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

Broadening access to both computational and educational resources is crit- ical to diffusing machine learning (ML) innovation. However, today, most ML resources and experts are siloed in a few countries and organizations. In this article, we describe our pedagogical approach to increasing access to applied ML through a massive open online course (MOOC) on Tiny Machine Learning (TinyML). We suggest that TinyML, applied ML on resource-constrained embedded devices, is an attractive means to widen access because TinyML leverages low-cost and globally (...) accessible hardware and encourages the development of complete, self-contained applications, from data collection to deployment. To this end, a collaboration between academia and industry produced a four part MOOC that provides application-oriented instruction on how to develop solutions using TinyML. The series is openly available on the edX MOOC platform, has no prerequisites beyond basic programming, and is designed for global learners from a variety of backgrounds. It introduces real-world applications, ML algorithms, data-set engineering, and the ethi- cal considerations of these technologies through hands-on programming and deployment of TinyML applications in both the cloud and on their own microcontrollers. To facili- tate continued learning, community building, and collaboration beyond the courses, we launched a standalone website, a forum, a chat, and an optional course-project com- petition. We also open-sourced the course materials, hoping they will inspire the next generation of ML practitioners and educators and further broaden access to cutting-edge ML technologies. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

In the Freedom Essay, Schelling provides four different accounts of the copula, two of which are largely implicit. In this paper, I focus on the first of these accounts, which I call the "mediated account." I argue that this explanation of the copula articulates a fundamental ontological structure in Schelling's philosophy. In the first half of the paper, I analyze the structural features of the account, drawing on Schelling's more extensive treatment in the Ages of the World. In the second (...) half of the paper, I argue that Schelling's fundamental distinction between that-which-exists and the ground of existence exhibits the same structure as the mediated account of the copula. This has implications for understanding the enigmatic relationship of these two principles to the Ungrund. I conclude by briefly suggesting other applications of this fundamental structure in Schelling's philosophy. (shrink)

In this essay, I give an analysis of the account of non-being in the Weltalter, focusing on the ways in which this account reflects Schelling’s new ontology of revelation. I begin by discussing the connection between non-being and the fundamental distinction between the principles in God. I then turn to the relationship of non-being to being in the Weltalter and show how a new meaning of being allows Schelling to distinguish non-being from nothing. The new meaning of being also makes (...) possible a distinction between essential non-being and de facto non-being; this distinction allows for the temporal sequence of revelation and the possibility of evil. I conclude by showing the implications of Schelling’s theory of non-being for his understanding of creation. (shrink)

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of the geospatial domain, (...) issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (shrink)

THIS IS A PRE-PUBLICATION VERSION OF THE PAPER. The New Testament speaks of our having faith rather than sight. This distinction is not made to distinguish faith from knowledge. Rather, it is to distinguish one kind of knowledge from another. We may know by trust in reliable authority; this knowledge is necessarily secondhand, but it is knowledge all the same. This, I argue, is the New Testament idea of faith. Another way of knowing is firsthand. Sight in the New Testament, (...) I argue, is a metonym for firsthand knowledge. In this article I consider the meaning of faith and sight in the relevant New Testament passages, with an extended exegesis of 2 Cor. 5:7 and Heb. 11:1. (shrink)

Each of the degenerating constitutions in Book VIII of Plato's Republic is the result of the disappearance of one of the four cardinal virtues. The failure of wisdom creates a timocracy; the failure of courage, an oligarchy; the failure of moderation, a democracy; the failure of justice, a tyranny. The degeneration shows that the disunited virtues are imperfect, though they have some power to stave off vice. Thus Book VIII implies a unity of the virtues thesis according to which perfect (...) virtues can only exist in a united state, but imperfect simulacra of virtue can exist in a disunited state. -/- Published 2011 in Apeiron: A Journal for Ancient Philosophy and Science. (Please note that the pagination in the uploaded document is not the same as the pagination in the published edition.). (shrink)

