In this paper, we argue that formal ontological relations avoid Bradley's reductio of relations, including his famous relation regress.

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand (...) four-dimensionalism. (shrink)

Foundational relations play an important role in the ontological foundations of conceptual modeling. Their investigation has been theoretically addressed in philosophical/ontological theories, and empirically offered in foundational ontologies (FOs). FOs are comprehensive theories that model the world as top-level entities and relations. Empirically, for modelers aiming to use foundational relations without an urge for entity types, FOs seem to be complex to comprehend, comply with, and integrate in practice. And since the practice of these (...) class='Hi'>relations is critical for conceptual modeling tasks, we present an approach that builds a well-founded entity-type free relations theory within a first-order-logic formalization, besides large complex FOs. The theory contributes to a minimal set of foundational ontological relations (FORT) by importing extant theories (mereotopology and location) and (re-)formalizing other relations (dependence, membership, constitution, and entity-location), while no FO has compromised this set. (shrink)

The purpose of this book is to address the controversial issues of whether we have a fixed set of ontological categories and if they have some epistemic value at all. Which are our ontological categories? What determines them? Do they play a role in cognition? If so, which? What do they force to presuppose regarding our world-view? If they constitute a limit to possible knowledge, up to what point is science possible? Does their study make of philosophy a (...) science? Departing from the novelty –but no exclusively- of considering distinctions to be the subject matter of thought and language -that is, of reference and meaning- the author arrives at a radical novel conception of the ontological categories. The observations and arguments presented in it constitute a strong case against established and well-rooted tenets, if not paradigms, of contemporary philosophy, beyond ontology and epistemology. The entailing conclusions, open the door to a revival of the discipline and the importance of its studies, as the science of the constitutive elements of knowledge of a non-empirical nature. (shrink)

Programming artificial intelligence to make fairness assessments of texts through top-down rules, bottom-up training, or hybrid approaches, has presented the challenge of defining cross-cultural fairness. In this paper a simple method is presented which uses vectors to discover if a verb is unfair or fair. It uses already existing relational social ontologies inherent in Word Embeddings and thus requires no training. The plausibility of the approach rests on two premises. That individuals consider fair acts those that they would be willing (...) to accept if done to themselves. Secondly, that such a construal is ontologically reflected in Word Embeddings, by virtue of their ability to reflect the dimensions of such a perception. These dimensions being: responsibility vs. irresponsibility, gain vs. loss, reward vs. sanction, joy vs. pain, all as a single vector. The paper finds it possible to quantify and qualify a verb as fair or unfair by calculating the cosine similarity of the said verb’s embedding vector against FairVec—which represents the above dimensions. We apply this to Glove and Word2Vec embeddings. Testing on a list of verbs produces an F1 score of 95.7, which is improved to 97.0. Lastly, a demonstration of the method’s applicability to sentence measurement is carried out. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

In this paper I will argue that critical theory needs to make its socio-ontological commitments explicit, whilst on the other hand I will posit that contemporary social ontology needs to amend its formalistic approach by embodying a critical theory perspective. In the first part of my paper I will discuss how the question was posed in Horkheimer’s essays of the 1930s, which leave open two options: (1) a constructive inclusion of social ontology within social philosophy, or else (2) a (...) program of social philosophy that excludes social ontology. Option (2) corresponds to Adorno’s position, which I argue is forced to recur to a hidden social ontology. Following option (1), I first develop a metacritical analysis of Searle, arguing that his social ontology presupposes a notion of 'recognition' which it cannot account for. Furthermore, by means of a critical reading of Honneth, I argue that critical theory could incorporate a socioontological approach, giving value to the constitutive socio-ontological role of recognition and to the socio-ontological role of objectification. I will finish with a proposal for a socio-ontological characterization of reification which involves that the basic occurrence of recognition is to be grasped at the level of background practices. (shrink)

