Axiom weakening is a novel technique that allows for fine-grained repair of inconsistent ontologies. In a multi-agent setting, integrating ontologies corresponding to multiple agents may lead to inconsistencies. Such inconsistencies can be resolved after the integrated ontology has been built, or their generation can be prevented during ontology generation. We implement and compare these two approaches. First, we study how to repair an inconsistent ontology resulting from a voting-based aggregation of views of heterogeneous agents. Second, we (...) prevent the generation of inconsistencies by letting the agents engage in a turn-based rational protocol about the axioms to be added to the integrated ontology. We instantiate the two approaches using real-world ontologies and compare them by measuring the levels of satisfaction of the agents w.r.t. the ontology obtained by the two procedures. (shrink)

Combinations of molecules, of biological individuals, or of chemical processes can produce effects that are not simply attributable to the constituents. Such non-redundant causality warrants recognition of those coherences as ontologically significant whenever that efficacy is relevant. With respect to such interaction, the effective coherence is more real than are the components. This ontological view is a variety of structural realism and is also a kind of process philosophy. The designation ‘process structural realism’ (PSR) seems appropriate.

Ontologies represent principled, formalised descriptions of agents’ conceptualisations of a domain. For a community of agents, these descriptions may differ among agents. We propose an aggregative view of the integration of ontologies based on Judgement Aggregation (JA). Agents may vote on statements of the ontologies, and we aim at constructing a collective, integrated ontology, that reflects the individual conceptualisations as much as possible. As several results in JA show, many attractive and widely used aggregation procedures are prone (...) to return inconsistent collective ontologies. We propose to solve the possible inconsistencies in the collective ontology by applying suitable weakenings of axioms that cause inconsistencies. (shrink)

Why is there a specific problem with biological individuality? Because the living realm contains a wide range of exotic particular concrete entities that do not easily match our ordinary concept of an individual. Slime moulds, dandelions, siphonophores are among the Odd Entities that excite the ontological zeal of the philosophers of biology. Most of these philosophers, however, seem to believe that these Odd Cases oblige us to refine or revise our common concept of an individual. They think, explicitly or tacitly, (...) that to be a living, evolutionary entity is to be a living individual. In this paper, we explore an alternative proposal: the variety and oddity of the forms of the living realm might be ontologically regimented through an increase in the categorial complexity of the living realm, by admitting, beside living individuals, living non-individuals or by acknowledging, more generally, that the evolutionary development of the living forms is not necessarily a process of building individuals, that life is not necessarily individuals-oriented. We claim that, from an ontological point of view, the spectacle of the living realm obliges us to take aggregativity seriously. (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)

Maddy's (1990) arguments against Aggregate Theory were undermined by the shift in her position in 1997. The present paper considers Aggregate Theory in the light of this, and the recent search for `New Axioms for Mathematics'. If Set Theory is the part-whole theory of singletons, then identifying singletons with their single members collapses Set Theory into Aggregate Theory. But if singletons are not identical to their single members, then they are not extensional objects and so are not a basis for (...) Science. Either way, the Continuum Hypothesis has no physical interest. (shrink)

Beginning with Aristotle, philosophers have taken artifacts to be ontologically deficient. This paper proposes a theory of artifacts, according to which artifacts are ontologically on a par with other material objects. I formulate a nonreductive theory that regards artifacts as constituted by - but not identical to - aggregates of particles. After setting out the theory, I rebut a number of arguments that disparage the ontological status of artifacts.

