink)

The ethos of Justin Smith’s Nature, Human Nature, & Human Difference is expressed in the narrative of Anton Wilhelm Amo (~1703-53), an African-born​ slave who earned his doctoral degree in Philosophy at a European university and went on to teach at the Universities of Jena and Halle. Smith identifies Amo as a time-marker for diverging interpretations of race: race as inherently tethered to physical difference and race as inherited essential difference. Further, these interpretations of race are fastened (...) to the discourse of science and human diversity within modern Europe. Smith’s thesis maintains that the rise of the concept of race in philosophy begins with a divorcing of the soul from human nature and a movement to a naturalistic classification of human beings through taxonomies (e.g. botany, mineralogy and zoology), which dissolved into this dichotomy: an essential difference between people of reason and people of nature. (shrink)

Moral sentimentalism can be understood as a metaethical theory, a normative theory, or some combination of the two. Metaethical sentimentalism emphasizes the role of affect in the proper psychology of moral judgment, while normative sentimentalism emphasizes the centrality of warm emotions to the phenomena of which these judgments properly approve. Neither form of sentimentalism necessarily implies a commitment to virtue ethics, but both have an elective affinity with it. The classical metaethical sentimentalists of the Scottish Enlightenment—such as David Hume and (...) Adam Smith—were all, to a greater or lesser extent, also virtue theorists. The connection is even stronger in the case of Enlightenment philosophers who were also normative sentimentalists , as with Frances Hutcheson. For Hutcheson, virtue simply is a habit of acting from the warm motive of universal benevolence. Today, neo-sentimentalist metaethicists such as Allan Gibbard, Justin D’Arms and Daniel Jacobson generally remain agnostic on the question of whether virtue ethics is superior to its deontological and consequentialist competitors. Michael Slote, however, has developed a comprehensive theory of sentimentalist care ethics in an unambiguously virtue-centered form. (shrink)

Table of contents for MONSTERS AND PHILOSOPHY, edited by Charles T. Wolfe (London 2005) -/- List of Contributors iii Acknowledgments vii List of Abbreviations ix -/- Introduction xi Charles T. Wolfe The Riddle of the Sphinx: Aristotle, Penelope, and 1 Empedocles Johannes Fritsche Science as a Cure for Fear: The Status of Monsters in 21 Lucretius Morgan Meis Nature and its Monsters During the Renaissance: 37 Montaigne and Vanini Tristan Dagron Conjoined Twins and the Limits of our Reason 61 Annie (...) Bitbol-Hespériès Degeneration and Hybridism in the Early Modern Species 109 Debate: Towards the Philosophical Roots of the Creation-Evolution Controversy Justin E. H. Smith Leibniz on the Unicorn and Various other Curiosities 131 Roger Ariew The Creativity of God and the Order of Nature: 153 Anatomizing Monsters in the Early Eighteenth Century Anita Guerrini The Status of Anomalies in the Philosophy of Diderot 169 Annie Ibrahim The Materialist Denial of Monsters 187 Charles T. Wolfe Cerebral Assymetry, Monstrosities and Hegel. 205 On the Situation of the Life Sciences in 1800 Michael Hagner The Lady Knight of the Perilous Place 217 Elfriede Jelinek Monster: More than a Word. . . From Portent to Anomaly, 231 the Extraordinary Career of Monsters Beate Ochsner Index 281 . (shrink)

When a liberal-democratic state signs a treaty or wages a war, does its whole polity do those things? In this article, we approach this question via the recent social ontological literature on collective agency. We provide arguments that it does and that it does not. The arguments are presented via three considerations: the polity's control over what the state does; the polity's unity; and the influence of individual polity members. We suggest that the answer to our question differs for different (...) liberal-democratic states and depends on two underlying considerations: the amount of discretion held by the state's officeholders; the extent to which the democratic procedure is deliberative rather than aggregative. (shrink)

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...) Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

The paper challenges the assumption, common amongst philosophers, that the reality described in the fundamental theories of microphysics is all the reality we have. It will be argued that this assumption is in fact incompatible with the nature of such theories. It will be shown further that the macro-world of three-dimensional bodies and of such qualitative structures as colour and sound can be treated scientifically on its own terms, which is to say not only from the perspective of psychology but (...) also ontologically. A new sort of emergentist position will be defended, one which yields the basis of a method for describing the perceptually salient macroscopic world in mathematical terms. Broadly, it will be argued that the macroscopic world exists in virtue of certain specific sorts of boundary-patterns in the field of what is captured by the theories of microphysics. (shrink)

