This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

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

Conflict over who belongs in women-only spaces is now part of mainstream political debate. Some think women-only spaces should exclude on the basis of sex, and others think they should exclude on the basis of a person’s self-determined gender identity. Many who take the latter view appear to believe that the only reason for taking the former view could be antipathy towards men who identify as women. In this paper, we’ll revisit the second-wave feminist literature on separatism, in order to (...) uncover the reasons for women-only spaces as feminists originally conceived them. Once these reasons are understood, those participating in debates over women-only spaces will be in a better position to adjudicate on whether shifting from sex to gender identity puts any significant interests at stake. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...) Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

Despite the end of the Cold War and the ascendancy of liberal democracy celebrated by Francis Fukuyama as “the end of history”, a growing number of scholars and political activists point to its inherent shortcomings. However, they have tended to dismiss it on the basis of one or two of its salient weaknesses. While this is a justifiable way to proceed, it denies the searching reader an opportunity to see the broad basis for the growing rejection of liberal democracy among (...) African political theorists. Consequently, in this article, I argue that from an African perspective, the almost hegemonic status of liberal democracy can be challenged on at least five grounds, namely, logical inconsistency, impracticability due to the largely communalistic outlook of many africans, inconsistency between affirmation and action, violation of the right to ethnic identity, and the moral imperative to assert the right to cultural emancipation. -/- I conclude by calling upon African and Africanist political theorists to utilise indigenous African political thought, coupled with emancipatory aspects of political thought from other parts of the world, to design practicable models of democracy for contemporary African states. I further conclude that in order to promote genuine inter-cultural dialogue on democratisation, people from Western cultures ought to acknowledge the equality of all cultures, and to recognise that systems of governance are part and parcel of those cultures. (shrink)

In The Philosophy of Logical Atomism Russell held the view that facts in the world are formally structured complexes, the structure of which matches the logical structure of correspondent propositions. Russell also seems to have denied that there are facts of identity and of diversity. This paper argues that Identity and Diversity can be understood as purely formal structures in Russellian facts. It considers Russell’s possible reasons for denying the existence of facts of identity and diversity and shows how problematic (...) these reasons are. In particular, I argue that identity statements are not tautologies, and their denial does not result into a contradiction. An important consequence of this thesis is that Metaphysics and Logic are not as tied up as Russell took them to be, but nevertheless these are good news for the old formal program for Metaphysics that lies at the very heart of what he called philosophical logic. (shrink)

Eleven top Deleuze scholars reclaim Deleuzian philosophy as moral philosophy Ethics plays a crucial, if subtle, role in Gilles Deleuze's philosophical project. Michel Foucault claimed that Anti-Oedipus was `a book of ethics, the first book of ethics to be written in France in quite a long time'. But what is the nature of the immanent ethics that is developed in Deleuze's thought? How does it differ from previous conceptions of ethics? And what paths does it open for future thought, given (...) the ethical challenges facing humanity in so many domains? Each of the eleven essays in this collection explores the ethical dimension of Deleuze's thought along a new and singular trajectory, and in so doing, attempts to reclaim his philosophy as an ethical philosophy. (shrink)

In this paper I consider the possibility of a kind of a priori cognition that serves the purposes of metaphysics, given that metaphysics involves the search for modal knowledge. Necessary or, better, modal knowledge is a priori; so metaphysical knowledge is likewise a priori. Here I argue that intuition is the route to modal knowledge in metaphysics, and I insist that conceivability or knowledge of conceptual truths does not lead towards the modal realm of metaphysics.

