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

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

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

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

Integrated information theory (IIT) is a candidate theory of consciousness that highlights the role of complex interactions between parts of a system as the basis of consciousness – and, due to its general information-theoretic formulation, is capable of making statements about consciousness in neural and non-neural systems alike. Here, we argue that a system radically different to a human brain, host to complex physiological and functional structures capable of integrating information, can be found in the meristems and vascular system of (...) higher plants. Following a pragmatic and ontologically innocent approach, neither taking for granted that plants are conscious nor dismissing the possibility that they are, we argue that the time is ripe to apply analysis tools inspired by IIT to plants, taking advantage of recent developments in both plant imaging and information theory. We introduce and discuss the relevant literature, and pro information and integration in plant behaviour, assessing the plausibility of plant sentience. If successful, these experiments could position plants as the next frontier in consciousness science, and urge us to rethink our perspectives on consciousness, how to measure it, and its prevalence amongst living beings. (shrink)

This essay’s main objective is to develop a theoretical, ontological basis for critical, social justice-oriented science education. Using Deleuze and Guattari’s notion of assemblages, rhizomes, and arborescent structures, this article challenges authoritarian institutional practices, as well as the subject of these practices, and offers a way for critical-social justice-oriented science educators and students to connect with sociopolitical contexts. Through diagramming institutional and community relationships using DG’s theory of assemblages, we envision new ontological spaces that bridge social and material entities. A (...) conceptualization of science education through DG’s philosophy of rhizomes and assemblages allows educators to merge critical, post-foundational perspectives with questions of ontology: not just what exists, but what could exist in terms of human social organizations, inorganic matter, microorganisms, and plant/animal populations. (shrink)

In his accounts of plant and animal generation Pierre Gassendi offers a mechanist story of how organisms create offspring to whom they pass on their traits. Development of the new organism is directed by a material “soul” or animula bearing ontogenetic information. Where reproduction is sexual, two sets of material semina and corresponding animulae meet and jointly determine the division, differentiation, and development of matter in the new organism. The determination of inherited traits requires a means of combining or (...) choosing among each parent's contributions, and towards this end, Gassendi outlines the nature of competition and dominance among animulae. Unlike his fellow mechanists, Gassendi can extend his mechanism to his heredity account, because his proposed vehicle for ontogenetic transmission is material. That proposal in turn relies on his atomist hypothesis. The relative uniformity of atoms allows animulae to operate equivalently across different modes of generation, spontaneous or otherwise. Further, his molecular model of atomic structures allows a material means of storing ontogenetic information received from the souls of parent organisms. These accounts—flawed and sketchy—unsurprisingly fail to specify how hereditary information might be borne physically, and in any case do not meet Gassendi's own empiricist standards. Yet this generation theory with pretensions to a materialist mechanism establishes Gassendi's firm commitment to a unity of the sciences through an atomist ontology that underlies all physical phenomena, including the organic. (shrink)

Russian abstract: В данном сборнике статей раскрывается формирование структурно-онтологического представления о таком явлении, как городское пространство. Наряду с соответствующей концептуализацией, также представлено и объяснено определение городского сообщества. Обоснована логика классификации городских сообществ. А также проанализированы факторы, обуславливающие их устойчивость. -/- English abstract: This collection of articles reveals the formation of a structural-ontological concept of such a phenomenon as urban space. Along with relevant conceptualization, the definition of an urban community is also presented and explained. The logic of classification of urban (...) communities is substantiated. And also analyzed the factors that determine their stability. (shrink)

Russian Abstract: Данный документ является сборником «заметок на полях», раскрывающих состав и содержание метода структурно-онтологического анализа. Указанный метод разработан для системного описания предметной области изучаемых явлений. Он включает специальную процедуру по построению структурно-онтологических матриц и алгоритм их описания. Междисциплинарная направленность метода продемонстрирована на примере анализа процесса социализации личности. English Abstract: This document is a collection of `marginal notes` revealing the composition and content of the structural ontological analysis method. The specified method is developed for a systemic description of the subject (...) matter area of the studied phenomena. It includes a special procedure for constructing structural-ontological matrices and an algorithm for their description. The interdisciplinary focus of the method is demonstrated by the example of an analysis of the personality socialization process. (shrink)