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)

Priority Monism, as defined by Jonathan Schaffer, has a number of components. It is the view that: the cosmos exists; the cosmos is a maximal actual concrete object, of which all actual concrete objects are parts; the cosmos is basic—there is no object upon which the cosmos depends, ontologically; ontological dependence is a primitive and unanalysable relation. In a recent attack, Lowe has offered a series of arguments to show that Monism fails. He offers up four tranches of argument, with (...) different focuses. These focal points are: being a concrete object; aggregation and dependence; analyses of ontological dependence; Schaffer’s no-overlap principle. These are all technical notions, but each figures at the heart of a cluster of arguments that Lowe puts forward. To respond, I work through each tranche of argument in turn. Before that, in the first section, I offer a cursory statement of Monism, as Schaffer presents it in his 2010 paper, Monism: The Priority of the Whole. I then respond to each of Lowe’s criticisms in turn, deploying material from Schaffer’s 2009 paper Spacetime: the One Substance, as well as various pieces of conceptual machinery from Lowe’s own works to deflect Lowe’s attacks. In the process of defending Monism from Lowe, I end up offering some subtle refinements to Schaffer’s view and explain how the resulting ‘hybrid’ view fares in the wider dialectic. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...) In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

The possibility of domain restrictions that allow the consistent use of majority-based aggregators for rankings of objects has been widely explored. This paper extends this exploration to structures in which equivalence relations or classifications are aggregated, and shows that there is very limited scope for such restrictions in the binary structure of Mirkin and in the unary structure of Maniquet and Mongin. We develop a hybrid structure that combines binary and unary conditions on the aggregator, and that allows the use (...) of a majority-based aggregator if and only if each object is eligible for inclusion in no more than two categories out of some greater number. We also show that in many circumstances, the surjectivity requirement of Maniquet and Mongin implicitly introduces binary conditions on the aggregator, and that their structure is entailed by the hybrid structure introduced here. (shrink)

We present an ontological analysis of the notion of group agency developed by Christian List and Philip Pettit. We focus on this notion as it allows us to neatly distinguish groups, organizations, corporations – to which we may ascribe agency – from mere aggregates of individuals. We develop a module for group agency within a foundational ontology and we apply it to organizations.

Suppose n Bayesian agents need to make a decision as a group. The groupas a whole is also supposed to be a Bayesian agent whose probabilities andutilities are derived or aggregated in reasonable ways from the probabilitiesand utilities of the group members. The aggregation could beex ante, i.e., interms of expected utilities, or it could be ex post, i.e., in terms of utilitiesonly, or in terms of utilities and probabilities separately. This study exploresthe ex post approach. Using the Bolker/Jeffrey (...) framework, we show thatex post aggregation is subject to an instability phenomenon. That is, it mayhappen that the group preference between actions ``flips back and forth'''' dependingon the level of detail in which the decision problem is described. Structurally verysimilar phenomena also occur elsewhere in social choice theory, in statistics (Simpson''sParadox), and in voting theory (Ostrogorski''s Paradox). (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Since the emergence of the innovative field of artificial intelligence in the 1960s, the late Hubert Dreyfus insisted on the ontological distinction between man and machine, human and artificial intelligence. In the different editions of his classic and influential book What computers can’t do, he posits that an algorithmic machine can never fully simulate the complex functioning of the human mind—not now, nor in the future. Dreyfus’ categorical distinctions between man and machine are still relevant today, but their relation has (...) become more complex in our increasingly data-driven society. We, humans, are continuously immersed within a technological universe, while at the same time ubiquitous computing, in the words of computer scientist Mark Weiser, “forces computers to live out here in the world with people” The cell phone reader. Peter Lang Publishing, New York, 2006, p 20). Dreyfus’ ideas are therefore challenged by thinkers such as Weiser, Kevin Kelly, Bruno Latour, Philip Agre, and Peter Paul Verbeek, who all argue that humans are much more intrinsically linked to machines than the original dichotomy suggests—they have evolved in concert. Through a discussion of the classical concepts of individuum and ‘authenticity’ within Western civilization, this paper argues that within the ever-expanding data-sphere of the twenty-first century, a new concept of man as ‘aggregate of data’ has emerged, which further erodes and undermines the categorical distinction between man and machine. This raises political and ethical questions beyond the confines of technology and artificial intelligence. Moreover, this seemingly never-ending debate on what computers should do provokes the philosophical necessity to once again define the concept of what it is to be ‘human.’. (shrink)