It was an empirical discovery that Phosphorus is Hesperus. According to Kripke, this was also the discovery of a necessary fact. Now, given Kripke’s theory of direct reference one could wonder what kind of discovery this is. For we already knew Phosphorus/Hesperus, and we also knew that any entity is, necessarily, identical to itself. So what is it that was discovered? I want to show that there is more to this widely known case than what usual readings, and critics, reveal; (...) and I want to show this under the Kripkean pattern that what was discovered is the plain fact of identity that Phosphorus is, and necessarily is, Hesperus. Moreover, I will show how both Kripkean theses, the necessity of identity and the direct theory of reference, should not be kept apart to understand the kind of discovery this is. In particular, understanding the kind of discovery we made will help us see how intuition is displayed in metaphysics, and how metaphysical impossibilities, and metaphysical modality in general, can be discerned by reason and separated from other modalities. The study of this discovery will help us see, in a line, how identity belongs to the inner and most profound structure of reality and to the most profound structure of cognition and language. (shrink)

I argue that the fundamental dogma that all necessary relations are internal is ungrounded. To motivate my argument, I analyse Moore’s classic ideas on internal relations and take them as an illustration of the common form of reasoning that can mislead us to conclude that all necessary relations are internal. That reasoning illicitly smuggles the idea that necessary properties and relations reflect on identity—in the sense that the loss of a necessary property/relation is a loss of identity—into the separate idea (...) that the loss of a necessary property/relation is a loss of essence. Essence, however, is not identity. So the way seems to be open for the existence of necessary properties/relations which do not belong to the essence of entities; that is, the existence of necessary but external relations. I then offer some examples of such relations. (shrink)

The late Kenyan Prof. H. Odera Oruka (1944-1995), from his base in the Department of Philosophy and Religious Studies at the University of Nairobi, contributed significantly to the growth of contemporary African philosophy, and helped locate African philosophy within the global philosophical discourse. His work in areas such as normative and applied ethics, political philosophy, epistemology, and, most notably, philosophic sagacity, continues to play a pivotal role in the current discourse on African philosophy. Prof. Oruka was also one of the (...) founders of Thought and Practice: A Journal of the Philosophical Association of Kenya. -/- The chapters in this volume examine various aspects of Oruka’s prolific contribution to philosophy in general, and to African philosophy in particular. Earlier versions of the chapters were presented at the three-day Odera Oruka International Symposium held from 19th to 21st November 2013, organised by the Department of Philosophy and Religious Studies at the University of Nairobi in collaboration with the Goethe Institute. (shrink)

Tropes, as distinguished from other possible kinds of entities such as universals, states of affairs, events and bare particulars, are best-suited to play the role of causal relata.

Abstract: Retama raetam (RR) is a traditional medicinal plant belongs to fabaceae family which grows in North Africa and East Mediterranean region. Locally, RR is used in several diseases including diabetes mellitus and hypertension. Thus, this study aims to investigate certain behavioral and central effects of methanolic extract of RR seeds in experimental animals (male Albino adult mice of 20 – 35 gm). Three exploratory behavioral models are used in this study, open field, elevated plus maze and light-dark box models, (...) in addition, picrotoxin induced seizure model in mice. In elevated plus-maze test of anxiety, a dose of 25 mg/kg of RR induced a significant increase in number of open arms entries and time spent on open arms of the maze compared to the control. In light-dark model, time spent on light area and number of light-dark transitions are significantly increased after treatment with 25 mg/kg RR extract of seeds. Open field model also revealed a significant increase in general motor activity of the mouse after 25 mg/kg of RR. On the other hand, a dose of 50 mg/kg of RR significantly induced a profound central and peripheral analgesic responses. In summary, this study concludes that RR seeds have a profound anxiolytic-like effect and analgesic response with delay in latency time of seizure induced by picrotoxin in mice. (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)

This article is a reply to Karori Mbugua’s article titled “The Problem of Hell Revisited: Towards a Gentler Theology of Hell” (Thought and Practice: A Journal of the Philosophical Association of Kenya, New Series, Vol.3 No.2, December 2011, pp.93-103). The present article does not in any way seek to argue for or against the existence of eternal damnation. Instead, it advances the view that while Mbugua raises important philosophical issues around the question of eternal damnation, those questions deserve a more (...) incisive treatment than Mbugua accorded them. The article further argues that as with all other matters touching on the way things are rather than the way they ought to be, the answer to the question as to whether or not eternal damnation exists cannot be determined by our opinions - its existence or nonexistence is an objective fact. Consequently, philosophers cannot revise the fact to their liking; what they can do is to accept or reject the doctrine of eternal damnation altogether on rational grounds, but with no assurance that the objective fact is on their chosen side. (shrink)