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

Objective – is to formulate a methodological discourse regarding the place and role of the language interconnected with the process of socialization of a person and develop a systemic idea of the corresponding functional features. -/- Materials & Methods – this discourse is formulated on the basis of a systemic idea of the personality socialization, which, in turn, is realized using the structural-ontological method of studying the subject matter field in interdisciplinary researches. This method involves the construction of special visual-graphic (...) matrices that reflect the interaction of the primary process and the material of the studied system. -/- Results. The work with the structural-ontological matrix made it possible to analyze the functions of the language in the context of such significant factors of socialization as complex psychodynamics, civilization space and the function of reflection. At the same time, reflection is considered at the level of two plans – primary (reflection-bond) and secondary (reflection-splitting). This made it possible to deduce the idea of the role of language beyond the traditional framework of working with text and analyze the place of the language in the context of activities to establish a connection between individuals, which is realized in a specific cooperative situation (Shchedrovitsky). In particular, the look at language as a specific tool of civilizational rationing, the mechanism of which is provided through reflection-communication. Thus, the language is examined through the prism of its systemic influence on the morphology of the psyche. -/- Conclusions – a structural-ontological analysis of the place and role of language in the process of personality socialization has led us to construction of a hypothesis about the phenomenon of language discontentment, as a tendency to distance away ego-consciousness in the process of individuation from linguistic ontology. The arguments were also advanced in favor of the assumption regarding the peculiarities of the influence of language discontentment on cultural activities and the psychodynamic contribution of this phenomenon in the midlife crisis (Jung). (shrink)

The concept of expression grounds a large portion of Spinoza’s metaphysics, giving further depth to seemingly foundational concepts such as substance, causality, attribute, and essence. Spinoza adopts the term “expression” in crucial contexts such as the definition of attribute, the essential dependence of modes on substance, and the striving or effort of a finite conatus. In this essay, I seek to interpret expression as an instance of relational or structural ontology, escaping the reductionist tendencies that would see it as (...) a mere result or combination of “more fundamental” properties such as causation, inherence, and conception. My interpretation of expression as a descriptive structural lens enriches our understanding of Spinoza’s metaphysics of substance and modes as a primarily structural ontology, which can only be read appropriately if its relata are conceived as ontologically dependent on the structure. (shrink)

For a long time it was believed that it was impossible to be realist about quantum mechanics. It took quite a while for the researchers in the foundations of physics, beginning with John Stuart Bell [Bell 1987], to convince others that such an alleged impossibility had no foundation. Nowadays there are several quantum theories that can be interpreted realistically, among which Bohmian mechanics, the GRW theory, and the many-worlds theory. The debate, though, is far from being over: in what respect (...) should we be realist regarding these theories? Two diff erent proposals have been made: on the one hand, there are those who insist on a direct ontological interpretation of the wave function as representing physical bodies, and on the other hand there are those who claim that quantum mechanics is not really about the wave function. In this paper we will present and discuss one proposal of the latter kind that focuses on the notion of primitive ontology. (shrink)

In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best (...) confirmed theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure. (shrink)