The relation-theory of mental acts proposes that a mental act is a kind of relative entity founded upon the mind and directed at the object of perception or thought. While most medieval philosophers recognized that there is something importantly relational about thought, they nevertheless rejected the view that mental acts are wholly relations. Rather, the dominant view was that a mental act is either in whole or part an Aristotelian quality added to the mind upon which such a relation (...) to the object can be founded. In this paper, I examine Durand of St.-Pourçain's defense of the relation-theory of mental acts against two objections raised against it: the first from John Duns Scotus, among others, and the second from an anonymous Thomist and Adam Wodeham. -/- . (shrink)

The research presented in this article is motivated by the increasing importance of complex human relations in linked data, either extracted from social networks, or found in existing databases. The FOAF vocabulary, targeted in our research, plays a central role in those data, and is a model for lightweight ontologies largely used in linked data, such as the DBpedia ontology and schema-org. We provide an overview of FOAF and other approaches for describing human relations, followed by a detailed (...) analysis and critique of the FOAF Relationship Vocabulary, the most important FOAF extension. We propose an explicit formal axiomatization of this vocabulary, and an ontological analysis concerning the properties used to describe human relationships. We analyze the distribution of human relations based on their epistemological status, and define an ontoepistemic meta-property as characteristic of some of these predicates. Our analysis is generalizable to semantic modeling of social networks. Additionally, the modeling patterns used in other relevant linked data vocabularies are analyzed for comparison. (shrink)

his article develops a framework for addressing racial ontologies in transnational perspective. In contrast to simple contextualist accounts, it is argued that a globally engaged metaphysics of race needs to address transnational continuities of racial ontologies. In contrast to unificationist accounts that aim for one globally unified ontology, it is argued that questions about the nature and reality of race do not always have the same answers across national contexts. In order address racial ontologies in global perspective, the article develops (...) a framework that accounts for both continuities and discontinuities by looking beyond the referents of narrowly defined core concepts. By shifting the focus from narrow concepts to richer conceptions of race, racial ontologies become comparable through globally related but nonetheless distinct mappings between conceptions and property relations. The article concludes by showing how this framework can generate novel insights in case studies from Asia, Europe, and Latin America. (shrink)

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

Amid the wide variety of interpretations of quantum mechanics, the notion of a fully coherent ontological interpretation has seen a promising evolution over the last few decades. Despite this progress, however, the old dualistic categorical constraints of subjectivity and objectivity, correlate with the metrically restricted definition of local and global, have remained largely in place – a reflection of the broader, persistent inheritance of these comfortable strictures throughout the evolution of modern science. If one traces this inheritance back to (...) its ancient roots in Plato and Aristotle, it is clear that the coherence, scientific utility, and historical durability of the various natural philosophies that followed have been directly proportional to their commitment, tacit or explicit, to object-oriented realism. As Simondon might put it, it is a commitment to the primacy of individuated substance over the process of individuation. For Whitehead, it is the misplaced assimilation of becoming to being, of potentiality to actuality. Quantum mechanics has challenged this commitment with a combined breadth and depth of force that far exceeds any other theory in the history of science. The theory’s objectively demonstrable empirical application is manifest only by way of a fundamentally subjective, context-dependent mechanism of measurement. More compelling still, actual system states are always actualizations of locally contextualized yet globally conditioned potential system states, such that “globally objective” reality is no longer merely the object of local measurement, but also its product. Thus, any coherent, ontological interpretation of quantum theory must include a conceptual framework by which objectivity and subjectivity, actuality and potentiality, global and local, being and becoming, individuated fact and process of individuation, are no longer understood as merely epistemic, mutually exclusive category pairs descriptive of an already extant, closed reality – but rather as mutually implicative ontological categories explicative of an ontogenetic, open reality-in-process. (shrink)

I think it would be fair to say that, until about 1900, philosophers were generally reluctant to admit the existence of what are nowadays called polyadic properties.1 It is important to recognize, however, that this reluctance on the part of pre-twentieth-century philosophers did not prevent them from theorizing about relations. On the contrary, philosophers from the ancient through the modern period have had much to say about both the nature and the ontological status of relations. In this (...) paper I examine the views of one such philosopher, namely, Albert the Great. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these (...) relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