The base units of the SI include six units of continuous quantities and the mole, which is defined as proportional to the number of specified elementary entities in a sample. The existence of the mole as a unit has prompted comment in Metrologia that units of all enumerable entities should be defined though not listed as base units. In a similar vein, the BIPM defines numbers of entities as quantities of dimension one, although without admitting these entities as base units. (...) However, there is a basic ontological distinction between continuous quantities and enumerable aggregates. The distinction is the basis of the difference between real and natural numbers. This paper clarifies the nature of the distinction: (i) in terms of a set of measurement axioms stated by Hölder; and (ii) using the formalism known in metrology as quantity calculus. We argue that a clear and unambiguous scientific distinction should be made between measurement and enumeration. We examine confusion in metrological definitions and nomenclature concerning this distinction, and discuss the implications of this distinction for ontology and epistemology in all scientific disciplines. (shrink)

When an entity ontologically depends on another entity, the former ‘presupposes’ or ‘requires’ the latter in some metaphysical sense. This paper defends a novel view, Dependence Deflationism, according to which ontological dependence is what I call an aggregative cluster concept: a concept which can be understood, but not fully analysed, as a ‘weighted total’ of constructive and modal relations. The view has several benefits: it accounts for clear cases of ontological dependence as well as the source of disagreement in controversial (...) ones; it gives a nice story about the evidential relevance of modal, mereological and set-theoretic facts to ontological dependence; and it makes sense of debates over the relation's formal properties. One important upshot of the deflationary account is that questions of ontological dependence are generally less deep and less interesting than usually thought. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in (...) such a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

This article’s purpose is to defend the depiction of ordinary-sized physical objects as mereological aggregates (MAs), to clarify what the ontology of an MA is, and to show why mereological essentialism (ME) applies to MAs that seem to be ubiquitous if we are to adopt what Frank Jackson calls “Serious Metaphysics” and refuse to broaden our ontology beyond what is (allegedly) bequeathed to us by physics and chemistry. To accomplish this goal, first, I clarify certain background issues that (...) inform what follows and I identify certain constraints that relate to the contemporary ambivalence towards ME. Second, I present a primer on Husserlian mereology that provides a superior account of parts and wholes than the inadequate approach identified in the previous section. Third, I will offer a defense of ME as the correct approach to providing an ontological account of MAs. Finally, I will evaluate two defeaters against my thesis. (shrink)

In various places we have defended the position that a new human organism, that is, an individual member of the human species, comes to be at fertilization, the union of the spermatozoon and the oocyte. This individual organism, during the ordinary course of embryological development, remains the same individual and does not undergo any further substantial change, unless monozygotic twinning, or some form of chimerism occurs. Recently, in this Journal Jason Morris has challenged our position, claiming that recent findings in (...) reproductive and stem cell biology have falsified our view. He objects to our claim that a discernible substantial change occurs at conception, giving rise to the existence of a new individual of the human species. In addition, he objects to our claim that the embryo is an individual, a unified whole that persists through various changes, and thus something other than a mere aggregate of cells. Morris raises a number of objections to these claims. However, we will show that his arguments overlook key data and confuse biological, metaphysical, and ethical questions. As a result, his attempts to rebut our arguments fail. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate therein. The theory is divided into two major categories of sub-theories: (sub-) theories of type SPAN and (sub-)theories of type SNAP. These theories represent two complementary perspectives on reality and result in distinct though compatible systems of categories. In SNAP we have enduring entities such as substances, qualities, roles, functions; in SPAN we have perduring entities such as (...) processes and their parts and aggregates. We argue that both kinds of ontological theory are required in order to give a non-reductionism account of complex domains of reality. (shrink)

It's well known that Leibniz characterizes bodies in two apparently incompatible ways. On the one hand, he asserts that a body is a real or well-founded phenomenon; on the other, he claims that a body is an aggregate of substances that possesses the reality of these same substances. In this essay I aim to defend an explanation of the relation that exists, according to Leibniz, between these two conceptions of body, an explanation that shows them to be compatible and, indeed, (...) complementary. In the first part of this paper I aim above all to show that Robert Adams and Donald Rutherford are wrong to think that these two conceptions are to be reconciled by recognizing that for Leibniz they apply to one and the same thing. (shrink)