Words form a fundamental basis for our understanding of linguistic practice. However, the precise ontology of words has eluded many philosophers and linguists. A persistent difficulty for most accounts of words is the type-token distinction [Bromberger, S. 1989. “Types and Tokens in Linguistics.” In Reflections on Chomsky, edited by A. George, 58–90. Basil Blackwell; Kaplan, D. 1990. “Words.” Aristotelian Society Supplementary Volume LXIV: 93–119]. In this paper, I present a novel account of words which differs from the atomistic and (...) platonistic conceptions of previous accounts which I argue fall prey to this problem. Specifically, I proffer a structuralist account of linguistic items, along the lines of structuralism in the philosophy of mathematics [Shapiro, S. 1997. Philosophy of Mathematics: Structure and Ontology. Oxford University Press], in which words are defined in part as positions in larger linguistic structures. I then follow Szabò [1999. “Expressions and Their Representations.” The Philosophical Quarterly 49 (195): 145–163] and Parsons [1990. “The Structuralist View of Mathematical Objects.” Synthese 84: 303–346] in further defining words as quasi-concrete objects according to a representation relation. This view aims for general correspondence with contemporary generative linguistic approaches to the study of language. (shrink)

Social groups—like teams, committees, gender groups, and racial groups—play a central role in our lives and in philosophical inquiry. Here I develop and motivate a structuralist ontology of social groups centered on social structures (i.e., networks of relations that are constitutively dependent on social factors). The view delivers a picture that encompasses a diverse range of social groups, while maintaining important metaphysical and normative distinctions between groups of different kinds. It also meets the constraint that not every arbitrary collection (...) of people is a social group. In addition, the framework provides resources for developing a broader structuralist view in social ontology. (shrink)

Whitehead’s cosmology centers on the self-creation of actual occasions that perish as they come to be, but somehow do combine to constitute societies that are persistent agents and/or patients. “Instance Ontology” developed by D.W. Mertz concerns unification of relata into facts of relatedness by specific intensions. These two conceptual systems are similar in that they both avoid the substance-property distinction: they differ in their understanding of how basic units combine to constitute complex unities. “Process Structural Realism” (PSR) draws from (...) both of these approaches in developing an account of how combinations of processes may produce ontologically significant coherences. When a group of processes achieves such closure that a set of states recurs continually, the effects of that coherence differ from what would occur in the absence of that closure. Such altered effectiveness is an attribute of the system as a whole, and would have consequences. This indicates that the network of processes, as a unit, has ontological significance. The closed network of processes, together with the conditions that prevail, constitute the form of definiteness of the coherence. That form continues to obtain as long as the coherence persists. Constituents contribute to, rather than share, that characteristic. Aspects of some recent research in systems biology, microeconomics, and social psychology illustrate the application of PSR. (shrink)

This essay explores the possibility of constructing a structural realist interpretation of spacetime theories that can resolve the ontological debate between substantivalists and relationists. Drawing on various structuralist approaches in the philosophy of mathematics, as well as on the theoretical complexities of general relativity, our investigation will reveal that a structuralist approach can be beneficial to the spacetime theorist as a means of deflating some of the ontological disputes regarding similarly structured spacetimes.

The agent-structure problem is a much discussed issue in the field of international relations. In his comprehensive analysis of this problem, Colin Wight deconstructs the accounts of structure and agency embedded within differing IR theories and, on the basis of this analysis, explores the implications of ontology - the metaphysical study of existence and reality. Wight argues that there are many gaps in IR theory that can only be understood by focusing on the ontological differences that construct (...) the theoretical landscape. By integrating the treatment of the agent-structure problem in IR theory with that in social theory, Wight makes a positive contribution to the problem as an issue of concern to the wider human sciences. At the most fundamental level politics is concerned with competing visions of how the world is and how it should be, thus politics is ontology. (shrink)

The phenomenon of rigid designation - in particular, de jure rigidity - is typically treated metaphysically. The picture is: reference is gained in a way that puts no constraints on what an object in other worlds, or counterfactual situations must be like, in order to be the referent of that term, other than 'being this thing'. This allows 'pure metaphysical' investigation into, and discovery of 'the nature' of the referent. It is argued that this presupposes a 'privileged' ontology, of (...) a sort that is far from obvious. An alternative picture of rigidity is sketched, terms have associated criteria of identity and criteria of application for counterfactual situations. A term is rigid when these coincide. Aside from being a better account of rigidity, it also undermines the picture of rigid terms allowing us to 'metaphysically' investigate the nature of the referent: matters of identity and essence for the referent are settled by these semantic constraints (though it can be done in a way that allows are a posteriori necessities). (shrink)

