How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (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)

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its (...) construction and maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying (...) attention to the relationships between (1) particulars and types, and (2) continuants and occurrents. (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)

Divine intention is an important problem for both philosophy and Kalam. This problem has two aspects as the subject and action of the intention. The intention of the subject occurs for the motion or the action itself. The intention of the action is to reach the motion or the action itself. According to this, when a person travels to Mecca to visit Kaaba, the visit is the intention of the subject and the journey is the intention of the action. In (...) this context, does Allah have an intention? And what are the intentions of the actions aris-ing from him? In the Islamic philosophy, the first question is handled as "intention of the sub-ject/divine intention” and the second question as "the intention of the actions/divine inten-tion of the actions". In order to answer the first question, we must examine all types of inten-tions. Each subject takes action to benefit them, to benefit others and to act for the sake of the goodness and kindness. Allah would be dependent being if he acted to benefit him and to make up for a flaw for the first of these intentions. In the second intention type, if Allah acted for someone else, this sit-uation would be on the degree of cause for the subject and he would be passive. For the third intention type which is to act to reach for perfection, it would deem Allah as a dependent being. The above-mentioned intentions are flawed. On the contrary, Allah is perfect and does not need any of these intentions to create. Thus, he is not subject to any of these possible inten-tions. These intentions are only used by imperfect subjects. Of course, it does not mean that Allah does not have intentions. According to Avicenna and Mulla Sadra, intention of Allah is the love towards his essence which is free from any flaw. According to this, all beings are entailed to the divine essence and they exist due to the love of essence of Allah. Allah has a direct intention as well as an indirect one. As mentioned before, Allah is in love with his essence. Allah loves the works and actions of his essence as well, according to the principal that one, who loves the essence, loves the works and actions of that essence as well. In this context, the love of essence of the Allah is a direct intention, while the love of his es-sence's works and actions is an indirect intention. After the divine intention is explained, we must also explain the intention of the divine ac-tions. According to both Mulla Sadra and Avicenna, since possible beings are flawed, their intention is to reach to certain perfections which are compatible with themselves. Mulla Sadra states that Allah bestows motivation to possible beings to advance towards the perfection and he claims that these beings make use of that motivation to be perfect. Therefore, possible beings try to make up their flaws and reach to perfection. Since Allah is the absolute perfect being, the final intention of the possible beings is Allah. In other words, all beings that seek for perfection, take example of him. The other intentions act as a primary tool to reach the final intention. How can flawed beings by essence reach to perfections compatible with them? Avicenna and Mulla Sadra stated different opinions on the search of perfection of the flawed beings in the Islam philosophy. According to Avicenna, beings change with extinction and creation. This change happens by accident and the substance stays constant. In accordance with this approach, this change and development is only possible with accidental motion. It occurs with the replacement between forms. But the theory of the Avicenna has some flaws. Because forms are not the intentions of each other and first hyle is not strong enough to have an intention. Thus, no form is superior to the other. It is also not possible to have substance development because the substance and es-sence of the material are constant. It only goes through changes in appearance with the acci-dental motion. It is clear that the changes in the appearance and the shape are not standards for perfection. On the other hand, Mulla Sadra's development theory, which is based on the fundamentality of existence, existential gradation and substantial motion, suggests that the material world is moving towards the perfection. The motion in the substance of material beings is reason of substantial and accidental developments. All beings try to promote themselves to a higher position by reaching perfection in accordance with their intentions. Thus, the theory of Avicenna focuses on the accidental and formal changes in the search of perfection of the material beings, while Mulla Sadra’s theory explains accidental changes as well as the essential ones. Mulla Sadra does not limit the explanation of which Allah is the intention of possible beings to ontological dimension. According to him, Allah is an intention of possible beings as well. He points out the Hadith Qudsi "I was a hidden treasure, I desired to be recognized so I created the creature" and states that "This (Hadith Qudsi) indicates that he is the subject and the in-tention of the universe in an ontological manner as well as the intention of the universe in an epistemological manner." Thus, according to Mulla Sadra, possible beings have two inten-tions, to reach to and understand Allah. (shrink)

The paper shows how the Bohmian approach to quantum physics can be applied to develop a clear and coherent ontology of non-perturbative quantum gravity. We suggest retaining discrete objects as the primitive ontology also when it comes to a quantum theory of space-time and therefore focus on loop quantum gravity. We conceive atoms of space, represented in terms of nodes linked by edges in a graph, as the primitive ontology of the theory and show how a non-local (...) law in which a universal and stationary wave-function figures can provide an order of configurations of such atoms of space such that the classical space-time of general relativity is approximated. Although there is as yet no fully worked out physical theory of quantum gravity, we regard the Bohmian approach as setting up a standard that proposals for a serious ontology in this field should meet and as opening up a route for fruitful physical and mathematical investigations. (shrink)

John Bell proposed an ontology for the GRW modification of quantum mechanics in terms of flashes occurring at space- time points. This article spells out the motivation for this ontology, inquires into the status of the wave function in it, critically examines the claim of its being Lorentz invariant, and considers whether it is a parsimonious but nevertheless physically adequate ontology.