J. L. Mackie distinguished himself in twentieth-century philosophy by presenting an important objection to the traditional free will explanation for why God would allow evil: If evil is due to the free choice of creatures, why wouldn’t an omnipotent God simply create free creatures who would choose better? Alvin Plantinga, in turn, distinguished himself with his critique of Mackie. Plantinga’s main point is that Mackie made a mistake in assuming that it is within the power of omnipotence fully to create (...) just any possible world. However, Mackie made a second questionable assumption which Plantinga does not critique, and which I aim to clarify in this article. Mackie assumes that a God, as construed by classical theistic belief, who could create either of two people—one of whom would freely choose right and the other of whom would freely choose wrong—must create the one who would freely choose right. This assumption motivates Plantinga’s own account of trans-world depravity, which suggests that every free creature God might have created would have sinned had God created them. I consider Plantinga’s suggestion highly improbable. More importantly, under Mackie’s assumption, if there is at least one possible creature who would choose rightly, then there is no possibility of God ever allowing any other creature to sin, which would seem to be incompatible with their having any free will. -/- This version of the paper does have the same pagination as the published version. Permission has been granted from the Editor of Philosophia Christi to upload this contribution according to Philosophy Documentation Center terms of use. Learn more about the Journal by going to wwwepsociety. org/philchristi. (shrink)

Augustine and William James both argue that religious faith can be both practical and rational even in the absence of knowledge. Augustine argues that religious faith is trust and that trust is a normal, proper, and even necessary way of believing. Beginning with faith, we then work towards knowledge by means of philosophical contemplation. James’ “The Will to Believe” makes pragmatic arguments for the rationality of faith. Although we do not know (yet) whether God exists, faith is a choice between (...) the risk of believing something false and the risk of not believing something true, and in the absence of convincing evidence we may decide for ourselves which risk we prefer. We may be able to experience God in the future and thereby gain knowledge, yet this may be contingent on our willingness to believe. There are key differences, however. Augustine is a Christian with a neo-Platonic bent, James an empiricist defending the religion of your choice. These differences may be less significant than they first appear. After explaining Augustine and then James I draw out the major points of comparison and contrast and suggest a few reasons their insights might be at least partially synthesized. -/- This is the accepted version of the following article: Mark J. Boone, “Augustine and William James on the Rationality of Faith,” The Heythrop Journal (online edition December 2018), which has been published in final form at [See First URL]. This article may be used for non-commercial purposes in accordance with the Wiley Self-Archiving Policy [See Second URL]. (shrink)

This paper is the submitted version. The published version of the paper is available using the DOI number 10.1111/heyj.14007.

Scholars have devoted considerable attention to the discovery by Justin D’Arms and Daniel Jacobson of a distinction between the fittingness of an emotion and the propriety of the same. Meanwhile, Christian theology has long been attentive to the relevance of Christian theology to the emotions. Although it seems that never so far have the twain discussions met, they should meet. A fitting emotion accurately construes a situation. Christian theology tells us something about the importance—or the lack thereof—of emotional fit for (...) the emotions involved in love. It is a desideratum for the emotions that they are fitting. But other desiderata for the emotional life sometimes overrule the desideratum of fit. Moreover, emotions sometimes have an effect on their own fittingness. As Kierkegaard shows, love construes its object as better than he presently is, but it also makes the object better. We should cultivate a disposition to loving emotions that are occasionally unfitting yet help to bring about better fit. I explain these things and consider how someone might go about cultivating loving emotions which are sometimes unfitting yet also restorative of fit. (shrink)

Augustine′s conversion to Christianity in A.D. 386 is a pivotal moment not only in his own life, but in Christian and world history, for the theology of Augustine set the course of theological and cultural development in the western Christian church. But to what exactly was Augustine converted? Scholars have long debated whether he really converted to Christianity in 386, whether he was a Platonist, and, if he adhered to both Platonism and Christianity, which dominated his thought. The debate of (...) the last thirteen decades spans an immense body of literature in multiple languages. In this literature, four major views on Augustine′s conversion may be discerned. The first view is associated with Gaston Boissier and Adolph von Harnack, and was famously championed by Prosper Alfaric: that Augustine in 386 converted to neo-Platonism but not to Christianity. Second, there is the view recently promoted by Catherine Conybeare: that Augustine in 386 converted to Christianity and rejected neo-Platonism. Third, there is the view that he converted to Christianity and was also a neo-Platonist; the most famous adherents of this view are Robert J. O′Connell and Pierre Courcelle. Finally, there is the view recently promoted by Carol Harrison: that Augustine committed to Christianity in 386, yet did not utterly reject neo-Platonism; rather, he aimed to develop a Christian faith that was informed by neo-Platonic insight. In this article, I first explain and distinguish these four general views, and then I explain why I prefer the fourth view. -/- More Info: This is the pre-peer reviewed version of Boone, Mark, "The Role of Platonism in Augustine's 386 Conversion to Christianity," Religion Compass 9.5 (May 2015), 151-61. This article has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/rec3.12149/abstract. (shrink)