Patient-centered care (PCC) is an approach to healthcare that values patients’ preference, need, and autonomy. The estimation of healthcare partly depends on how well PCC is implemented. In addition, the result of clinical research can inform the assessment of the implementation of PCC. In clinical research, health-related quality of life (HRQL) theoretical models offer a conceptual toolbox that informs clinical research and guides the hypotheses generation. Wilson and Cleary (1995) developed the most widely used HRQL theoretical model (Bakas et al., (...) 2012). Ontological assumptions about causation in Wilson and Cleary’s model will influence which kind of hypotheses will be generated. I will argue that Wilson and Cleary’s model instilled a kind of causal bias into hypothesis generation in clinical research on HRQL. Causation from biomedical factors to non-biomedical factors is frequently hypothesized while causation from non-biomedical factors to biomedical factors is rarely hypothesized. It leads to that the interdependence and interaction between constituent parts of patients are ignored, which is an obstacle to the implementation of PCC. In addition, I will propose a revised HRQL theoretical model which avoids the causal bias brought by Wilson and Cleary’s model. By doing so, I leave room for the improvement of the practice of healthcare by analyzing the ontological assumptions about causation. (shrink)

Preference relations are intensively studied in Economics, but they are also approached in AI, Knowledge Representation, and Conceptual Modelling, as they provide a key concept in a variety of domains of application. In this paper, we propose an ontological foundation of preference relations to formalise their essential aspects across domains. Firstly, we shall discuss what is the ontological status of the relata of a preference relation. Secondly, we investigate the place of preference relations within a (...) rich taxonomy of relations (e.g. we ask whether they are internal or external, essential or contingent, descriptive or nondescriptive relations). Finally, we provide an ontological modelling of preference relation as a module of a foundational (or upper) ontology (viz. OntoUML). The aim of this paper is to provide a sharable foundational theory of preference relation that foster interoperability across the heterogeneous domains of application of preference relations. (shrink)

This paper is focused on the possibility of a dialogue between Object-Oriented Ontology (OOO) and phenomenology, a dialogue concerning the problem of objects and relations. In the first part, the author shows what is interesting in OOO from a phenomenological perspective and why it should be considered as a challenge for contemporary philosophy. The second part develops the phenomenological perspective of the author, a perspective based on Merleau-Ponty’s “carnal” phenomenology, as well as some suggestions coming from the Italian school (...) of Gaetano Kanizsa. The third part is dedicated to the objections of the author to the OOO view regarding the separation between objects and relations: a separation which leads to Harman’s quadruple object. In the concluding portion, the author shows that, despite evident differences between phenomenological and OOO’s views of relations, OOO offers new starting points for phenomenological reflections, thanks to its specific focus on objects and its pluralistic view of reality. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power (...) and great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

The last 20 years have witnessed a deepening of the imbrication between capital and the university. This paper seeks to map one point at which this binding occurs: in critical theory. Recently scholars in strategic management have turned to processual and relational ontologies in an attempt to reimagine the logics of profit, value, and growth. These same ontologies have appealed to critical geographers as a means of reconceiving space as unfixed. Drawing on a case study of Deleuze’s appropriation in management (...) literature, I show how such ontologies presuppose a vitalism that necessarily reproduces and obscures the structures of exploitation. (shrink)

The basic kinds of physical causality that are foundational for other kinds of causality involve objects and the causal relations between them. These interactions do not involve events. If events were ontologically significant entities for causality in general, then they would play a role in simple mechanical interactions. But arguments about simple collisions looked at from different frames of reference show that events cannot play a role in simple mechanical interactions, and neither can the entirely hypothetical causal relations (...) between events. These arguments show that physics, which should be authoritative when it comes to the metaphysics of causality, gives no reasons to believe that events are causal agents. Force relations and some cases of energy-momentum transfer are examples of causal relations, with forces being paradigmatic in the macroscopic world, though it is conceivable that there are other kinds of causal relation. A relation between two objects is a causal relation if and only if when it is instantiated by the two objects there is a possibility that the objects that are the terms of the relation could change. The basic metaphysics of causality is about objects, causal relations, changes in objects, and a causal primitive. The paper also includes a discussion of the metaphysics of forces and a discussion of the metaphysics of energy and momentum exchanges. (shrink)