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)

Despite their shared origins, medicine and dentistry are not always two sides of the same coin. There is a long history in medical philosophy of defining disease and various medical models have come into existence. Hitherto, little philosophical and phenomenological work has been done considering dental caries and periodontitis as examples of disease and illness. A philosophical methodology is employed to explore how we might define dental caries and periodontitis using classical medical models of disease – the naturalistic (...) and normativist. We identify shared threads and highlight how the features of these highly prevalent dental diseases prevent them fitting in either definition. The article describes phenomenology and the current thought around the phenomenology of illness, exploring how and why these dental illnesses might integrate into a phenomenological model. We discover that there are some features particular to dental caries and periodontitis: ubiquity, preventability and hyper-monitorablility. Understanding the differences that these dental diseases have compared to many other classically studied diseases leads us to ethical questions concerning how we might manage those who have symptoms and seek treatment. As dental caries and periodontitis are common, preventable and hyper-monitorable, it is suggested that these features affect the phenomenology of these illnesses. For example, if we experience dental illness when we have consciously made decisions that have led to it, do we experience them differently to those rarer illnesses that we cannot expect? Other diseases share these features are discussed. This paper highlights the central differences between the classical philosophical notion of disease in medicine and the dental examples of caries and periodontitis. It suggests that a philosophical method of conceptualising medical illness - phenomenology - should not be applied to these dental illnesses without thought. A phenomenological analysis of any dental illness is yet to be done and this paper highlights why a separate strand of phenomenology should be explored, instead of employing those that are extant. The article concludes with suggestions for further research into the nascent field of the phenomenology of dental illness and aims to act as a springboard to expose the dental sphere to this philosophical method of analysis. (shrink)

In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...) formulated as quasi-Newtonian, via the postulation of forces proportional to acceleration; advocates of the guidance approach defend the notion that the theory is essentially first-order and incorporates some concepts akin to those of Aristotelian physics. Here I analyze whether the desideratum of an interpretation of Bohmian mechanics that is both explanatorily adequate and not committed to configuration space realism favors one of these two approaches to the theory over the other. Contrary to some recent claims in the literature, I argue that the quasi-Newtonian approach based on the idea of a quantum potential does not come out the winner. (shrink)

Scientific realists don’t standardly discriminate between, say, biology and fundamental physics when deciding whether the evidence and explanatory power warrant the inclusion of new entities in our ontology. As such, scientific realists are committed to a lush rainforest of special science kinds (Ross, 2000). Viruses certainly inhabit this rainforest – their explanatory power is overwhelming – but viruses’ properties can be explained from the bottom up: reductive explanations involving amino acids are generally available. However, reduction has often been taken (...) to lead to a metaphysical downgrading, so how can viruses keep their place in the rainforest? 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 trout and turkeys, but philosophically gerrymandered objects like trout-turkeys do not qualify. (shrink)

Individualists about social ontology hold that social facts are “built out of” facts about individuals. In this paper, I argue that there are two distinct kinds of individualism about social ontology, two different ways individual people might be the metaphysical “builders” of the social world. The familiar kind is ontological individualism. This is the thesis that social facts supervene on, or are exhaustively grounded by, facts about individual people. What I call anchor individualism is the alternative thesis that (...) facts about individuals put in place the conditions for a social entity to exist, or the conditions for something to have a social property. Examples include conventionalist theories of the social world, such as David Hume’s theories of promises, money, and government, and collective acceptance theories, such as John Searle’s theory of institutional facts. Anchor individualism is often conflated with ontological individualism. But in fact, the two theses are in tension with one another: if one of these kinds of individualism is true, then the other is very unlikely to be. My aim in this paper is to clarify both, and argue that they should be sharply distinguished from one another. (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)

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (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)

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)

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)

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)

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)

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.