The general idea of strong foundationalism is that knowledge has a foundation in well warranted beliefs which do not derive any warrant from other beliefs and that all our other beliefs depend on these foundational ones for their warrant. Although inerrancy posits Scripture as a solid foundation for theology, the idea that the doctrine of biblical inerrancy involves a strong foundationalist epistemology is deeply problematic. In fact, inerrancy does not require any particular view of the structure of knowledge, and notable (...) sources on inerrancy tout it in ways inconsistent with most forms of strong foundationalism. (shrink)

While some scholars neglect the theological component to William James’s ethical views in “The Moral Philosopher and the Moral Life,” Michael Cantrell reads it as promoting a divine command theory (DCT) of the foundations of moral obligation. While Cantrell’s interpretation is to be commended for taking God seriously, he goes a little too far in the right direction. Although James’s view amounts to what could be called (and what Cantrell does call) a DCT because on it God’s demands are necessary (...) and sufficient for the highest obligations, this is a view with characteristics unusual for a DCT. It only holds for some obligations; on it moral obligation does not derive from God’s authority; it is not obvious that James believes the God required by it even exists; we do not know what God’s demands are; and, finally, since we do not know them, we cannot act on them. -/- (Lest there be any confusion, the titular phrase "taking God seriously, but not too seriously" describes William James' view of God and morality, not my own view.). (shrink)

At the heart of two recent theological traditions are hermeneutical principles which are not only consistent but are integrated in the hermeneutics of Augustine. According to the doctrine of biblical inerrancy as it has been recently articulated by Evangelicals, Scripture has an original meaning, and that meaning is not open to the possibility of error. According to some thinkers in postmodern theology, including Jean-Luc Marion, the meaning of Scripture transcends its original meaning. After examining postmodernism and inerrancy, I consider their (...) harmony in the writings of Augustine, who takes original meaning as a guide for understanding that biblical meaning which transcends it. An Augustinian hermeneutic consistent with inerrancy is thus an alternative to the more typical non-inerrantist postmodern theologies. (shrink)

Although current educational priorities tend to avoid strong moral positions, one of the world's most venerable yet persistently influential moral traditions not only lays out a number of major moral principles but also incorporates them into its pedagogy. Confucius teaches us about the importance of seeking knowledge, learning how to learn, applying ancient wisdom to contemporary situations, valuing virtue over material gain, following the Golden Rule, and living by our principles. He also has ways of assessing his own students' progress (...) in these matters. Confucius' pedagogy is an interesting model to consider and contrast with contemporary models. This chapter introduces these principles and assessments from the Analects and draws out some comparisons to and contrasts with two alternative theories in western moral thought, Augustine and John Dewey. -/- The accepted version of the paper is included here. Pagination does not match the published version. (shrink)

THIS IS A PRE-PUBLICATION VERSION OF THE PAPER and does not have the same pagination as the published version. -/- It is sometimes said that religious belief and empiricism are different or even incompatible ways of believing. However, William James and notable twentieth-century philosophers representing Buddhism, Hinduism, Islam, Judaism, and Christianity have argued that there is a high degree of compatibility between religious faith and empiricism. Their analyses suggest that there are three characteristics of empiricism—that an empiricist bases his beliefs (...) on past experience, that he seeks to test his beliefs in future experience, and that he holds his beliefs with a degree of tentativeness in case future experience should uncover evidence against them. The epistemological insights of these philosophers, along with Augustine, show that Christian theology is consistent with empiricism. Indeed, reliance on faith fails to distinguish Christianity from science, and Christian theology is even to a significant extent both verifiable and falsifiable. (shrink)

