This book is an anthology with the following themes. Non-European Tradition: Bussanich interprets main themes of Hindu ethics, including its roots in ritual sacrifice, its relationship to religious duty, society, individual human well-being, and psychic liberation. To best assess the truth of Hindu ethics, he argues for dialogue with premodern Western thought. Pfister takes up the question of human nature as a case study in Chinese ethics. Is our nature inherently good (as Mengzi argued) or bad (Xunzi’s view)? (...) class='Hi'>Pfister ob- serves their underlying agreement, that human beings are capable of becoming good, and makes precise the disagreement: whether we achieve goodness by cultivating autonomous feelings or by accepting external precepts. There are political consequences: whether government should aim to respect and em- power individual choices or to be a controlling authority. Early Greek Thinking: Collobert examines the bases of Homeric ethics in fame, prudence, and shame, and how these guide the deliberations of heroes. She observes how, by depending upon the poet’s words, the hero gains a quasi- immortality, although in truth there is no consolation for each person’s inevi- table death. Plato: Santas examines Socratic Method and ethics in Republic 1. There Socrates examines definitions of justice and tests them by comparison to the arts and sciences. Santas shows the similarities of Socrates’ method to John Rawls’ method of considered judgments in reflective equilibrium. McPherran interprets Plato’s religious dimension as like that of his teacher Socrates. McPherran shows how Plato appropriates, reshapes, and extends the religious conventions of his own time in the service of establishing the new enterprise of philosophy. Ac- cording to Taylor, Socrates believes that humans in general have the task of helping the gods by making their own souls as good as possible, and Socrates’ unique ability to cross-examine imposes on him the special task of helping others to become as good as possible. This conception of Socrates’ mission is Plato’s own, consisting in an extension of the traditional conception of piety as helping the gods. Brickhouse and Smith propose a new understanding of Socratic moral psychology—one that retains the standard view of Socrates as an intellectualist, but also recognizes roles in human agency for appetites and passions. They compare and contrast the Socratic view to the picture of moral psychology we get in other dialogues of Plato. Hardy also proposes a new, non-reductive understanding of Socratic eudaimonism—he argues that Socrates invokes a very rich and complex notion of the “Knowledge of the Good and Bad”, which is associated with the motivating forces of the virtues. Rudebusch defends Socrates’ argument that knowledge can never be impotent in the face of psychic passions. He considers the standard objections: that knowledge cannot weigh incom- mensurable human values, and that brute desire, all by itself, is capable of moving the soul to action. Aristotle: Anagnostopoulos interprets Aristotle on the nature and acquisition of virtue. Though virtue of character, aiming at human happiness, requires a complex awareness of multiple dimensions of one’s experience, it is not properly a cognitive capacity. Thus it requires habituation, not education, according to Aristotle, in order to align the unruly elements of the soul with reason’s knowledge of what promotes happiness. Shields explains Aristotle’s doctrine that goodness is meant in many ways as the doctrine that there are different analyses of goodness for different types of circumstance, just as for being. He finds Aristotle to argue for this conclusion, against Plato’s doctrine of the unity of the Good, by applying the tests for homonymy and as an immediate cons- equence of the doctrine of categories. Shields evaluates the issue as unresolved at present. Russell discusses Aristotle’s account of practical deliberation and its virtue, intelligence (phronesis). He relates the account to contemporary philo- sophical controversies surrounding Aristotle’s view that intelligence is neces- sary for moral virtue, including the objections that in some cases it is unnecessary or even impedes human goodness. Frede examines the advantages and disadvantages of Aristotle’s virtue ethics. She explains the general Greek con- ceptions of happiness and virtue, Aristotle’s conception of phronesis and compares the Aristotle’s ethics with modern accounts. Liske discusses the question of whether the Aristotelian account of virtue entails an ethical-psy- chological determinism. He argues that Aristotle’s understanding of hexis allows for free action and ethical responsibility : By making decisions for good actions we are able to stabilize our character (hexis). Hellenistic and Roman: Annas defends an account of stoic ethics, according to which the three parts of Stoicism—logic, physics, and ethics—are integrated as the parts of an egg, not as the parts of a building. Since by this analogy no one part is a foundation for the rest, pedagogical decisions may govern the choice of numerous, equally valid, presentations of Stoic ethics. Piering interprets the Cynic way of life as a distinctive philosophy. In their ethics, Cynics value neither pleasure nor tradition but personal liberty, which they achieve by self-suffi- ciency and display in speech that is frank to the point of insult. Plotinus and Neoplatonism: Gerson outlines the place of ordinary civic virtue as well as philosophically contemplative excellence in Neoplatonism. In doing so he attempts to show how one and the same good can be both action-guiding in human life and be the absolute simple One that grounds the explanation of everything in the universe. Delcomminette follows Plotinus’s path to the Good as the foundation of free will, first in the freedom of Intellect and then in the “more than freedom” of the One. Plotinus postulates these divinities as not outside but within each self, saving him from the contradiction of an external foundation for a truly free will. General Topics: Halbig discusses the thesis on the unity of virtues. He dis- tinguishes the thesis of the identity of virtues and the thesis of a reciprocity of virtues and argues that the various virtues form a unity (in terms of reciprocity) since virtues cannot bring about any bad action. Detel examines Plato’s and Aristotle’s conceptions of normativity : Plato and Aristotle (i) entertained hybrid theories of normativity by distinguishing functional, semantic and ethical normativity, (ii) located the ultimate source of normativity in standards of a good life, and thus (iii) took semantic normativity to be a derived form of normativity. Detel argues that hybrid theories of normativity are—from a mo- dern point of view—still promising. Ho ̈ffe defends the Ancient conception of an art of living against Modern objections. Whereas many Modern philosophers think that we have to replace Ancient eudaimonism by the idea of moral obligation (Pflicht), Ho ̈ffe argues that Eudaimonism and autonomy-based ethics can be reconciled and integrated into a comprehensive and promising theory of a good life, if we enrich the idea of autonomy by the central elements of Ancient eudaimonism. Some common themes: The topics in Chinese and Hindu ethics are perhaps more familiar to modern western sensibilities than Homeric and even Socratic. Anagnostopoulos, Brickhouse and Smith, Frede, Liske, Rudebusch, and Russell all consider in contrasting ways the role of moral character, apart from intellect, in ethics. Brickhouse / Smith, Hardy, and Rudebusch discuss the Socratic con- ception of moral knowledge. Brickhouse / Smith and Hardy retain the standard view of the so called Socratic Intellectualism. Shields and Gerson both consider the question whether there is a single genus of goodness, or if the term is a homonym. Bussanich, McPherran, Taylor, and Delcomminette all consider the relation between religion and ethics. Pfister, Piering, Delcomminette, and Liske all consider what sort of freedom is appropriate to human well-being. Halbig, Detel, and Ho ̈ffe propose interpretations of main themes of Ancient ethics. (shrink)