These three volumes, entitled Essays On Values, bring together fortyone recent articles by researchers at the Nova Institute of Philosophy (IFILNOVA). They are a small sample of everything that, in the last four years, the Institute’s researchers have published, in English, in indexed journals and collections of essays with peer review. As a whole, they reflect very well the research work that is done at IFILNOVA. Section I. of Volume 1 gathers six articles that deal directly with the question “what (...) are values?”, the question that guides all the work of the institute’s different laboratories and research groups. The first article, by Susana Cadilha and Vítor Guerreiro, results from work developed in the Laboratory of Ethics and Political Philosophy (EPLab); the second, by João Constâncio, from the Lisbon Nietzsche Group; the third, by Alexandra Dias Fortes, from the Lisbon Wittgenstein Group; the third and fifth, by Nuno Fonseca, and Maria Filomena Molder, from the Aesthetics and Philosophy of Art Group of the Laboratory of Culture and Value (CultureLab); the last, by Erich H. Rast, from the Philosophy of Language and Argumentation Theory Group and the Lisbon Mind, Cognition & Knowledge Group of the Laboratory of Argumentation, Cognition, and Language (ArgLab). Section II. brings together three articles by members of the Lisbon Nietzsche Group. Since 2010, the Lisbon Nietzsche Group has completed several funded projects, and has established itself as a leading international research group on Nietzsche’s thought. The three articles demonstrate the crucial importance of the question of values in Nietzsche’s work, always thought from the perspective of the possibility of a “transvaluation of all values”. Maria João Mayer Branco’s article focuses on the value of introspection, and how Nietzsche anticipates Wittgenstein’s “expressivist” view of the “the Peculiar Grammar of the Word ‘I’” and the impossibility of private languages. Marta Faustino’s article considers the theme of affirmation and the value of life through the interpretation of Nietzsche’s reflection on truthfulness, intellectual honesty and courage in the light of Michel Foucault’s work on parrhesia. Pietro Gori’s article studies how Nietzsche creates a new anthropological ideal based on his enquiry into the values of the “good European”. The area of Wittgenstein studies has had a strong influence on the institute since the time when it was a philosophy of language institute. The Wittgensteinian distinction between facts and values was decisive in defining the question of values as the central issue of IFILNOVA’s research project, replacing the focus on philosophy of language. More recently, the focus of research at the Lisbon Wittgenstein Group has been on epistemic values, in particular in their connection with the question of religious belief. In Section III., Nuno Venturinha’s article examines, in the light of an epistemological standpoint, the way Wittgenstein thinks about the possibility of translation. Robert Vinten’s article argues that Wittgenstein’s thought contains elements for a critique of the concept of justice and of the liberal political visions of both Richard Rorty and Chantal Mouffe, despite the fact that both have drawn inspiration from Wittgenstein. Benedetta Zavatta’s article questions the value of mythology by thinking of it as a disease of language – not only in Wittgenstein, but also in a whole philosophical tradition that preceded him. The existence of a research group in ancient philosophy is a recent but very promising development in the life of IFILNOVA. Section IV. includes two articles by members of the group. Paulo Alexandre Lima’s article considers the critique of misology and the value of discourse in Plato’s Phaedo. Hélder Telo’s article examines the pedagogical and protreptic value of imperfection in Plato’s work. (shrink)

I want to make sense of the view that singular causation involves a metaphysical necessary connection. By this I understand, where A and B are particulars, that ifA causes B then in every possible world in which A (or an A-indiscernible) or B (or a B-indiscernible) occurs, A (or an Aindiscernible) and B (or a B-indiscernible) occur. In the singularist approach that I will favour causal facts do not supervene on laws, causal relata are best understood as tropes, causation is (...) founded on the nature of its terms, and the necessity thus involved does not entail essentialism, determinism, and other usual problems. (shrink)