In the second part of this essay, I aim to show that Leibniz, in asserting that bodies are aggregates of substances, wants to affirm something about bodies insofar as they exist a parte rei or in reality: in reality a body is not a being, but a multitude of beings or substances. And this, on my view, is precisely what leads Leibniz to assert that bodies are phenomena: since a body is not in reality a being, but many beings, it (...) follows that a body, conceived as a being, is something that exists only objectively in the soul. That is, a body, conceived as a single thing, is not something real, but an imaginary being, a creature of the mind, a phenomenon. (shrink)

Este texto surge de un intercambio epistolar mantenido con David Armstrong a propósito de su libro Universals. An Opinionated lntroduction. Se presenta en forma de diálogo y ha sido dividido en seis temas. El primero trata el problema de si las diferentes teorías ontológicas, al postular diferentes relaciones básicas, se hallan también en diferentes condiciones para afrontar el argumento del regreso infinito planteado por Bradley. El segundo presenta una duda. Los universales que postula Armstrong, tales como masa, carga electromagnética, etc., (...) son "agregativos": admiten la categoría de cantidad. Pero se supone que los universales no admiten dicha categoría. Pareciera, pues, que los "universales" postulados por Armstrong no constituyen auténticos universales. El tercer tema concierne a la relación entre la teoría del haz y el Principio de identidad de los indiscernibles. El cuarto trata la opinión de Armstrong según la cual la teoría del haz se vería obligada a postular el carácter autosubsistente de los universales. El quinto consiste en la discusión acerca de si la teoría del haz debe admitir la existencia de hechos. Finalmente, el sexto concierne a la naturaleza de los tropos. This text originates in an exchange of letters I held with David Armstrong when his book Universals. An Opinionated Introduction was published. It is offered as a dialogue and has been divided into six topics. The first one deals with the problem of whether different ontological theories, which posit different basic relations, are also differently prepared to deal with Bradley's infinito regress argument. The second one raises a doubt. Those universals posited by Armstrong, such as mass, electric charge, etc., are "aggregative", which means they are subject to the category of quantity. But universals are not supposed to differ quantitatively. Thus, those "universals" favored by Armstrong become suspect of not being real universals. The third one addresses the relation between the Bundle Theory and the Identity of Indiscernibles. The fourth one deals with Armstrong's opinion according to which the bundle theorist is forced to conceive of universals as self subsistant entities. The fifth one discusses whether the Bundle Theory has to accept the existence of facts. Finally, the sixth one deals with tropes. (shrink)

BACKGROUND -/- Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces (...) of knowledge available in a formal (and thus computable) manner. -/- RESULTS -/- We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. -/- CONCLUSIONS -/- We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities (...) such as organisms, geographic features, or qualities as they exist at some given moment of time. A SPAN ontology comprehends perduring entities such as processes and their parts and aggregates as they unfold themselves through some temporal interval. We give an axiomatic account of the theory of directly depicting ontologies and of the core parts of the metaontological fragment within which they are embedded. (shrink)

Does Aquinas have a theory of social ontology? It is not easy to answer this question. On the one hand, Aquinas never discusses the ontology of those entities that we today consider significant for social ontology. On the other hand, though, there are places where Aquinas addresses the mereological question of the relation between aggregates and the individuals that compose them, and these places are significant for bringing to light what Aquinas had to say, if anything, about (...) social ontology. In the end, Aquinas grants social aggregates a place within Aristotelian ontology. My claim here is stronger, however. As a follower of Aristotle, Aquinas cannot avoid having a theory of social ontology, however inchoate this theory may be. In this paper, I show that his theory is metaphysical in character rather than cognitive or linguistic; nevertheless, it also considers the three primitives that, according to John Searle, are at the basis of any social construction, namely collective intentionality, assignment of function, and constitutive rules and procedures. I shall prove that Aquinas’s theory lies between reductionism and realism when it answers the question of the nature of social aggregates, and between naturalism and constructionism when it comes to explaining their origin. (shrink)