This paper takes a detailed look at the Republic’s Divided Line analogy and considers how we should respond to its most contentious implication: that pistis and dianoia have the same degree of ‘clarity’ (σαφήνεια). It argues that we must take this implication at face value and that doing so allows us to better understand both the analogy and the nature of dianoia.

This paper examines the soul-turning metaphor in Book 7 of Plato’s Republic. It argues that the failure to find a consistent reading of how the metaphor is used has contributed to a number of long-standing disagreements, especially concerning the more famous metaphor with which it is intertwined, the Cave allegory. A full reading of the metaphor, as it occurs throughout Book 7, is offered, with particularly close attention to what is one of the most difficult and stubbornly divisive passages in (...) Book 7, 532b6–d1. (shrink)

This paper defends a reading of eikasia—the lowest kind of cognition in the Divided Line—as a kind of empirical cognition that Plato appeals to when explaining, among other things, the origin of ethical error. The paper has two central claims. First, eikasia with respect to, for example, goodness or justice is not different in kind to eikasia with respect to purely sensory images like shadows and reflections: the only difference is that in the first case the sensory images include representations (...) of value properties. Second, eikasia is not the bare awareness of images or simply a label for an error (mistaking image for original) but a kind of empirical, image-confined cognition, and one that has an important part to play in characterising the cognitive abilities of the non-rational parts of the soul. (shrink)