This paper is a historical, legal and philosophical analysis of the concept of human dignity in German and Kenyan constitutional law. We base our analysis on decisions of the Federal Constitutional Court of Germany, in particular its take on life imprisonment and its 2006 decision concerning the shooting of hijacked airplanes, and on a close reading of the Constitution of Kenya. We also present a dialogue between us in which we offer some critical remarks on the concept of human dignity (...) in the two constitutions, each one of us from his own philosophical perspective. (shrink)

Este artículo defiende que toda acción es un suceso que entraña, responsabilidad agente. Toda acción es el suceso que es el "hacer" de alguien. La responsabilidad del agente que define una acción es el tipo que justifica el premio-castigo. Esto implica que la acción es, en todos los casos, revocable y socialmente sancionada, igual que lo es la responsabilidad que la define. Más aún, si la identidad personal se ha de comprender dentro del reino de la acción, las teorías de (...) corte narrativo, más que las aproximaciones mentalistas, se encuentran mucho mejor posicionadas para llevar a cabo esta labor de comprensión.Este artículo defiende que toda acción es un suceso que entraña, responsabilidad agente. Toda acción es el suceso que es el "hacer" de alguien. La responsabilidad del agente que define una acción es el tipo que justifica el premio-castigo. Esto implica que la acción es, en todos los casos, revocable y socialmente sancionada, igual que lo es la responsabilidad que la define. Más aún, si la identidad personal se ha de comprender dentro del reino de la acción, las teorías de corte narrativo, más que las aproximaciones mentalistas, se encuentran mucho mejor posicionadas para llevar a cabo esta labor de comprensión.This paper argues that an action is an event that essentially conveysagent responsibility. Any action is the event that is someone’s doing. Andagent responsibility, which defines action, is the kind of responsibility that justifiesreward and punishment. This means that action is, in all cases, defeasileand socially santioned, such as it is the type of responsibility that defines action.Moreover, if pesonal identity is to be understood within the frame ofaction, narrativist kind of theories, rather than mentalist approaches, are in amuch better position to do the job. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

Batı’da teorik felsefe; Analitik Felsefe (AF), Kıta Felsefesi (KF) ve Felsefe Tarihi (FT) olmak üzere üçe ayrılır. Fakat üçünde de işler yolunda değildir. AF, felsefenin bir bilim olabileceği iddiasından kuşku duyduğu için gerçek dünyayla ilgilenmiyorken başından beri uygun bir teorik yöntem izlemeyen Kıta Felsefesinin uygulanışı, belirli politik ve etik yargılara hizmet edecek şekilde özelleştirilmiştir. FT çalışmalarının gidişatı ise eldeki eserin nesnel değerinden daha çok ilgili filozofun ait olduğu ulus veya kültüre göre bölgesel bir temelde gelişmiştir. Felsefede ilerleme sağlanacaksa bu ancak (...) bahsi geçen tuzaklardan kaçınılarak gerçekleşebilir. (shrink)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review the (...) paper and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

Primitives are both important and unavoidable, and which set of primitives we endorse will greatly shape our theories and how those theories provide solutions to the problems that we take to be important. After introducing the notion of a primitive posit, I discuss the different kinds of primitives that we might posit. Following Cowling (2013), I distinguish between ontological and ideological primitives, and, following Benovsky (2013) between functional and content views of primitives. I then propose that these two distinctions cut (...) across each other leading to four types of primitive posits. I then argue that theoretical virtues should be taken to be meta-theoretical ideological primitives. I close with some reflections on the global nature of comparing sets of primitives. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