Two ancient sages show how even the most salacious fiction can be spiritually beneficial, for it shows our need for virtue and for grace. The first is the Roman philosopher Plutarch. Among ancient moral philosophers who were concerned with the effects of bad behavior in fiction, Plutarch distinguishes himself by showing how we can benefit morally from such stories. To do so we must approach them with a critical mind and from the right perspective; only then will we have the (...) discernment to separate the good from the bad, to learn to embrace and imitate virtue but flee from vice. The second is Augustine. A comparison of his writings with Plutarch’s produces not only a valuable theological extension of Plutarch’s thought, but also a valuable Christian perspective on the arts. According to Augustine, the pursuit of virtue only gets us so far, and on its own it cannot get us to a happy life. In particular, fiction such as this shows us that we need virtue; but it also shows us that we are not virtuous; so it also shows us that we need grace. -/- I first expound the concerns of ancient philosophers with the epic fiction of their own day. Then I consider Plutarch’s advice on how to benefit from bad behavior portrayed in fiction. Next, I apply his advice to the reimagined Battlestar Galactica. Finally, I show that Galactica illustrates Augustine’s argument in The City of God that happiness cannot be found in this life and how it thus points to our need for grace. -/- Note: The attached file does not have the same pagination as the published article. If you need to cite this article by page number, please consult Volume 2, Issue 1 of Imaginatio et Ratio. (shrink)

Original meaning generally and authorial intent specifically are relevant to textual meaning. The author is not dead—a reasonable common-sense view in the absence of extremely good contrary evidence. If anyone should offer such evidence, they will not be able to take credit for it—at least not for writing it down! Accordingly, humanities teachers should train students to understand original meaning and authorial intent. This is one reason the humanities will continue to be relevant to other fields of study. Finally, this (...) is one reason to support a critical thinking pedagogy. I also connect these considerations to some of the major textual and cultural issues in South Asia. THE VERSION AVAILABLE HERE IS THE ACCEPTED MANUSCRIPT, NOT THE SAME AS THE FINAL PUBLISHED VERSION. (shrink)

American Pragmatist philosopher William James and subcontinent Islamic philosopher Allama Iqbal both believe that religious experiences are an important class of those experiences with which empiricism is concerned. They both explain and defend religious belief on empirical grounds and argue that the ultimate empirical justification of a religious belief must come by looking at its fruits. This is no accident, for James influenced Iqbal on this very point. -/- However, they diverge in some matters. James defends the right to diverse (...) religious belief and eventually articulates his own account based on religious experience—an account which is intentionally philosophical and not reliant on any religious authority. Iqbal, however, reconsiders and defends Islam understood along largely traditional lines. -/- I compare and contrast James’ and Iqbal’s religious epistemologies in order to understand both of them better and, hopefully, enrich contemporary reflection on faith and reason through a better awareness of the past dialogue on the subject. -/- This is the accepted version of the following article: “William James and Allama Iqbal on Empirical Faith;” The Heythrop Journal 61.5 (2020): 775-787, which has been published in final form at the URL provided. This article may be used for non-commercial purposes in accordance with the Wiley Self-Archiving Policy [see second URL]. (shrink)

Alvin Plantinga’s Warrant and Proper Function gives two major definitions of warrant. One states that reliable cognitive faculties aimed at true belief and functioning properly in the right environment are necessary and sufficient for warrant; the other definition only states that they are necessary. The latter definition is the more important one. There are different kinds of knowledge, and justification is necessary for some beliefs to be warranted. Even a belief warranted by proper function can receive a higher degree of (...) warrant by justification. This implies that natural theology has a useful role within the contours of a Plantingian epistemology. (Please note that the pagination here does not match the pagination in the published edition.). (shrink)

NOW OPEN-ACCESS! In Reason, Authority, and the Healing of Desire in the Writings of Augustine, Mark Boone explains Augustine’s theology of desire in a cross-section of his writings. He shows that Augustine's writings consistently teach a Platonically informed, yet distinctively Christian, theology of desire.