In book 10 of the Republic we find a new argument for the division of the soul. The argument’s structure is similar to the arguments in book 4 but, unlike those arguments, it centres on a purely cognitive conflict: believing and disbelieving the same thing, at the same time. The argument presents two interpretive difficulties. First, it assumes that a conflict between a belief and an appearance—e.g. disbelieving that a stick partially immersed in water is, as it appears, bent—entails a (...) conflict between beliefs. Prima facie, there is only one belief, the belief that contradicts the appearance. Second, it is unclear what parts of the soul Plato intends to divide between: some argue that it is, as in book 4, a partition between a rational and a non-rational part; others argue that it is a new partition between a higher and a lower subdivision of the rational part. This paper offers solutions to both difficulties through an analysis of what Plato means by φαινόμενα, ‘appearances’, and δόξαι, ‘beliefs’. It is argued, first, that the relevant appearances are entirely sensory but nonetheless sufficiently belief-like to (a) warrant being called δόξαι and (b) oppose, by themselves, our beliefs; there is no need for a third mental state, a belief that assents to the appearance. A second claim concerns a central line in the argument, 602e4–6, that has served as the primary evidence that the partition is within the rational part of the soul. Those who wish to avoid this conclusion generally resort to alternative, and less natural, translations of 602e4–6. It is argued that this is unnecessary: once we have correctly understood sensory appearances, we see that the standard translation of 602e4–6 in fact entails a division between a rational and a non-rational part of the soul. (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)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

I offer a reading of the two conceptions of the good found in Plato’s Protagoras: the popular conception—‘the many’s’ conception—and Socrates’ conception. I pay particular attention to the three kinds of goods Socrates introduces: (a) bodily pleasures like food, drink, and sex; (b) instrumental goods like wealth, health, or power; and (c) virtuous actions like courageously going to war. My reading revises existing views about these goods in two ways. First, I argue that the many are only ‘hedonists’ in a (...) very attenuated sense. They do not value goods of kind (b) simply as means to pleasures of kind (a); rather, they have fundamentally different attitudes to (a) and (b). Second, the hedonism that Socrates’ defends includes a distinction between kinds of pleasures: (a) bodily pleasures and (c) the pleasures of virtuous actions. This distinction between kinds of pleasures—some that do and some that do not exert the ‘power of appearance’—allows Socrates to address one of the central beliefs in the popular conception of akrasia, namely that it involves a special kind of unruly desire: non-rational appetites for pleasures like food, drink, or sex. Socrates replaces the motivational push of non-rational appetites with the epistemic pull of the appearance of immediate pleasures like food, drink, and sex. (shrink)

In this paper I discuss the translation of a line in Plato's description of the ‘greatest accusation’ against imitative poetry, Republic 606a3–b5. This line is pivotal in Plato's account of how poetry corrupts its audience and is one of the Republic's most complex and interesting applications of his partite psychology, but it is misconstrued in most recent translations, including the most widely used. I argue that an examination of the text and reflections on Platonic psychology settle the translation decisively.

Reading Kripke's "Wittgenstein on Rules and Private Language", at first one can easily get confused about his claim that the problem discovered was a sort of ontological skepticism. Contrary to the opinion of a great number of contemporary philosophers who hold that rule-following brings up merely epistemological problems I will argue that the scepticism presented by Kripke really is ontological because it is concerned with the exclusion of certain facts. The first section in this paper is dedicated to a presentation (...) of Kripke's paradox with a clarification of the position of "plus/quus-talk" in the argument. Section two is engaged in one of his classical direct solutions: the dispositional theory which will serve as a preparation for the last section. Section three is concerned with Kripke's solution to the skeptical problem, ending with the question of whether he is giving a real solution. In section four, I will try to give an answer to those questions, distinguishing between two different versions of the problem given by the paradox; a wrong one and a correct one. Readers who are really fed up with the sceptical problem and its sceptical solution can skip section one, two and three, concentrating instead on my own argument for the real nature of the problem. In section five, I will pick up on some ideas from Norwich, who tries to give a "straight solution" to the paradox reanimating some weaker version of a dispositional theory of meaning. I will argue that Horwich's solution is misleading because he aims at the wrong version of the paradox. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (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)

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)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

This commentary examines the role of sustainability in the latest draft of the WHO pandemic accord, highlighting its notable absence from the official list of guiding principles despite being mentioned frequently throughout the text. It argues that sustainability should be explicitly acknowledged as a core principle and given a clear definition tailored to pandemic preparedness, and proposes defining sustainability as ensuring that immediate emergency responses don't compromise future pandemic preparedness and response capabilities. Including sustainability as a guiding principle would serve (...) two key purposes: validating the relevance of ethical principles in the accord's provisions and emphasizing the importance of long-term planning in pandemic preparedness. The commentary notes that while humans naturally discount future consequences, sustainable pandemic planning requires considering impacts beyond the next pandemic. It recommends coupling any reforms, such as intellectual property changes, with alternative innovation incentives to maintain a balanced approach to pandemic preparedness and response. (shrink)

