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)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics (...) advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart. (shrink)

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude (...) with a description of how the body fluids ontology initiative may provide support to basic and translational science. (shrink)

Nihilism is the thesis that no composite objects exist. Some ontologists have advocated abandoning nihilism in favor of deep nihilism, the thesis that composites do not existO, where to existO is to be in the domain of the most fundamental quantifier. By shifting from an existential to an existentialO thesis, the deep nihilist seems to secure all the benefits of a composite-free ontology without running afoul of ordinary belief in the existence of composites. I argue that, while there are (...) well-known reasons for accepting nihilism, there appears to be no reason at all to accept deep nihilism. In particular, deep nihilism draws no support either from the usual arguments for nihilism or from considerations of parsimony. (shrink)

Archimedes of Syracuse has long provided a touchstone for considering how we make and acquire knowledge. Since the early Roman chroniclers of Archimedes’ life, and especially intensively since Descartes, scholars have described, sought, or derided the Archimedean point, defining and redefining its epistemic role. “Knowledge,” at least within modernity, is rhetorically tied to the figure of the Archimedean point, a place somewhere outside a regular and constrained world of experience. If this figure still leads to useful ways of thinking about (...) knowing, we are left with the question of how different modes of making knowledge approach their “Archimedean” points. The question is especially important today as a renewed .. (shrink)

My topic is the materialist appropriation of empiricism – as conveyed in the ‘minimal credo’ nihil est in intellectu quod non fuerit in sensu (which interestingly is not just a phrase repeated from Hobbes and Locke to Diderot, but is also a medical phrase, used by Harvey, Mandeville and others). That is, canonical empiricists like Locke go out of their way to state that their project to investigate and articulate the ‘logic of ideas’ is not a scientific project: “I shall (...) not at present meddle with the Physical consideration of the Mind” (Essay, I.i.2, in Locke 1975; which Kant gets exactly wrong in his reading of Locke, in the Preface to the A edition of the first Critique). Indeed, I have suggested elsewhere, contrary to a prevalent reading of Locke, that the Essay is not the extension to the study of the mind of the methods of natural philosophy; that he is actually not the “underlabourer” of Newton and Boyle he claims politely to be in the Epistle to the Reader (Wolfe and Salter 2009, Wolfe 2010). Rather, Locke says quite directly if we pay heed to such passages, “Our Business here is not to know all things, but those which concern our Conduct” (Essay, I.i.6). There would be more to say here about what this implies for our understanding of empiricism (see Norton 1981 and Gaukroger 2005), but instead I shall focus on a different aspect of this episode: how a non-naturalistic claim which falls under what we now call epistemology (a claim about the senses as the source of knowledge) becomes an ontology – materialism. That is, how an empiricist claim could shift from being about the sources of knowledge to being about the nature of reality (and/or the mind, in which case it needs, as David Hartley saw and Denis Diderot proclaimed more overtly, an account of the relation between mental processes and the brain). (David Armstrong, for one, denied that there could be an identification between empiricism and materialism on this point: eighteenth-century history of science seems to prove him wrong: see Armstrong 1968 and 1978.) Put differently, I want to examine the shift from the logic of ideas in the seventeenth century (Locke) to an eighteenth-century focus on what kind of ‘world’ the senses give us (Condillac), to an assertion that there is only one substance in the universe (Diderot, giving a materialist cast to Spinozism), and that we need an account of the material substrate of mental life. This is neither a ‘scientific empiricism’ nor a linear developmental process from philosophical empiricism to natural science, but something else again: the unpredictable emergence of an ontology on empiricist grounds. (shrink)