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)

Notions such as śūnyatā, catuṣkoṭi, and Indra's net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nāgārjuna considered two levels of reality: one called conventional reality, and the other ultimate reality. Within this framework, śūnyatā refers to the claim that at the ultimate level objects are devoid of essence or "intrinsic properties", but are interdependent by virtue of their relations to other objects. Catuṣkoṭi refers to the claim (...) that four truth values, including contradiction, are admissible in reasoning. Indra's net refers to the claim that every part of a whole is reflective of the whole. Here we present category theoretic constructions that are reminiscent of these Buddhist concepts. The universal mapping property definition of mathematical objects, wherein objects of a universe of discourse are defined not in terms of their content, but in terms of their relations to all objects of the universe is reminiscent of śūnyatā. The objective logic of perception, with perception modeled as [a category of] two sequential processes (sensation followed by interpretation), and with its truth value object of four truth values, is reminiscent of the Buddhist logic of catuṣkoṭi. The category of categories, wherein every category has a subcategory of sets with zero structure within which every category can be modeled, is reminiscent of Indra's net. Our thorough elaboration of the parallels between Buddhist philosophy and category theory can facilitate better understanding of Buddhist philosophy, and bring out the broader philosophical import of category theory beyond mathematics. (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)

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)

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)

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)

There are prominent resemblances between issues addressed by Simone de Beauvoir in her early essay on moral philosophy, Pyrrhus and Cineas (1944), and issues attracting the attention of contemporary feminist ethicists, especially those concerned with the ethics of care. They include a focus on relationships, interaction, and mutual dependency. Both emphasize concrete ethical challenges rooted in everyday life, such as those affecting parents and children. Both are critical of the level of abstraction and insensitivity to the situation of the moral (...) agent in utilitarianism and Kantian ethics. And both condemn the “moral point of view,” i.e. the assumption that it is possible to speak with a universal voice on behalf of humanity. These resemblances are explored in this article. (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)

This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...) for formal ontology. We provide examples to support this thesis from the domain of biomedicine. (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)

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)

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)

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)

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)

Intellectual history still quite commonly distinguishes between the episode we know as the Scientific Revolution, and its successor era, the Enlightenment, in terms of the calculatory and quantifying zeal of the former—the age of mechanics—and the rather scientifically lackadaisical mood of the latter, more concerned with freedom, public space and aesthetics. It is possible to challenge this distinction in a variety of ways, but the approach I examine here, in which the focus on an emerging scientific field or cluster of (...) disciplines—the ‘life sciences’, particularly natural history, medicine, and physiology —is, not Romantically anti-scientific, but resolutely anti-mathematical. Diderot bluntly states, in his Thoughts on the interpretation of nature, that “We are on the verge of a great revolution in the sciences. Given the taste people seem to have for morals, belles-lettres, the history of nature and experimental physics, I dare say that before a hundred years, there will not be more than three great geometricians remaining in Europe. The science will stop short where the Bernoullis, the Eulers, the Maupertuis, the Clairauts, the Fontaines and the D’Alemberts will have left it.... We will not go beyond.” Similarly, Buffon in the first discourse of his Histoire naturelle speaks of the “over-reliance on mathematical sciences,” given that mathematical truths are merely “definitional” and “demonstrative,” and thereby “abstract, intellectual and arbitrary.” Earlier in the Thoughts, Diderot judges “the thing of the mathematician” to have “as little existence in nature as that of the gambler.” Significantly, this attitude—taken by great scientists who also translated Newton or wrote careful papers on probability theory, as well as by others such as Mandeville—participates in the effort to conceptualize what we might call a new ontology for the emerging life sciences, very different from both the ‘iatromechanism’ and the ‘animism’ of earlier generations, which either failed to account for specifically living, goal-directed features of organisms, or accounted for them in supernaturalistic terms by appealing to an ‘anima’ as explanatory principle. Anti-mathematicism here is then a key component of a naturalistic, open-ended project to give a successful reductionist model of explanation in ‘natural history’, a model which is no more vitalist than it is materialist—but which is fairly far removed from early modern mechanism. (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)

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)

Two major lines of argument support the notion that Hildegard of Bingen’s metaphysics is peculiarly gynocentric. Contra the standard commentary on her work, the focus is not on the notion of viriditas; rather, the first line of argument presents a specific delineation of her ontology, demonstrating that it is a graded hierarchy of beings, many of which present feminine aspects of the divine, and all of which establish the metaphysical notion of interpenetrability. The second line of argument specifically contrasts (...) her thought to that of Aquinas and Meister Eckhart, noting areas of similarity and difference. It is concluded that the visionary origins of Hildegard’s work may have to some extent precluded our understanding of it, and that her work merits consideration not only philosophically and theologically but from the standpoint of its early presentation of a gynocentric worldview. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into (...) hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (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)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. 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 COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease (...) Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (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)

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)