Philosophical orthodoxy holds that pains are mental states, taking this to reflect the ordinary conception of pain. Despite this, evidence is mounting that English speakers do not tend to conceptualize pains in this way; rather, they tend to treat pains as being bodily states. We hypothesize that this is driven by two primary factors—the phenomenology of feeling pains and the surface grammar of pain reports. There is reason to expect that neither of these factors is culturally specific, however, and thus (...) reason to expect that the empirical findings for English speakers will generalize to other cultures and other languages. In this article we begin to test this hypothesis, reporting the results of two cross-cultural studies comparing judgments about the location of referred pains between two groups—Americans and South Koreans—that we might otherwise expect to differ in how they understand pains. In line with our predictions, we find that both groups tend to conceive of pains as bodily states. (shrink)

Distinguishes two senses of 'judgment' on the one hand as meaning a state of 'conviction' or 'belief', and on the other hand as meaning an act of 'affirmation' or 'assertion'. Certainly conviction and assertion stand in close relation to each other, but they delineate two heterogeneous logical spheres, and thereby divide the total field of the theory of judgment into two neighbouring but separate sub-fields. Once this is done it is shown to have implications for our understanding especially of the (...) phenomenon of negation, and of the distinction between negation as affirmation of a negative state of affairs, and negation as act of contradicting the judgment someone else has made. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

Since the noun phrase `artificial intelligence' (AI) was coined, it has been debated whether humans are able to create intelligence using technology. We shed new light on this question from the point of view of themodynamics and mathematics. First, we define what it is to be an agent (device) that could be the bearer of AI. Then we show that the mainstream definitions of `intelligence' proposed by Hutter and others and still accepted by the AI community are too weak even (...) to capture what is involved when we ascribe intelligence to an insect. We then summarise the highly useful definition of basic (arthropod) intelligence proposed by Rodney Brooks, and we identify the properties that an AI agent would need to possess in order to be the bearer of intelligence by this definition. Finally, we show that, from the perspective of the disciplines needed to create such an agent, namely mathematics and physics, these properties are realisable by neither implicit nor explicit mathematical design nor by setting up an environment in which an AI could evolve spontaneously. (shrink)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process that (...) is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

Ernst Mach's atomistic theory of sensation faces problems in doing justice to our ability to perceive and remember complex phenomena such as melodies and shapes. Christian von Ehrenfels attempted to solve these problems with his theory of "Gestalt qualities", which he sees as entities depending one-sidedly on the corresponding simple objects of sensation. We explore the theory of dependence relations advanced by Ehrenfels and show how it relates to the views on the objects of perception advanced by Husserl and by (...) the Gestalt psychologists. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics (...) domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

The current rise of neurodevelopmental disorders poses a critical need to detect risk early in order to rapidly intervene. One of the tools pediatricians use to track development is the standard growth chart. The growth charts are somewhat limited in predicting possible neurodevelopmental issues. They rely on linear models and assumptions of normality for physical growth data – obscuring key statistical information about possible neurodevelopmental risk in growth data that actually has accelerated, non-linear rates-of-change and variability encompassing skewed distributions. Here, (...) we use new analytics to profile growth data from 36 newborn babies that were tracked longitudinally for 5 months. By switching to incremental (velocity-based) growth charts and combining these dynamic changes with underlying fluctuations in motor performance – as the transition from spontaneous random noise to a systematic signal – we demonstrate a method to detect very early stunting in the development of voluntary neuromotor control and to flag risk of neurodevelopmental derail. (shrink)

Perhaps the question “What is philosophy?” can only be posed late in life, when old age has come, and with it the time to speak in concrete terms. It is a question one poses when one no longer has anything to ask for, but its consequences can be considerable. One was asking the question before, one never ceased asking it, but it was too artificial, too abstract; one expounded and dominated the question, more than being grabbed by it. There are (...) cases in which old age bestows not an eternal youth, but on the contrary a sovereign freedom, a pure necessity where one enjoys a moment of grace between life and death, and where all the parts of the machine combine to dispatch into the future a trait that traverses the ages: Turner, Monet, Matisse. The elderly Turner acquired or conquered the right to lead painting down a deserted path from which there was no return, and that was no longer distinguishable from a final question. In the same way, in philosophy, Kant’s Critique of Judgment is a work of old age, a wild work from which descendants will never cease to flow.We cannot lay claim to such a status. The time has simply come for us to ask what philosophy is. And we have never ceased to do this in the past, and we already had the response, which has not varied: philosophy is the art of forming, inventing, and fabricating concepts. But it was not only necessary for the response to take note of the question; it also had to determine a time, an occasion, the circumstances, the landscapes and personae, the conditions and unknowns of the question. One had to be able to pose the question “between friends” as a confidence or a trust, or else, faced with an enemy, as a challenge, and at the same time one had to reach that moment, between dog and wolf, when one mistrusts even the friend. Gilles Deleuze was professor of philosophy at the University of Paris VIII, Vincennes-St.-Denis, until his retirement in 1987. Among his books translated into English are the two-volume Capitalism and Schizophrenia , the two-volume Cinema , The Logic of Sense , and Expressionism in Philosophy: Spinoza . Daniel W. Smith is a doctoral candidate in philosophy at the University of Chicago. He is at work on a study of the philosophy of Deleuze, and is translating Deleuze’s Francis Bacon: Logique de la sensation. Arnold I. Davidson, executive editor of Critical Inquiry, teaches philosophy at the University of Chicago and is currently Marta Sutton Weeks Fellow at the Stanford Humanities Center. (shrink)