The rational explanation of the Eucharist is at the centre of a revived debate in philosophical theology. After describing gunk-relational ontology, I show how it allows us to understand transubstantiation differently than other traditional and contemporary accounts, from which it draws a few points but combining them in a new way. In gunk-relational ontology every substance is its own relations, which constitute a gunky fundamental reality. The liturgical celebration of the Last Supper therefore creates a new relational situation for (...) the bread: the substance of the bread (its relations) profoundly changes its nature. (shrink)

Formal ontology as a main branch of metaphysics investigates categories of being. In the formal ontological approach to metaphysics, these ontological categories are analysed by ontological forms. This analysis, which we illustrate by some category systems, provides a tool to assess the clarity, exactness and intelligibility of different category systems or formal ontologies. We discuss critically different accounts of ontological form in the literature. Of ontological form, we propose a character- neutral relational account. In this (...) metatheory, ontological forms of entities are their standings in internal relations whose holding is neutral on the character of their relata. These relations are “formal ontological relations”. Entities belong to ontological categories because they stand in the same formal ontological relations. We hold a nominalist relationalism about ontological categories and forms. We conclude by showing that our metatheory is useful for understanding categorial fundamentality/non- fundamentality, different formal ontologies, and for unifying metaphysical questions. (shrink)

Political theory and philosophy need to widen their view of the space in which what matters politically takes place, and I suggest that integrating the conditions of sustainability of all affected—that is, all participants in nature's relations—is a necessary first step in this direction. New materialists and posthumanists have challenged how nature and politics have traditionally been construed. While acknowledging the significance of their contributions, I critically examine the ethical and political implications of their ontological project. I focus (...) particularly on how the decentering of human agency that they advocate for raises a set of concerns that need to be addressed in developing an appropriate ecological ethics. I argue that the latter must be attuned to the vulnerability of living beings who participate in relationships that sustain life on earth. This brings me to conclude that qualitative distinctions between the worlds ofbiosandtechneare necessary. This is because we need to think critically about ways of evaluating types of relationships so that we can assess them and establish which are worth nurturing and protecting and which are not. (shrink)

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ (...) and ‘part of ’. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...) formal ontological principles as a first step towards finding answers to this question. (shrink)

"Ontology" focuses on three ways ground and ontology are said to relate. One way involves ground's ability to provide a safe and sane way of admitting certain kinds of things in our theories. Another way involves ground's ability to show how we should measure ontological simplicity. And a third way involves ground's ability to restrict what things or kinds of things can depend on other things or kinds.

Utilizing Einstein’s comparison of General Relativity and Descartes’ physics, this investigation explores the alleged conventionalism that pervades the ontology of substantival and relationist conceptions of spacetime. Although previously discussed, namely by Rynasiewicz and Hoefer, it will be argued that the close similarities between General Relativity and Cartesian physics have not been adequately treated in the literature—and that the disclosure of these similarities bolsters the case for a conventionalist interpretation of spacetime ontology.

In this paper, I examine the book "Relations: Ontology and Philosophy of Religion" which is a collection of invited and selected papers dealing with both ontology and the philosophy of religion. It aims at showing how the two disciplines can fruitfully interact and provide useful tools for philosophical investigation. The background is relational ontology and analytical philosophy.

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

This book is an attempt to understand the human being, using the method of critical ontology. The human person, as an embodied conscious being, stands in triple relationality with the world around them, maintains the author. I-exist, I-know and I-act are respectively the ontic, epistemic and ethic relationality of our being.

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

In order to develop the ontology of tendencies for use in the representation of medical knowledge, tendencies are compared with other kinds of entities possessing the realizable-realization-structure, specifically: dispositions, propensities, abilities and virtues. The peculiarities of tendencies are discussed and a standard schema of tendency ascription is developed in order to represent the relations between the ascriptions of tendency tokens to particulars and the ascriptions of tendency types to universals. Two non-standard cases and their epistemic variants are discussed.