Published in extended form as "Endurants and Perdurants in Directly Depicting Ontologies", -/- We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate in such processes. For this purpose we distinguish between ontologies and metaontology. Ontologies are based on very simple directly depicting languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct (...) though compatible systems of categories. In a SNAP (snapshot) ontology we have the enduring entities in a given domain as they exist to be inventoried at some given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontology are required, together with the meta-ontology which joins them together. On the level of meta-ontology we are able to impose constraints on ontologies of a sort which can support efficient processing of large amounts of data. (shrink)

The background thesis is that an implicit ontology of the people and the relation between the people and the state often shapes how we think in normative terms about politics. This article attempts to defend that thesis in relation to Rawls. The argument is that the rejection of an image of the people as a group agent connects with his objection to utilitarianism and the rejection of an image of the people as a mere aggregate connects with his objection (...) to libertarianism. Rawls, it is argued, holds by an in-between picture and it is this that explains many of his most distinctive commitments. Key Words: Rawls • social ontology • group agent • solidarism • singularism • civicity. (shrink)

According to several prominent philosophers, pleasure and pain come in measurable quantities. This thesis is controversial, however, and many philosophers have presented or felt compelled to respond to arguments for the conclusion that it is false. One important class of these arguments concerns the problem of aggregation, which says that if pleasure and pain were measurable quantities, then, by definition, it would be possible to perform various mathematical and statistical operations on numbers representing amounts of them. It is sometimes (...) argued that such operations cannot be sensibly applied to pleasure and pain, and that sentences expressing such operations must be false or meaningless. The purpose of this paper is to present, explain, and rebut several versions of this argument. In the first section, I present a generic version of the argument. In the second section, I present a defense of its key premise based on a case involving comparisons of relief from pain, and explain why I think it fails. In the third section, I present and rebut another defense, based on a pair of analogies with temperature. In the final section, I present a third defense, based on an analogy with spatial distances. I then present my reasons for rejecting it. Along the way, I explain my reasons for thinking that pleasure and pain are amenable to interval measurement. (shrink)

Bertrand Russell’s _Principles of Mathematics_ (1903) gives rise to several interpretational challenges, especially concerning the theory of denoting concepts. Only relatively recently, for instance, has it been properly realised that Russell accepted denoting concepts that do not denote anything. Such empty denoting concepts are sometimes thought to enable Russell, whether he was aware of it or not, to avoid commitment to some of the problematic non-existent entities he seems to accept, such as the Homeric gods and chimeras. In this paper, (...) I argue first that the theory of denoting concepts in _Principles of __Mathematics_ has been generally misunderstood. According to the interpretation I defend, if a denoting concept shifts what a proposition is about, then the aggregate of the denoted terms will also be a constituent of the proposition. I then show that Russell therefore could not have avoided commitment to the Homeric gods and chimeras by appealing to empty denoting concepts. Finally, I develop what I think is the best understanding of the ontology of _Principles of __Mathematics_ by interpreting some difficult passages. (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)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in (...) publicly available databases. Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

Following Gadamer, Dilthey’s philosophy of the social world is beset by an implicit subjectivism which puts into question the very possibility of shared understanding. This subjectivism is taken to lie behind Dilthey’s emphasis on empathy (or “re-experiencing”), which becomes a condition of our understanding of others and knowledge of the socio-historical world generally. I argue that Dilthey does not give primacy to subjectivity, particularly in his later works. Dilthey’s own notion of sociality, accounted for in terms of the common realm (...) of “objective spirit,” is akin to Gadamer’s own anti-subjectivist account of the human sciences and understanding. Through objective spirit, Dilthey shows that understanding cannot be conceived in terms of an aggregation of individual mental acts but is instead an irreducibly social accomplishment. (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)

In previous works, an ontology of properties for quantum mechanics has been proposed, according to which quantum systems are bundles of properties with no principle of individuality. The aim of the present article is to show that, since quasi-set theory is particularly suited for dealing with aggregates of items that do not belong to the traditional category of individual, it supplies an adequate meta-language to speak of the proposed ontology of properties and its structure.