The number of positions identified with structural realism in philosophical debates about scientific knowledge has grown significantly in the past decade, particularly with respect to the metaphysical or ‘ontic’ approach (OSR). In recent years, several advocates of OSR have proposed a novel understanding of it in order to side-step a serious challenge faced by its original formulation, eliminative OSR. I examine the conceptual basis of the new, noneliminative view, and conclude that it too faces a serious challenge, resulting in a (...) dilemma for ontic structuralists regarding the ontological status of objects and properties, and the relative “ontological priority” of these entities with respect to the relations in which they stand. (shrink)

This paper studies European chemists’ shifting ontologies of materials by comparing the ways in which they classified materials. The focus is on plant materials, their different identities, and the changing ways chemists sorted out and ordered plant materials in the eighteenth and early nineteenth centuries. The main goals of the paper are to follow the development of plant materials from ordinary, everyday materials and commodities in the early eighteenth century to purified carbon compounds and organic substances familiar (...) only to experts in the 1830s, and to reconstruct chemists’ ways of classifying these objects in different practical and intellectual contexts.The study of changes in European chemists’ ways of classifying plant materials over more than a century brings to the foreground a trajectory of ontological shifts that is ‘punctuated’ in the 1750s, the 1790s, and the 1830s. Early eighteenth-century plant materials, which were commodities of the apothecary trade and other arts and crafts, were elevated epistemically as compound components or ‘proximate principles’ of plants in the 1750s, reduced to organic compounds in the 1790s, and replaced by carbon compounds in the 1830s. The last, third transformation of the epistemic constitution of materials and the mode of their classification was accompanied by a deep transformation of the material culture of plant chemistry. After the late 1830s, many of the eighteenth-century vegetable commodities disappeared from chemists’ agenda or were split into different substances individuated and identified in new ways. Coal tar products, and new organic artefacts containing chlorine or bromine, entered the chemical laboratory in the 1820s and became fused with the purified rest of the previous plant and animal substances. The material objects of the new culture of organic chemistry became detached from the materials applied in the extant arts and crafts. It was only in the late 1850s, with the rise of the synthetic dye industry, that a great number of these laboratory substances became involved in industrial production.Keywords: Commodities and scientific objects; Historical ontology; Classification; Plant chemistry; Organic chemistry. (shrink)

W.V. Quine, a champion of philosophical naturalism and pioneer of mathematical logic, was one of the most important philosophers of the 20th century. This volume provides a full picture of the development of Quine's views on structure and how it permeates and shapes his attitude to a range of philosophical questions.

'Structural realism' is a buzzword in the scientific realism debate. Various positions with diverse motivations fall under this label. A much advertised distinction is between epistemic and ontological forms of structuralism. This paper scrutinizes the alleged dichotomy between these two 'alternatives', and criticises the considerations that have been taken to motivate the ontic variety over the epistemic. I will argue that ontological structural realism is not called for within the traditional realism debate.

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.