The Enarrationes in Psalmos is the collection of Augustine’s commentaries and sermons on the Psalms. Although Augustine is often at his philosophical best here, bearing various resemblances to the Platonists and other philosophers, he also articulates a distinctively Christian view on what we should desire, on how desire has gone wrong, and on how it is healed. The renewal of desire takes place as a result of and through the unity of Christ and the church, which is the guiding theme (...) of the Enarrationes. Augustine’s Preaching and the Healing of Desire in the Enarrationes in Psalmos traces this theology of desire as it connects to Augustine’s Christology, his ecclesiology, his account of happiness and well-being, and his eschatology. The book closes with some suggestions on what the church can learn today from the Enarrationes in the areas of psychology and wellbeing, biblical exegesis, and homiletics. (shrink)

The success of the early music movement has long raised questions about performing historical works: Should musicians perform on period instruments and try to reconstruct the original style? If a historically “authentic” performance is impossible or undesirable, what should be the goal of the early music movement? I turn to Gadamer to answer these questions by constructing the outlines of a hermeneutics of early music performance. In the first half of the paper, I examine Gadamer’s critique of historical reconstruction and (...) argue that this critique sheds light on mistaken tendencies and misunderstandings within the early music movement, but it does not discredit the movement as such. In the second half of the paper, I attempt to show how Gadamer’s dialogical account of historical consciousness provides a framework for understanding what historically informed performance is seeking to accomplish, as well as its advantage over a Nietzschean approach. (shrink)

Review article on Philipp Höfele's book "Wollen und Lassen: Zur Ausdifferenzierung, Kritik und Rezeption des Willensparadigmas in der Philosophie Schellings" (Freiburg: Alber, 2019). The book demonstrates why Schelling is not an uncritical predecessor of Nietzsche and the will to power, as Heidegger alleges. Instead, Schelling displays an ambivalent attitude toward willing—affirming it in some forms, critiquing or rejecting it in others. Above all, Schelling’s thought on the will has many layers of complexity: it includes not only a variety of forms (...) of willing, but also “fringe phenomena” like non-willing or Gelassenheit that are ordinarily placed in opposition to will. Moreover, Schelling’s philosophy of will is distinctive in not conceiving willing and letting-be as either-or alternatives, as Heidegger tends to do. Especially in the late lectures, Schelling brings them together, showing how non-voluntary phenomena like Gelassenheit make an authentic willing possible. (shrink)

In this paper I investigate the relationship between the serious and the playful elements in Socrates’ character as these unfold within the context of Xenophon’s Symposium. For the Greeks, the concept of value is attached to the meaning of seriousness, and this accounts for the natural preference for the serious over the playful. Despite the potential rivalry of the playful and philosophy, Socrates mixes the playful with the serious in such a way as to conceal their boundary. This mixing serves (...) the purpose of education, by both attracting us to Socrates and placing us at a distance from the intended meaning of his words. (shrink)

Review article on Alexander Schnell’s book “Hinaus: Entwürfe zu einer phänomenologischen Metaphysik und Anthropologie” (Würzburg: Königshausen & Neumann, 2011). According to Schnell, an exclusively descriptive phenomenology is not enough; phenomenology must also be constructive. He thus outlines an ambitious project for constructive phenomenology that promises (1) to provide an ultimate justification for knowledge and (2) to ground a phenomenological metaphysics and anthropology, each of which is centered on the “image” (Bild). Insofar as Schnell fills in the details of this outline, (...) his analysis is careful, provocative, and filled with insight. (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)

This book is a new interpretation of Schelling's path-breaking 1809 treatise on freedom, the last major work published during his lifetime. The treatise is at the heart of the current Schelling renaissance—indeed, Heidegger calls it "one of the most profound works of German, thus of Western, philosophy." It is also one of the most demanding and complex texts in German Idealism. By tracing the problem of ground through Schelling's treatise, this book provides a unified reading of the text, while unlocking (...) the meaning of its most challenging passages through clear, detailed analysis. This analysis shows how Schelling's implicit distinction between senses of ground is the key to his project of constructing a system that can satisfy reason while accommodating objects that seem to defy rational explanation—including evil, the origins of nature, and absolute freedom. This allows Schelling to unite reason and mystery, providing a rich model for philosophizing about freedom and evil today. (shrink)

This is a model of consciousness. The hard problem of consciousness, what it feels like, is answered. The work builds on medical research analyzing the source and mechanisms associated with our feelings. It goes further by describing a generic model with wide applicability. The model is fully consistent with medical pathways in humans, but easily extends to animals and AI. The essence of the model is the interplay between associative memory and physiology. The model is a clear and concrete counterexample (...) to the famous philosophical objections to a scientific explanation. (shrink)

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)

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)

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)