It is often thought that the boundaries and properties of art-kinds are determined by the things we say and think about them. More recently, this tendency has manifested itself as concept-descriptivism, the view that the reference of art-kind terms is fixed by the ontological properties explicitly or implicitly ascribed to art and art-kinds by competent users of those terms. Competent users are therefore immune from radical error in their ascriptions; the result is that the ontology of art must begin (...) and end with conceptual analysis. Against this tendency towards concept-driven ontology, I offer a trio of objections derived from: the cultural and temporal variability of concepts of art, the systematic tendency, on the part of would-be ontological assessors, to err on the side of familiar categories or, conversely, to exaggerate minor differences between familiar and unfamiliar practices, and the influence artworld precedents exert over expert and folk concepts alike. These considerations, I argue, mandate an epistemic humility that is simply unavailable to the concept-descriptivist. (shrink)

This paper elaborates on relationalism about space and time as motivated by a minimalist ontology of the physical world: there are only matter points that are individuated by the distance relations among them, with these relations changing. We assess two strategies to combine this ontology with physics, using classical mechanics as example: the Humean strategy adopts the standard, non-relationalist physical theories as they stand and interprets their formal apparatus as the means of bookkeeping of the change of the (...) distance relations instead of committing us to additional elements of the ontology. The alternative theory strategy seeks to combine the relationalist ontology with a relationalist physical theory that reproduces the predictions of the standard theory in the domain where these are empirically tested. We show that, as things stand, this strategy cannot be accomplished without compromising a minimalist relationalist ontology. (shrink)

Ontological pluralism is the view that there are different fundamental ways of being. Trenton Merricks has recently raised three objections to combining pluralism with a generic way of being enjoyed by absolutely everything there is: first, that the resulting view contradicts the pluralist’s core intuition; second, that it is especially vulnerable to the charge—due to Peter van Inwagen—that it posits a difference in being where there is simply a difference in kind; and, third, that it is in tension with various (...) historically influential motivations for pluralism. I reply to each of these objections in turn. My replies will help to bring out the true nature of the pluralist’s basic commitments. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at (...) the same time, (ii) through its association with specific players and a specific occasion, tied to time and history. We discover other abstract patterns of this sort especially in the domains of law and commerce. This essay draws on the work in social ontology, we of Hernando de Soto and of John Searle to develop an ontology of the social world based on an analysis of the peculiar interdependence between quasi-abstract patterns and their representations in documents of different sorts. (shrink)

The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the view (...) of brands as mere marks or names and interpret them as emergent products with properties that afford branding in the sense of Gibson’s ecological psychology. Brand strength is a function of the degree to which brands occupy defensible niches in product space. Branding as a process involves changing external or internal boundaries of products. Several arguments are proposed in favor of brand realism. The fragments of an ontology of marketing are developed in a broadly Aristotelian framework. Brand realism has significant implications for a new understanding of issues ranging from the effects of advertising to financial brand valuation, the nature of trademarks, and marketing strategy in general. It permits one to treat brand equity as a real phenomenon not dependent on associations, attitudinal states such as brand loyalty, or spurious constructs such as brand character or personality. (shrink)

This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes.

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is (...) an essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of (...) the ontology within the ACGT project thus far. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been (...) little effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. We describe our efforts towards developing an Emotion Ontology (EMO) to serve the affective science community. We here focus on conformity to the BFO upper ontology and disambiguation of polysemous terminology. (shrink)

Do we suddenly become justified in treating robots like humans by positing new notions like “artificial moral agency” and “artificial moral responsibility”? I answer no. Or, to be more precise, I argue that such notions may become philosophically acceptable only after crucial metaphysical issues have been addressed. My main claim, in sum, is that “artificial moral responsibility” betokens moral responsibility to the same degree that a “fake orgasm” betokens an orgasm.