First published in 1995. Routledge is an imprint of Taylor & Francis, an informa company.

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of the geospatial domain, (...) issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

In their paper “Sixteen Days” Barry Smith and Berit Brogaard try to answer the question: when does a human being begin to exist? In this paper we will address some methodological issues connected with this exercise in ontology. We shall begin by sketching the argument of “Sixteen Days”. We shall then attempt to characterize what is special about the ontological realism of “Sixteen Days” as contrasted to the linguistic constructivism which represents the more dominant current in contemporary analytic philosophy. (...) This will allow us to infer guidelines for assessing the quality of ontological theories of various types. We shall argue that ontological parsimony, groundedness, faithfulness to ordinary language, consistency with science, coherence, and fruitfulness are at least part of the adequacy criteria for such theories. These criteria will then be applied to the theory presented in “Sixteen Days”, and they will lead us to some revisions of this theory as well as to some reflections on its ethical implications. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available for (...) integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. (shrink)

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of (...) implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation. (shrink)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This essay contains an attempt to trace the evolution of the concept of wisdom as found in the thought of Aristotle and Aquinas in terms of how the philosophical concept of wisdom as an intellectual virtue is understood and used to express the theological concept of wisdom as a gift of the Holy Spirit. The main aim is to understand how Aquinas derived the concept of wisdom from Aristotle's metaphysics and developed it in his mysticism. This research is based on (...) a close study of Book Six of Aristotle's Nichomachean Ethics, the corresponding sections of Aquinas' Sententia libri Ethicorum and question forty-five of the second part of the second part of Aquinas' Summa Theologiae. The insights gained from the study are then used to decipher the theoretical meaning of Augustine's famous saying: "love and do what thou wilt" and to expound on the practical value of wisdom for religious leaders. (shrink)

In this essay, I consider Sally Haslanger’s social constructivist account of race and propose a modification to the nature of hierarchy specified. According to Haslanger, race will cease to exist post-hierarchy, given that she builds in a requirement of synchronic hierarchy for the existence of race. While Haslanger maintains that racial identity would linger beyond hierarchical treatment in the form of ethnicity, I will suggest this fails to provide adequate conceptual justice for the cultures and aesthetics which emerged out of (...) past oppression. In response, I propose a modification which would allow us to recognize the possibility of post-hierarchical races. (shrink)

In this paper I address the phenomenon of syncretism with respect to Chinese religions. An analysis of the syncretism that takes place between the three major Chinese religious traditions is first done in its personal and social dimensions. The social structure of Chinese religion is then used as a framework to understand how Buddhism and Daoism were made compatible with Confucianism. All this will serve as a background for the case study of Macau, where Chinese religious syncretism is very much (...) alive. Three popular religious festivals are celebrated annually and simultaneously on the eighth day of the fourth lunar month, namely, zuilongjie (醉龍節) Feast of the Drunken Dragon, tangongdan (譚公誕) Tam Kung Festival and fodanjie (佛誕節) Feast of the Buddha. (shrink)

Symposium on Nietzsche's Constructivism (Routledge, 2018), replies to Adler, Cabrera, Doyle, Migotti, Sinhababu, Pedersen.