Between 1934 and 1937 Maurice Blondel, the French Roman Catholic philosopher best known for his 1893 work, Action, published a trilogy of writings. Out of these writings came a theological ontology of tremendous force, creativity, and coherence. The purpose of the present dissertation is to reassess the viability of Blondel's ontology for contemporary theology. The retrieval begins with John Milbank's 1990 investigation of Blondel's early philosophy. While Milbank focuses on the strengths of Blondel, he also highlights some critical (...) weaknesses. The dissertation argues that Blondel later came to recognize and correct these weaknesses in his trilogy. ;La pensee, the first volume of the trilogy, discusses the nature and development of thought. Recognizing the ontological structure of thought leads Blondel to present his doctrine of the transnatural elan for assimilation to God. The transnatural desire for God is compared with Henri de Lubac's notion of naturae desiderium and then applied to the modern problem of the relationship between nature and supernature. ;The second installment of the trilogy, L'etre et les etres , explores the mysterious relation of Being and beings. Blondel situates the discussion within the language of creation, identifying Being as Creator and beings as creatures. The analogy of creation allows him to forge the proper relationship between Being and beings. After Blondel's death, two different schools of thought emerged on the mystery of being: Karl Rahner's Thomism and Jean-Luc Marion's new phenomenology. Each school is reviewed and critiqued from a Blondelian perspective. ;The trilogy concludes with a long-awaited revision of L'action . It begins by distinguishing the idea of action from action itself and establishing the ontological difference of action. Action is presented ontologically as enacted power, which is investigated in its individual, social, and metaphysical forms. Individual action is identified as making, practicing, and contemplating. Social action is studied next, with the conclusion that the social being of enacted power is determined by either a philosophy of peace or violence. Finally, divine action is evaluated with regards to the language of causality and absolute power. Blondel proposes instead to describe God's activity in terms of pure action. (shrink)

ABSTRACTLadyman and Ross’s account of the metaphysical component of ontic structural realism was associated with a unificationist view of the connection between fundamental physics and special sciences. The aim of the present article is to assess the sense of unification that is at issue in Ladyman and Ross’s definition of metaphysics. Given the ontic core of Ladyman and Ross’s version of structural realism, it should be assumed that the unifying endeavour is worthwhile only if the connective links that underpin unification (...) are metaphysically significant. Ladyman and Ross employed information-theoretic notions, e.g. ‘projectibility’, to account for the significance of real patterns, which underpin unification. I build upon McAllister’s engagements with the same topic, to argue that these notions fail to accomplish this objective. (shrink)

Could space consist entirely of extended regions, without any regions shaped like points, lines, or surfaces? Peter Forrest and Frank Arntzenius have independently raised a paradox of size for space like this, drawing on a construction of Cantor’s. I present a new version of this argument and explore possible lines of response.

This paper discusses attributively limited concrete objects such as disturbances (holes, folds, scratches etc), tropes, and attitudinal objects, which lack the sort of spatial location or part structures expected of them as concrete objects. The paper proposes an account in terms of (quasi-Fregean) abstraction, which has so far been applied only to abstract objects.

Do numbers, sets, and so forth, exist? What do mathematical statements mean? Are they literally true or false, or do they lack truth values altogether? Addressing questions that have attracted lively debate in recent years, Stewart Shapiro contends that standard realist and antirealist accounts of mathematics are both problematic. As Benacerraf first noted, we are confronted with the following powerful dilemma. The desired continuity between mathematical and, say, scientific language suggests realism, but realism in this context suggests seemingly intractable epistemic (...) problems. As a way out of this dilemma, Shapiro articulates a structuralist approach. On this view, the subject matter of arithmetic, for example, is not a fixed domain of numbers independent of each other, but rather is the natural number structure, the pattern common to any system of objects that has an initial object and successor relation satisfying the induction principle. Using this framework, realism in mathematics can be preserved without troublesome epistemic consequences. Shapiro concludes by showing how a structuralist approach can be applied to wider philosophical questions such as the nature of an "object" and the Quinean nature of ontological commitment. Clear, compelling, and tautly argued, Shapiro's work, noteworthy both in its attempt to develop a full-length structuralist approach to mathematics and to trace its emergence in the history of mathematics, will be of deep interest to both philosophers and mathematicians. (shrink)

The aim of this paper is to offer two novel solutions to two perennial problems of categorial ontology, namely, the problem of the categorial structure: how are the categories related to one another? And the problem of categorial completeness: how is the completeness of a proposed list of categories justified? First, I argue that a system of categories should have a structure such that there is a most basic category that is a bearer of all other categories (...) and that has what I shall call “combinatorial conditions”. To do so, I compare this approach to categorial structure with the approaches given by substantialist, mereological, factualist, and geo ontologies. Second, I argue that the problem of categorial completeness is only a problem for certain ontologies. In this connection, I explore views on categorial completeness proposed by substantialists and geo-ontologists. Lastly, I conclude that factualism does a better job of accounting for categorial structure and categorial completeness than other categorial ontologies. (shrink)