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

The Realist that investigates questions of ontology by appeal to the quantificational structure of language assumes that the semantics for the privileged language of ontology is externalist. I argue that such a language cannot be (some variant of) a natural language, as some Realists propose. The flexibility exhibited by natural language expressions noted by Chomsky and others cannot obviously be characterized by the rigid models available to the externalist. If natural languages are hostile to externalist treatments, then the (...) meanings of natural language expressions serve as poor guides for ontological investigation, insofar as their meanings will fail to determine the referents of their constituents. This undermines the Realist’s use of natural languages to settle disputes in metaphysics. (shrink)

Many philosophers of science are ontologically committed to a lush rainforest of special science entities ), but are often reticent about the criteria that determine which entities count as real. On the other hand, the metaphysics literature is much more forthcoming about such criteria, but often links ontological commitment to irreducibility. We argue that the irreducibility criteria are in tension with scientific realism: for example, they would exclude viruses, which are plausibly theoretically reducible and yet play a sufficiently important role (...) in scientific accounts of the world that they should be included in our ontology. In this paper, we show how the inhabitants of the rainforest can be inoculated against the eliminative threat of reduction: by demonstrating that they are emergent. According to our account, emergence involves a screening off condition as well as novelty. We go on to demonstrate that this account of emergence, which is compatible with theoretical reducibility, satisfies common intuitions concerning what should and shouldn't count as real: viruses are emergent, as are trouts and turkeys, but philosophically gerrymandered objects like trout-turkeys do not qualify. (shrink)

Suppose you own a garden-variety object such as a hat or a shirt. Your property right then follows the ageold saw according to which possession is nine-tenths of the law. That is, your possession of a shirt constitutes a strong presumption in favor of your ownership of the shirt. In the case of land, however, this is not the case. Here possession is not only not a strong presumption in favor of ownership; it is not even clear what possession is. (...) Possessing a thing like a hat or a shirt is a rather straightforward affair: the person wearing the hat or shirt possesses the shirt or the hat. But what is possession in the case of land? This essay seeks to provide an answer to this question in the form of an ontology of landed property. (shrink)

Drawing from Arjen Kleinherenbrink's recent book, Against Continuity: Gilles Deleuze's Speculative Realism (2019), this paper undertakes a detailed review of Kleinherenbrink's fourfold "externality thesis" vis-à-vis Deleuze's machine ontology. Reading Deleuze as a philosopher of the actual, this paper renders Deleuzean syntheses as passive contemplations, pulling other (passive) entities into an (active) experience and designating relations as expressed through contraction. In addition to reviewing Kleinherenbrink's book (which argues that the machine ontology is a guiding current that emerges in Deleuze's (...) work after Difference and Repetition) alongside much of Deleuze's oeuvre, we relate and juxtapose Deleuze's machine ontology to positions concerning externality held by a host of speculative realists. Arguing that the machine ontology has its own account of interaction, change, and novelty, we ultimately set to prove that positing an ontological "cut" on behalf of the virtual realm is unwarranted because, unlike the realm of actualities, it is extraneous to the structure of becoming-that is, because it cannot be homogenous, any theory of change vis-à-vis the virtual makes it impossible to explain how and why qualitatively different actualities are produced. (shrink)

This paper investigates the connection between temporal attitudes (attitudes characterised by a concern (or lack thereof) about future and past events), beliefs about temporal ontology (beliefs about the existence of future and past events) and temporal preferences (preferences regarding where in time events are located). Our aim is to probe the connection between these preferences, attitudes, and beliefs, in order to better evaluate the normative status of these preferences. We investigate the hypothesis that there is a three-way association between (...) (a) being present-biased (that is, preferring that positive events are located in the present, and negative events are located in the non-present), (b) believing that past and future events do not exist and (c) tending to have present-focused rather than non-present-focused temporal attitudes. We find no such association. This suggests that insofar as temporal preferences and temporal attitudes are connected to the ways we represent time, they are not connected to the ways we represent temporal ontology; rather, they are more likely connected to the ways we represent relative movement in, or of, time. This has important consequences for, first, explaining why we exhibit these preferences and, second, for their normative evaluation. (shrink)