The physical realm is causally closed, according to physicalists like me. But why is it causally closed, what metaphysically explains causal closure? I argue that reductive physicalists are committed to one explanation of causal closure to the exclusion of any independent explanation, and that as a result, they must give up on using a causal argument to attack mind–body dualism. Reductive physicalists should view dualism in much the way that we view the hypothesis that unicorns exist, or that the Kansas (...) City Royals won the 2003 World Series: false, but not objectionable in any distinctively causal way. My argument turns on connections between explanation, counterfactuals, and inductive confirmation. (shrink)

Confucian education is best captured by the programme described in the Great Learning. Education is presented first as the process of self-cultivation for the sake of developing virtuous character. Self-cultivation then allows for virtue to be cultivated in the familial, social and international dimensions. My central thesis is that Confucianism can serve as a universal framework of educating people for the common good in its promotion of personal cultivation for the sake of human progress. On this account the common good (...) specifically refers to the social order accomplished by the virtuous behaviour found in the members of society. In this paper I argue that the Confucian notion of “lesser learning” sheds light on the concept of general education and the notion of “greater learning” improves our understanding of liberal education. Under this analysis the necessity of general education is assured although its importance should not be overly exaggerated. Furthermore, the objectives of liberal education deserve greater emphasis due to their historical importance and enduring relevance to promoting the common good of universal humanity. (shrink)

One of the standard puzzles in ordinary-object metaphysics concerns what happens when an object and one of its undetached parts apparently begin to coincide. I distinguish two versions of this puzzle: the problem of extraordinary undetached parts and the problem of ordinary undetached parts. Then I present a novel phasalist solution to the problem of ordinary undetached parts. My solution is designed to supplement the recently-defended view that ordinary undetached parts exist but extraordinary ones do not.

In contemporary debates in religious epistemology, theistic philosophers provide differing responses to the evidentialist argument against religious beliefs. Plantinga’s strategy is to argue that evidence is not needed to justify religious beliefs while Swinburne’s strategy is to argue that religious beliefs can be justified by evidence. However, in Aquinas’ account of religious epistemology, he seems to employ both strategies. In his account of religious knowledge by faith, he argues that evidence is unnecessary for religious beliefs. But in his account of (...) religious knowledge by science, he argues that there is evidence for religious beliefs. In this paper, I argue that there is no real dichotomy between Plantinga’s and Swinburne’s responses to the evidentialist argument. From a Thomistic perspective, Reformed Epistemology and Natural Theology are different but compatible responses to Evidentialism. (shrink)

In this paper we use an experimental approach to investigate how linguistic conventions can emerge in a society without explicit agreement. As a starting point we consider the signaling game introduced by Lewis. We find that in experimental settings, small groups can quickly develop conventions of signal meaning in these games. We also investigate versions of the game where the theoretical literature indicates that meaning will be less likely to arise—when there are more than two states for actors to transfer (...) meaning about and when some states are more likely than others. In these cases, we find that actors are less likely to arrive at strategies where signals have clear conventional meaning. We conclude with a proposal for extending the use of the methodology of experimental economics in experimental philosophy. (shrink)

A promising but underexplored view about normative reasons is contrastivism, which holds that considerations are fundamentally reasons for things only relative to sets of alternatives. Contrastivism gains an advantage over non-contrastive theories by holding that reasons relative to different sets of alternatives can be independent of one another. But this feature also raises a serious problem: we need some way of constraining this independence. I develop a version of contrastivism that provides the needed constraints, and that is independently motivated by (...) the widespread idea that reasons involve the promotion of various kinds of objectives. (shrink)

This paper argues that Nietzsche is a panpsychist. Panpsychism holds that mental features are ubiquitous and fundamental in reality. I first argue that Nietzsche’s rejection of Cartesian dualism leads him to substance monism. To better understand his monism, I examine Nietzsche’s rejection of Newtonian atomism. Nietzsche holds that bundles of forces, or will to power, are more fundamental than hard, extended atoms. So, will to power is fundamental. I then investigate Nietzsche’s remarks on organic and inorganic nature to show that (...) he believes both are will to power. So, will to power is ubiquitous. The final step to panpsychism is to show that Nietzsche believes will to power exhibits mental qualities. If all goes well, it should emerge that Nietzsche thinks mental features are fundamental and ubiquitous in reality. (shrink)

Many philosophers believe that the criteria of identity over time for ordinary objects entail that such objects are permanent members of certain sortal kinds. The sortal kinds in question have come to be known as substance sortal kinds. But in this article, I defend a criterion of identity that is suited to phasalism, the view that alleged substance sortals are in fact phase sortals. The criterion I defend is a sortal‐weighted version of a change‐minimizing criterion first discussed by Eli Hirsch. (...) I present this criterion and then argue that it withstands attempts to show that it is inferior to non‐phasalist rivals. (shrink)

I argue that God lacks the standing to blame or punish people for their sin if theological determinism is true, and that this is so even if sinners deserve both blame and punishment for sins God determines them to commit (and thus even if theological determinism is compatible with human free will and moral responsibility). I then respond to two recent objections to this conclusion, one by John Ross Churchill, the other by Patrick Todd. I conclude by noting several implications (...) of the position here defended. (shrink)