This excellent book focuses on a decisive moment in Schelling's philosophical development: his 1801 dispute with Eschenmayer shortly before publishing Presentation of My System, the inaugural text of his identity philosophy. Carl August Eschenmayer was a German physician whose Kant-inspired writings in the philosophy of nature greatly influenced Schelling, especially with respect to the doctrine of the potencies. As Berger and Whistler demonstrate, the 1801 controversy has significant implications for understanding the trajectory of German Idealism and its debates on methodology, (...) the meaning of identity, and the place of nature in philosophy. (shrink)

This collection is the first volume published by Cambridge University Press devoted exclusively to Schelling scholarship. It contains eleven essays on diverse topics in Schelling’s philosophy, covering the entirety of his philosophical development, but mostly focusing on writings up to 1815. A number of the contributors are well-established scholars best known for their work on other thinkers in German Idealism. The volume thus offers readings of Schelling that are especially sensitive to his relationship to other figures in classical German philosophy. (...) Perhaps the richest contribution in the volume is Manfred Frank’s essay on Schelling’s theory of identity, which covers the theory’s historical sources, its application to the mind-body problem, and Schelling’s disagreement with Hegel. In any case, the wide historical range of these essays and the diversity of their topics offer an excellent overview of Schelling’s philosophical development. (shrink)

This book aims to present a richer alternative to the popular conception of freedom as the power to choose by giving an account of freedom in Schiller, Schelling, and Hegel. Despite my points of criticism (especially with regard to moral responsibility and the freedom to do evil), the contributions of the book are significant. By posing and developing the question of the relationship between freedom and actuality, Schindler introduces a problem that any complete account of freedom must address. At the (...) same time, Schindler provides us with a useful framework for relating Schelling and Hegel on freedom. Finally, the book gives an overview of the potential richness that a fuller conception of freedom provides. (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.

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 Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

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.

(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)

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 has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (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)

This chapter offers a new criticism of the Mind argument that is both decisive and instructive. It introduces a plausible principle (γ) that places a requirement on one’s having a choice about an event whose causal history includes only other events. Depending on γ’s truth-value, the Mind argument fails in such a way that one or the other of the two main species of libertarianism is the best approach to the metaphysics of freedom. Libertarians argue the compatibility of freedom and (...) indeterminism, and their biggest obstacle is the Mind argument that argues an incompatibility between the two. The chapter aims to build a case for the truth of γ, and so for nonreductive libertarianism. This is achieved by defending it from the best objections that have been brought to light, thereby emphasizing γ’s prima facie plausibility. (shrink)

YouTube has been implicated in the transformation of users into extremists and conspiracy theorists. The alleged mechanism for this radicalizing process is YouTube’s recommender system, which is optimized to amplify and promote clips that users are likely to watch through to the end. YouTube optimizes for watch-through for economic reasons: people who watch a video through to the end are likely to then watch the next recommended video as well, which means that more advertisements can be served to them. This (...) is a seemingly innocuous design choice, but it has a troubling side-effect. Critics of YouTube have alleged that the recommender system tends to recommend extremist content and conspiracy theories, as such videos are especially likely to capture and keep users’ attention. To date, the problem of radicalization via the YouTube recommender system has been a matter of speculation. The current study represents the first systematic, pre-registered attempt to establish whether and to what extent the recommender system tends to promote such content. We begin by contextualizing our study in the framework of technological seduction. Next, we explain our methodology. After that, we present our results, which are consistent with the radicalization hypothesis. Finally, we discuss our findings, as well as directions for future research and recommendations for users, industry, and policy-makers. (shrink)

Two hundred and sixty-three subjects each gave examples for one of five geographic categories: geographic features, geographic objects, geographic concepts, something geographic, and something that could be portrayed on a map. The frequencies of various responses were significantly different, indicating that the basic ontological terms feature, object, etc., are not interchangeable but carry different meanings when combined with adjectives indicating geographic or mappable. For all of the test phrases involving geographic, responses were predominantly natural features such as mountain, river, lake, (...) ocean, hill. Artificial geographic features such as town and city were listed hardly at all for geographic categories, an outcome that contrasts sharply with the disciplinary self-understanding of academic geography. However, geographic artifacts and fiat objects, such as roads, cities, boundaries, countries, and states, were frequently listed by the subjects responding to the phrase something that could be portrayed on a map. In this paper, we present the results of these experiments in visual form, and provide interpretations and implications for further research. (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.