Twentieth century philosophers introduced the distinction between “objective rightness” and “subjective rightness” to achieve two primary goals. The first goal is to reduce the paradoxical tension between our judgments of (i) what is best for an agent to do in light of the actual circumstances in which she acts and (ii) what is wisest for her to do in light of her mistaken or uncertain beliefs about her circumstances. The second goal is to provide moral guidance to an agent who (...) may be uncertain about the circumstances in which she acts, and hence is unable to use her standard moral principle directly in deciding what to do. This paper distinguishes two important senses of “moral guidance”; proposes criteria of adequacy for accounts of subjective rightness; canvasses existing definitions for “subjective rightness”; finds them all deficient; and proposes a new and more successful account. It argues that each comprehensive moral theory must include multiple principles of subjective rightness to address the epistemic situations of the full range of moral decision-makers, and shows that accounts of subjective rightness formulated in terms of what it would reasonable for the agent to believe cannot provide that guidance. -/- . (shrink)

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

Much problem solving and learning research in math and science has focused on formal representations. Recently researchers have documented the use of unschooled strategies for solving daily problems -- informal strategies which can be as effective, and sometimes as sophisticated, as school-taught formalisms. Our research focuses on how formal and informal strategies interact in the process of doing and learning mathematics. We found that combining informal and formal strategies is more effective than single strategies. We provide a theoretical account of (...) this multiple strategy effect and have begun to formulate this theory in an ACT-R computer model. We show why students may reach common impasses in the use of written algebra, and how subsequent or concurrent use of informal strategies leads to better problem-solving performance. Formal strategies facilitate computation because of their abstract and syntactic nature; however, abstraction can lead to nonsensical interpretations and conceptual errors. Reapplying the formal strategy will not repair such errors; switching to an informal one may. We explain the multiple strategy effect as a complementary relationship between the computational efficiency of formal strategies and the sense-making function of informal strategies. (shrink)

ABSTRACT The idea that two words can be instances of the same word is a central intuition in our conception of language. This fact underlies many of the claims that we make about how we communicate, and how we understand each other. Given this, irrespective of what we think words are, it is common to think that any putative ontology of words, must be able to explain this feature of language. That is, we need to provide criteria of identity for (...) word-types which allow us to individuate words such that it can be the case that two particular word-instances are instances of the same word-type. One solution, recently further developed by Irmak, holds that words are individuated by their history. In this paper, I argue that this view either fails to account for our intuitions about word identity, or is too vague to be a plausible answer to the problem of word individuation. (shrink)

It has been a common assumption that words are substances that instantiate or have properties. In this paper, I question the assumption that our ontology of words requires posting substances by outlining a bundle theory of words, wherein words are bundles of various sorts of properties (such as semantic, phonetic, orthographic, and grammatical properties). I argue that this view can better account for certain phenomena than substance theories, is ontologically more parsimonious, and coheres with claims in linguistics.

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

The aim of this paper is to provide a conceptual framework that will help in understanding and evaluating, along social and ethical lines, the issue of killing day-old male chicks and two alternative directions of responsible innovations to solve this issue. The following research questions are addressed: Why is the killing of day-old chicks morally problematic? Are the proposed alternatives morally sound? To what extent do the alternatives lead to responsible innovation? The conceptual framework demonstrates clearly that there is a (...) moral “lock-in”, and why the killing of day-old chicks is indeed an issue. Furthermore, it is shown that both alternative directions address some important objections with regard to the killing of day-old chicks, but that they also raise new dilemmas. It also becomes clear that the framework enables and secures anticipation, reflection, deliberation with and responsiveness to stakeholders, the four dimensions of responsible innovation, in a structured way. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (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)

Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...) andere im Bereich der Biologie und Biomedizin von der OBO Foundry. Es soll aufgezeigt werden, wie die Verpflichtung zu speziellen Kriterien der Ontologieentwicklung die Nützlichkeit und Effektivität der Ontologien positiv beeinflusst, indem die Pflege der terminologischen Systeme und ihre Interoperabilität vereinfacht werden. -/- Ergebnisse: SNOMED CT und die OBO Foundry unterscheiden sich grundlegend in ihren Ansätzen und Zielen. Unabhängig davon kann jedoch ein allgemeiner Trend zur strengeren Formalisierung und Fokussierung auf Interoperabilität zwischen unterschiedlichen Domänen und ihren Repräsentationen beobachtet werden. (shrink)