Michael Jubien’s Ontology, Modality, and the Fallacy of Reference is an interesting and lively discussion of those three topics. In ontology, Jubien defends, to a first approximation, a Quinean conception: a world of objects that may be arbitrarily sliced or summed. Slicing yields temporal parts; summing yields aggregates, or fusions. Jubien is very unQuinean in his explicit Platonism regarding properties and propositions, but concerns about abstracta are peripheral to much of the argumentation in the book.1 His version of (...) the doctrine that arbitrary mereological sums exist is nonstandard in that he views it as a convention (albeit a useful one) that we treat sums of objects as themselves being objects. Indeed, he views the concept of objecthood itself as being conventional. The world consists fundamentally of stuff, which we divide into things in any way that suits our purposes. In modality, Jubien’s views are to a first approximation Chisholmian: he holds the doctrine of mereological essentialism, according to which anything.. (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)

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data (...) on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)

This comment discusses Kaidesoja and raises the issue whether his analysis justifies stronger conclusions than he presents in the book. My comments focus on four issues. First, I argue that his naturalistic reconstruction of critical realist transcendental arguments shows that transcendental arguments should be treated as a rare curiosity rather than a general argumentative strategy. Second, I suggest that Kaidesoja’s analysis does not really justify his optimism about the usefulness of causal powers ontology in the social sciences. Third, I (...) raise some doubts about the heuristic value of Mario Bunge’s social ontology that Kaidesoja presents as a replacement for critical realist ontology. Finally, I propose an alternative way to analyze failures of aggregativity that might better serve Kaidesoja’s purposes than the Wimsattian scheme he employs in the book. (shrink)

ABSTRACT This paper reconstructs William of Ockham's (c. 1287–1347) account of the ontology of social groups. Across his writings, Ockham mentions kingdoms, religious orders, crowds, people, armies, and corporations. Using the political community as a case-study against the background of Ockham’s metaphysics of parts and wholes, it is argued that at least some social groups are identical to a plurality of many human beings who have decided to order themselves with respect to another in some particular way. In this (...) regard, a social group is a structured aggregate that is nothing over and above its existing and ordered parts, and, at least in the case of the political community, is like an artefact inasmuch as it is partly dependent on the volitional acts of its members to exist at all. (shrink)

It has long been acknowledged that one of the most original aspects of Ockham’s account of knowledge is his contention that bodies of scientific knowledge are aggregates but without much explanation as to why he holds this view. In this chapter, I argue that a plausible philosophical motivation lies in the inner structure of his mental ontology, namely, in the intellect’s habits, acts, and their objects, which are the true and necessary principles and conclusions of demonstrations. Ockham upholds what (...) I call a “Principle of Object-Act-Habit-Specification,” according to which kinds of habits and their acts are determined by the objects they grasp. This principle entails that if a body of scientific knowledge contains two or more sentences, it can only have aggregate unity. Furthermore, I look at the logical and determinate orders that gather together the sentences of various aggregate bodies of scientific knowledge. (shrink)

The misconception that the application of statistical methods makes psychology a science is examined. Criticisms of statistical methods involving issues related to the generalization of aggregate-level findings to individuals, the impoverished language of numbers, the application of questions to methods, and the logic of statistical hypothesis testing are reviewed. It is not suggested, however, that statistical methods be abandoned. Instead, it is suggested that shortcomings of statistical methods indicate the importance of making ontological considerations a primary concern. Methodological considerations in (...) the absence of an understanding of the truth or ontological status of what is being studied will inevitably undermine psychologists’ efforts at understanding what it is to be human. Whereas the use of statistical methods in psychological research does not make the discipline a science, the truthful affiliation of methodology with ontology may. (shrink)