This article investigates the problem of the identity of the parts of space in Newton’s natural philosophy, as well as the holistic or structuralist nature of Newton’s ontology of space. Additionally, this article relates the lessons reached in this historical and philosophical investigation to analogous debates in contemporary space-time ontology. While previous contributions, by Nerlich, Huggett, and others, have proven to be informative in evaluating Newton’s claims, it will be argued that the underlying goals of Newton’s views have (...) largely eluded prior analysis and that Newton’s approach is similar, and lends support, to several current structuralist trends in the conception of space-time ontology. (shrink)

Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation (...) of the FGM Ontology (FGMO) in 2016. Here, we present a revised and expanded version of the FGM Ontology, which includes enrichments along four dimensions: (1) documenting recent FGMs applications; (2) reorganising the framework to incorporate an updated representation of types of manufacturing processes; (3) enriching the axioms of the ontology; and (4) importing mid-level ontologies from the Common Core Ontologies (CCO) and Product Life Cycle (PLC) Ontologies. The work is being carried out within the framework of the Industry Ontology Foundry (IOF), and the ontology is conformant to Basic Formal Ontology (BFO). (shrink)

Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated only once. By (...) serving as a lingua franca for database integration this benchmark taxonomy would ensure that all databases calibrated in its terms would be automatically compatible with each other. We describe one strategy for creating such a lingua franca, in which philosophical ontology plays a central role. (shrink)

What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas (...) were developed prior to the scientific discoveries of the modern era, he approached the objects and relations of everyday reality with the same ontological seriousness with which scientists today approach the objects of physics. We shall seek to show that what Aristotle has to say about these commonsensical objects and relations can, when translated into more formal terms, be of use also to contemporary ontologists. More precisely, we shall argue that his ideas can contribute to the development of a rigorous theory of those social and institutional components of everyday reality – the settings of human behavior – which are the subject of this volume. When modern-day philosophers turn their attentions to ontology they begin not with Aristotle but rather, in almost every case, with a set-theoretic ontology of the sort which is employed in standard model-theoretic semantics. Set-theoretic ontology sees the world in atomistic terms: it postulates a lowest level of atoms or urelements, from out of which successively higher levels of set-theoretic objects are then constructed. The approach to ontology to be defended here, in contrast, starts not with atoms but with the mesoscopic objects by which we are surrounded in our normal day-to-day.. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

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

This essay presents an alternative to contemporary substantivalist and relationist interpretations of quantum gravity hypotheses by means of an historical comparison with the ontology of space in the seventeenth century. Utilizing differences in the spatial geometry between the foundational theory and the theory derived from the foundational, in conjunction with nominalism and platonism, it will be argued that there are crucial similarities between seventeenth century and contemporary theories of space, and that these similarities reveal a host of underlying conceptual (...) issues that the substantival/relational dichotomy fails to distinguish. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...) are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (shrink)

My aim in this paper is to draw Plotinus and Derrida together in a comparison of their respective appropriations of the famous “receptacle” passage in Plato's Timaeus (specifically, Plotinus' discussion of intelligible matter in Enneads 2.4 and Derrida's essay on Timaeus entitled “Kh ō ra”). After setting the stage with a discussion of several instructive similarities between their general philosophical projects, I contend that Plotinus and Derrida take comparable approaches both to thinking the origin of the forms and to problematizing (...) the stability of the sensible/intelligible opposition. With these parallels in focus, I go on to explain how examining such points of contact can help us to dismantle the canonical constructs of “Plotinus the metaphysician” and “Derrida the anti-metaphysician” that have obscured important connections between Neoplatonism and deconstruction, and suppressed latent resources within the Platonic tradition itself for deconstructing the dualistic ontology of so-called “Platonic metaphysics.”. (shrink)