The aim of natural language ontology is to uncover the ontological categories and structures that are implicit in the use of natural language, that is, that a speaker accepts when using a language. This article aims to clarify what exactly the subject matter of natural language ontology is, what sorts of linguistic data it should take into account, how natural language ontology relates to other branches of metaphysics, in what ways natural language ontology is important, and what may be (...) distinctive of the ontological categories and structures reflected in natural language. (shrink)

This essay provides an opinionated survey of some recent developments in the literature on ontological dependence. Some of the most popular definitions of ontological dependence are formulated in modal terms; others in non-modal terms (e.g., in terms of the explanatory connective, ‘because’, or in terms of a non-modal conception of essence); some (viz., the existential construals of ontological dependence) emphasise requirements that must be met in order for an entity to exist; others (viz., the essentialist construals) focus (...) on conditions that must be satisfied in order for an entity to be the very entity it is at each time at which it exists; some are rigid, in the sense that they concern a relation between particular entities; others are generic, in the sense that they involve only a relation between an entity and some entities or other, which bear certain characteristics. I identify three potential measures of success with respect to which these different definitions of ontological dependence can be evaluated and consider the question of how well they in fact meet these desiderata. I end by noting that certain challenges face even the most promising essentialist construals of ontological dependence. (shrink)

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

According to standard trope nominalism, there are simple tropes that do not have parts or multiply distinct aspects. Douglas Ehring’s reductio ad absurdum against this standard view concludes that there are no simple tropes. In this paper, we provide a response to Ehring defending the standard view. Ehring’s argument may be refuted by (1) distinguishing the ontological form of tropes from their contribution to the ontological content of the world, and (2) construing tropes as having primitive identity. At (...) the same time, standard trope nominalism is elaborated on by distinguishing between ontological form and content, for which there are also independent reasons. (shrink)

The dominant view amongst contemporary Western philosophers about the essence of a natu­ ral object is that it is constituted by its intrinsic properties. The ontological approach salient in the African philosophical tradition, in contrast, accounts for a thing’s essence by appeal to its relational properties. The Afro­relational ontology is under­developed, with the primary aim of this article being to help rectify that weakness. Specifically, this article’s aims are: to articulate an African approach to understanding the essence of a (...) concrete, natural thing in terms of its relationships; to illustrate the Afro­relational approach with the examples of the self and of water; to contrast the Afro­relational characterization of the essence of the self and of water with a typically Western construal in terms of their intrinsic properties; and finally to provide an initial defence of the Afro­relational approach, both by responding to some objections facing it and by providing some new, positive reasons to take it seriously. (shrink)

The relation of ontological dependence or grounding, expressed by the terminology of separation and priority in substance, plays a central role in Aristotle’s Categories, Metaphysics, De Anima and elsewhere. The article discusses three current interpretations of this terminology. These are drawn along the lines of, respectively, modal-existential ontological dependence, essential ontological dependence, and grounding or metaphysical explanation. I provide an opinionated introduction to the topic, raising the main interpretative questions, laying out a few of the exegetical and (...) philosophical options that influence one’s reading, and locating questions of Aristotle scholarship within the discussion of ontological dependence and grounding in contemporary metaphysics. (shrink)

Ingarden’s puzzle is: how can we come to know what is essentially involved in an act of knowing? As starting point he takes what he holds to be a particular good candidate example of such an act, namely an act of perceiving an apple. Here we have act and object standing in a certain first-level relation to each other. We now in a second level act of reflection, make this first-level relation into an object, and strive to apprehend this object (...) as an instantiation of the essence knowledge. But how, on this basis, could we ever establish that we had indeed grasped this essence, and that this is indeed the appropriate essence? Surely, through some third-level act of reflection on this second-level act. We expound from an ontological point of view Ingarden's idea as to how this regress can be avoided. (shrink)