The Kurdish movement has revitalised the idea of democracy. Under the most difficult of circumstances – squeezed between ISIS on one side and the Turkish armed forces on the other – a radical form of democracy has been implemented that has inspired many both inside and outside the region. Introducing the special issue “Rethinking Democracy in Kurdistan”, this article explores the ingenious challenge to the nation-state system posed by this new democratic theory and practice, focusing on the prison writings of (...) Abdullah Öcalan. These remarkable texts are read as proposing a new philosophy of world-history which decisively breaks with Marxism, displaces the central place of Europe, and drastically extends the point in time at which philosophies of history typically begin. (shrink)

While there seems to be much evidence that perceptual states can occur without being conscious, some theorists recently express scepticism about unconscious perception. We explore here two kinds of such scepticism: Megan Peters and Hakwan Lau's experimental work regarding the well-known problem of the criterion -- which seems to show that many purported instances of unconscious perception go unreported but are weakly conscious -- and Ian Phillips' theoretical consideration, which he calls the 'problem of attribution' -- the worry that many (...) purported examples of unconscious perception are not perceptual, but rather merely informational and subpersonal. We argue that these concerns do not undermine the evidence for unconscious perception and that this sceptical approach results in a dilemma for the sceptic, who must either deny that there is unconscious mentality generally or explain why perceptual states are unique in the mind such that they cannot occur unconsciously. Both options, we argue, are problematic. (shrink)

For centuries it has been a mainstay of European and American moral thought that keeping promises—and the allied activity of upholding contracts—is one of the most important requirements of morality. On some historically powerful views the obligation to uphold promises or contracts not only regulates private relationships, but also provides the moral foundation for our duty to support and obey legitimate governments. Some theorists believe that the concept of keeping promises has gradually moved to center stage in European moral thought. (...) They see this movement as part of an historical shift from a moral conception in which an individual’s duties are mainly externally imposed and unalterable, to a conception in which duties are largely chosen by the individual. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

Atualmente, biotecnologias são empregadas na forma de protocolos a fim de sincronizar o crescimento folicular e a ovulação, bem como permitir que vacas atuem como receptoras de embriões visando melhorar o potencial genético do rebanho. O objetivo desse estudo foi avaliar o efeito da utilização de implantes intravaginais de progesterona de 1º, 2º e 3º uso no protocolo de transferência de embriões em tempo fixo (TETF) sobre a taxa de prenhez em receptoras girolandas. O experimento ocorreu em uma fazenda localizada (...) no município de São Sebastião do Maranhão (MG). Foram utilizadas 74 vacas submetidas aos seguintes protocolos: No dia 0 (D0) administrou-se 2 ml de 17β-Estradiol e progesterona e foi colocado o implante intravaginal de progesterona. Estes implantes foram colocados de forma aleatória, sendo de 1° uso (grupo 1; n=15), 2° (grupo 2; n=24) ou 3° (grupo 3; n=35).No D8, os implantes foram retirados e administrou-se 2 ml PGF2α; 1,5 ml de eCG e 1 ml de 17β-Estradiol e progesterona. A inovulação dos embriões in vitroo correu no D (16) para todas as vacas que apresentaram um corpo lúteo. As variáveis qualitativas (prenhe ou não prenhe) foram comparadas em tabelas de contingência e analisadas pelo teste de qui-quadrado a 5% de probabilidade. Neste estudo não houve diferença estatística entre os grupos protocolados em relação ao aproveitamento como receptoras: 1º uso (53,3%), 2º (79,2%) e 3º (68,65). Ademais, observou-se uma taxa de prenhez entre os grupos de 37,5% para o 1º uso, 42,1% para o 2º e 33,3% para o 3º (P>0,05). Dentre as vantagens ao reaproveitamento dos implantes multiusos destaca-se a redução dos custos dos protocolos hormonais, já que a progesterona é o hormônio mais oneroso, desta forma, a maximização do uso reduz o valor final do protocolo sem prejuízos a taxa de prenhez. (shrink)