In Lowe’s Four-Category Ontology, instantiation is a basic formal ontological relation between particulars (objects, modes) and their kinds (kinds, attributes). Therefore, instantiation must be considered as a metaphysically necessary relation, which also rules out the metaphysical possibility of kind change. Nevertheless, according to Lowe, objects obtain their identity conditions in a more general level than specific natural kinds, which allows for kind change. There also seems to be actual examples of kind change. The advocate of Four-Category Ontology is (...) obliged to resolve the tension between these mutually incompatible claims. In this article, we argue that the only viable option for the advocate of Four-Category Ontology is to bite the bullet and stick to the necessity of each of the most specific natural kind to the object instantiating it. As a major drawback, the four-category ontologist does not have any credible means to allow for kind change or determination of the identity conditions in a more general level. (shrink)

This thesis articulates an analytic version of the ontology of idealism, according to which universal phenomenal consciousness is all there ultimately is, everything else in nature being reducible to patterns of excitation of this consciousness. The thesis’ key challenge is to explain how the seemingly distinct conscious inner lives of different subjects—such as you and me—can arise within this fundamentally unitary phenomenal field. Along the way, a variety of other challenges are addressed, such as: how we can reconcile idealism (...) with the fact that we all inhabit a common external world; why this world unfolds independently of our personal volition or imagination; why there are such tight correlations between measured patterns of brain activity and reports of experience; etc. The core idea of this thesis can be summarized thus: we, as well as all other living organisms, are dissociated alters of universal phenomenal consciousness, analogously to how a person with Dissociative Identity Disorder (DID) manifests multiple disjoint centers of subjectivity also called ‘alters.’ We, and all other living organisms, are surrounded by the transpersonal phenomenal activity of universal consciousness, which unfolds beyond the dissociative boundary of our respective alter. The inanimate world we perceive around us is the extrinsic appearance—i.e. the phenomenal image imprinted from across our dissociative boundary—of this activity. The living organisms we share the world with are the extrinsic appearances of other alters. (shrink)

In the Netherlands and Belgium, it is lawful for voluntary euthanasia to be offered on the grounds of psychiatric suffering. A recent case that has sparked much debate is that of Aurelia Brouwers, who was helped to die in the Netherlands on account of her suffering from borderline personality disorder. It is sometimes claimed that whether or not a mentally ill person’s wish to die is valid hinges on whether or not that wish is a symptom of the person’s mental (...) disorder. This article addresses the philosophical problems raised by this claim, with a specific focus on the diagnosis of borderline personality disorder. After considering descriptivist and causal conceptualizations of mental disorder, I argue that the current approach to borderline personality disorder in psychiatry precludes the possibility of dissociating the wish to die from the disorder. I then examine the implications of this analysis for the question of whether or not the request for voluntary euthanasia in the case of borderline personality disorder can be considered valid. Ultimately, I conclude that the inability to dissociate the wish to die from the disorder does not invalidate the wish in the case of borderline personality disorder. (shrink)

This is an exploration of the importance of the collocation approach in investigating language. It underpins a new conception of grammar that is: (i) intrinsically connected with lexis; (ii) investigates the language as it is naturally used in life; (iii) can be developed as a corpus-driven grammar. The collocation approach in language exploration is also examined from the perspective of some recent developments in the philosophy of language. In conclusion, I defend the identity between philosophical ontology, linguistic ontology (...) and computational ontology. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from (...) the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

I argue that a two-dimensional model of social objects is uniquely positioned to deliver explanations for some of the puzzling metaphysical features of words. I consider how a type-token model offers explanations for the metaphysical features of words, but I give reasons to find the model wanting. In its place, I employ an alternative model from social ontology to explain the puzzling data and questions that are generated from the metaphysical features of words. In the end I chart a (...) new path that foregrounds the agent-dependence and social conditions for word kinds. (shrink)