In recent years, a hierarchical view of reality has become extremely influential. In order to understand the world as a whole, on this view, we need to understand the nature of the fundamental constituents of the world. We also need to understand the relations that build the world up from these fundamental constituents. Building pluralism is the view that there are at least two equally fundamental relations that together build the world. It has been widely, though tacitly, assumed in a (...) variety of important metaphysical debates. However, my primary aim in this paper is to argue that this has been a mistake. I will show that serious problems concerning the relationship between building and fundamentality afflict pluralism and are likely fatal to it. I claim that, for better or worse, our best hope is building singularism, the view that there is a single most fundamental building relation. I conclude by examining the advantage that singularist accounts enjoy over their pluralist rivals. (shrink)

Realities are structured categorially, and comprehension of our internal and external conditions do not appear to be global or unitary. Rather, both human and non human animals function within their worlds and understand these by categorizing their experiences. Drawing upon many areas of life, the authors consider the ontological, mereological and multi-faceted structure of experience to explore how an understanding of categories can further knowledge.

Moving beyond both realist and anti-realist accounts of mathematics, Shapiro articulates a "structuralist" approach, arguing that the subject matter of a mathematical theory is not a fixed domain of numbers that exist independent of each other, but rather is the natural structure, the pattern common to any system of objects that has an initial object and successor relation satisfying the induction principle.

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

Phenomenologists call for the abandoning of all philosophical theorizing in favor of a descriptive study of the "things themselves" as they are given. On its face, such a study of appearances would appear to have little to contribute to ontology, traditionally understood as the science of being and its most fundamental categories. But phenomenologists have not hesitated to draw ontological conclusions from their phenomenological investigations. Phenomenology and its ontological pretensions have come under attack, however, from philosophers of a wide (...) variety of persuasions . ;The project of this dissertation is to re-examine the relationship of phenomenology, conceived as a philosophical method, to ontology. I proceed by undertaking systematic critical examinations of the attempts of thee central figures in the phenomenological tradition to arrive at categorial ontological results upon the basis of phenomenological investigations. At issue are Brentano's descriptive psychological studies of so-called mental phenomena in Psychology from an Empirical Standpoint , Husserl's static transcendental phenomenological study of the structures of pure consciousness in Ideas I, II, and III, and Sartre's phenomenological ontology of consciousness in Being and Nothingness. For each of these cases, I attempt to ascertain the precise way in which the application of phenomenological methods gives rise to specific ontological claims or "results". In none of these cases, I argue, does the thinker in question succeed in producing ontological assertions in a sufficiently phenomenological fashion. All, that is, depart to some extent from the phenomenological ideal of an ontology arrived at in accordance with an unprejudiced examination and description of "the things themselves". In the final chapter I ask whether the particular failures of these thinkers to have formulated ontological claims in a phenomenologically satisfactory manner implies the general failure of all phenomenological approaches to ontology. I argue that while principled reasons can be given why a truly phenomenological ontology must remain an unattainable ideal, it is an ideal that philosophers ought not abandon. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

We use the primitive ontology framework of Allori et al. to analyze the quantum information-theoretic interpretation of Bub and Pitowsky. There are interesting parallels between the two approaches, which differentiate them both from the more standard realist interpretations of quantum theory. Where they differ, however, is in terms of their commitments to an underlying ontology on which the manifest image of the world supervenes. Employing the primitive ontology framework in this way makes perspicuous the differences between the (...) quantum information-theoretic interpretation, and the various realist interpretations of quantum theory. It also allows us to identify a sense in which the commitments of quantum information-theoretic interpretation are underspecified. Several possible ways of completing the interpretation are presented, and it is suggested that the most likely strategy would leave the information-theoretic interpretation such that it would fail to qualify as a theory, according to the primitive ontology approach. (shrink)