This paper motivates taking seriously the possibility that brains are basically protean: that they make use of neural structures in inventive, on-the-fly improvisations to suit circumstance and context. Accordingly, we should not always expect cognition to divide into functionally stable neural parts and pieces. We begin by reviewing recent work in cognitive ontology that highlights the inadequacy of traditional neuroscientific approaches when it comes to divining the function and structure of cognition. Cathy J. Price and Karl J. Friston, and Colin (...) Klein identify the limitations of relying on forward and reverse inferences to cast light on the relation between cognitive functions and neural structures. There is reason to prefer Klein’s approach to that of Price and Friston’s. But Klein’s approach is neurocentric - it assumes that we ought to look solely at neural contexts to fix cognitive ontology. Using recent work on mindreading as a case study, we motivate adopting a radically different approach to cognitive ontology. Promoting the Protean Brain Hypothesis, we posit the possibility that we may need to look beyond the brain when deciding which functions are being performed in acts of cognition and in understanding how the brain contributes to such acts by adapting to circumstance. (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)

Virtually everyone who has advanced an ontology of art has accepted a constraint to the effect that claims about ontology should cohere with the sort of appreciative claims made about artworks within a mature and reflective version of critical practice. I argue that such a constraint, which I agree is appropriate, rules out a one-size-fits-all ontology of contemporary visual art (and thus of visual art in general). Mature critical practice with respect to contemporary art accords artists a significant degree of (...) stipulative authority regarding the features and boundaries of their works. This results in ontological variation among visual artworks. Any claim to the effect that all works belong to the same ontological category will thus come out false or uninformative. Interesting, substantive claims about ontological status can be made only in relation to specific works; that is, we must consider the ontological status of each contemporary artwork individually. The only general ontological claim that can be made about visual artworks (and also about artworks in other forms) is that they belong to the sort of thing that artists create. But this is not a substantive ontological claim. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The problem of merging several ontologies has important applications in the Semantic Web, medical ontology engineering and other domains where information from several distinct sources needs to be integrated in a coherent manner.We propose to view ontology merging as a problem of social choice, i.e. as a problem of aggregating the input of a set of individuals into an adequate collective decision. That is, we propose to view ontology merging as ontology aggregation. As a first step in this direction, we (...) formulate several desirable properties for ontology aggregators, we identify the incompatibility of some of these properties, and we define and analyse several simple aggregation procedures. Our approach is closely related to work in judgment aggregation, but with the crucial difference that we adopt an open world assumption, by distinguishing between facts not included in an agent’s ontology and facts explicitly negated in an agent’s ontology. (shrink)

This paper will present an analysis of the relational aspect of Brentano’s last theory of intentionality. My main thesis is that Brentano, at the end of his life, considered relations (relatives) without existent terms to be genuine relations (relatives). Thus, intentionality is a non-reducible real relation (the thinking subject is a non-reducible real relative) regardless of whether or not the object exists. I will use unpublished texts from the Brentanian Nachlass to support my argument.

In this article, we analyse the ontological import of adding classes to set theories. We assume that this increment is well represented by going from ZF system to NBG. We thus consider the standard techniques of reducing one system to the other. Novak proved that from a model of ZF we can build a model of NBG (and vice versa), while Shoenfield have shown that from a proof in NBG of a set-sentence we can generate a proof in ZF (...) of the same formula. We argue that the first makes use of a too strong metatheory. Although meaningful, this symmetrical reduction does not equate the ontological content of the theories. The strong metatheory levels the two theories. Moreover, we will modernize Shoenfields proof, emphasizing its relation to Herbrands theorem and that it can only be seen as a partial type of reduction. In contrast with symmetrical reductions, we believe that asymmetrical relations are powerful tools for comparing ontological content. In virtue of this, we prove that there is no interpretation of NBG in ZF, while NBG trivially interprets ZF. This challenges the standard view that the two systems have the same ontological content. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological (...) theorizing in abstract fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

A brief description of ontology and of its relation to the work of Jean-Luc Nancy.