Today, in any mature information society, we live neither online nor offline but on life, that is, we increasingly live in that special space that is both analogue and digital, both online and offline. Imagine someone asking whether the water is fresh or salty in the estuary where the river meets the sea. That someone has not understood the special nature of the place. Our information society is that place. And our technologies are perfectly evolved to take advantage of it, (...) like mangroves growing in brackish water. In the mangrove society, machine-readable data, new forms of agency and interactions are constantly evolving. The consequences of such a radical transformation are many, but one is particularly significant and rich in consequences: how should we design the mangrove society, when it comes to the relationship between the natural and the digital? In this text, I argue that the digital blue is a great ally of the environmental green. The two work best in tandem. And if the world will enjoy a sustainable development for the environment that is also socially preferable for humanity, it will be because the green and the blue will have created a virtuous circle of nature and technology. It can be done. There is just no time to waste. (shrink)

This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In (...) an appendix, however, Brentano puts forward an even more radical suggestion, inspired by the physics of Kelvin. According to this final view, space itself is an accident of a deeper substance: the present time. (shrink)

After some suggestions about how to clarify the confused metaphysical distinctions between dispositional and non-dispositional or categorical properties, I review some of the main interpretations of QM in order to show that – with the relevant exception of Bohm’s minimalist interpretation – quantum ontology is irreducibly dispositional. Such an irreducible character of dispositions must be explained differently in different interpretations, but the reducibility of the contextual properties in the case of Bohmian mechanics is guaranteed by the fact that the (...) positions of particles play the role of the categorical basis, a role that in other interpretations cannot be filled by anything else. In Bohr’s and Everett-type interpretations, dispositionalism is instrumentalism in disguise. (shrink)

The beliefs of economists are not solely determined by empirical evidence in direct relation to the theories and models they hold. Economists hold 'ontological presuppositions', fundamental ideas about the nature of being which direct their thinking about economic behaviour. In this volume, leading philosophers and economists examine these hidden presuppositions, searching for a 'world view' of economics. What properties are attributed to human individuals in economic theories, and which are excluded? Does economic man exist? Do markets have an essence? Do (...) macroeconomic aggregates exist? Is the economy a mechanism, the functioning of which is governed by a limited set of distinct causes? What are the methodological implications of different ontological starting points? This collection, which establishes economic ontology as a coordinated field of study, will be of great value to economists and philosophers of social sciences. (shrink)

It is widely believed that at least two developments in the last third of the 20th century have given dispositionalism—the view that powers, capacities, potencies, etc. are irreducible real properties—new credibility: (i) the many counterexamples launched against reductive analyses of dispositional predicates in terms of counterfactual conditionals and (ii) a new anti-Humean faith in necessary connections in nature which, it is said, owes a lot to Kripke’s arguments surrounding metaphysical necessity. I aim to show in this paper that necessity is, (...) in fact, of little help for the dispositionalists. My argument makes use of one of the above mentioned counterexamples against Humean reduction: antidotes. Turning the tables, I ask how the dispositionalists themselves can deal with antidotes. The result will be to show that if the dispositionalists are to demystify antidote cases, they must make plausible a conceptualisation of dispositions that does not invoke any kind of necessity. I will cautiously suggest that the anti-Humean link dispositions bring to the world has to be thought of in terms of (Newtonian) forces. (shrink)

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)

‘Eruv’ is a Hebrew word meaning literally ‘mixture’ or ‘mingling’. An eruv is an urban region demarcated within a larger urban region by means of a boundary made up of telephone wires or similar markers. Through the creation of the eruv, the smaller region is turned symbolically (halachically = according to Jewish law) into a private domain. So long as they remain within the boundaries of the eruv, Orthodox Jews may engage in activities that would otherwise be prohibited on the (...) Sabbath, such as pushing prams or wheelchairs, or carrying walking sticks. There are eruvim in many towns and university campuses throughout the world. There are five eruvim in Chicago, five in Brooklyn, twenty three in Queens and Long Island, and at least three in Manhattan. The US Supreme Court is (like most other major US Federal Government buildings) located within the eruv of Washington DC. In many cases, not all of those living within or near the area of an actual or proposed eruv will themselves be Orthodox Jews, and this has sometimes led to protests against eruv creation. It is such protests which triggered the writing of this essay. (shrink)