Perceivers generally show a poor ability to detect changes, a condition referred to as “Change Blindness” . They are, in addition, “blind to their own blindness”. A common explanation of this “Change Blindness Blindness” is that it derives from an inadequate, “photographical” folk-theory about perception. This explanation, however, does not account for intra-individual variations of CBB across trials. Our study aims to explore an alternative theory, according to which participants base their self-evaluations on two activity-dependent cues, namely search time and (...) perceived success in prior trials. These cues were found to influence self-evaluation in two orthogonal ways: success-feedback influenced self-evaluation in a global, contextual way, presumably by recalibrating the norm of adequacy for the task. Search time influenced it in a local way, predicting the success of a given trial from its duration. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Abortion is arguably the most controversial and divisive moral issue of modern times, but up until now the debate has taken place almost exclusively within a Western cultural, religious and philosophical context. For the past three decades in the West arguments both for and against abortion have been mounted by groups of all kinds, from religious fundamentalists to radical feminists and every shade of opinion in between. Rather than mutual understanding, however, the result has been the polarisation of opinion and (...) the deepening of entrenched positions. In the face of this deadlock a new perspective is urgently required. Buddhism is an ancient tradition which over the centuries has refined its distinctive beliefs and values in the course of a long interaction with the major cultures of Asia. As Buddhism continues to engage the attention of the West, the time is now opportune for its views on abortion to be heard. This is the first book to explore the abortion question from a range of Buddhist cultural and ethical perspectives. The approach is interdisciplinary and will be of relevance to those working in fields such as law, ethics, medicine, philosophy, religion, the social sciences and women's studies. (shrink)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

This paper presents an account of the ethical and conceptual relationship between free speech and press freedom. Many authors have argued that, despite there being some common ground between them, these two liberties should be treated as properly distinct, both theoretically and practically. The core of the argument, for this “unbundling” approach, is that conflating free speech and press freedom makes it too easy for reasonable democratic regulations on press freedom to be portrayed, by their opponents, as part of a (...) programme of illiberal censorship. While we acknowledge the important grain of truth in that argument, we try to show how the alternative, “unbundling” approach can also be used to undermine or mischaracterise democratically justifiable opposition to media regulations in despotic regimes. In light of the problems on both sides, we defend a contextually-variable account of the relation between these two liberties. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.

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.

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

Der Sammelband umfasst Aufsätze zu den Grundfragen, Anwendungen und Grenzen des Unterrichts des Argumentierens, in allen Fächern und mit Fokus auf die Fächer Philosophie und Ethik. Dabei werden Fragen wie diese behandelt: Welchen Zielen dient das Argumentieren und welche verfolgt der Unterricht des Argumentierens? In welchem Verhältnis stehen diese zu anderen Zielen des Unterrichts? Welche Kenntnisse, Fähigkeiten und Tugenden des Argumentierens sollen eingeübt werden und wie? Die vorgeschlagenen Antworten sind nicht nur für Personen aus der Fachdidaktik, sondern auch aus der (...) Philosophie und der Schullehrpraxis aller Fächer interessant. Der Band trägt damit auch zur stärkeren Etablierung des Felds der Argumentationsdidaktik bei. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (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.

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (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)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

According to the principle of Conjunction Closure, if one has justification for believing each of a set of propositions, one has justification for believing their conjunction. The lottery and preface paradoxes can both be seen as posing challenges for Closure, but leave open familiar strategies for preserving the principle. While this is all relatively well-trodden ground, a new Closure-challenging paradox has recently emerged, in two somewhat different forms, due to Backes :3773–3787, 2019a) and Praolini :715–726, 2019). This paradox synthesises elements (...) of the lottery and the preface and is designed to close off the familiar Closure-preserving strategies. By appealing to a normic theory of justification, I will defend Closure in the face of this new paradox. Along the way I will draw more general conclusions about justification, normalcy and defeat, which bear upon what Backes :2877–2895, 2019b) has dubbed the ‘easy defeat’ problem for the normic theory. (shrink)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

Deleuze argued that a fundamental mutation in the concept of time occurred in Kant. In antiquity, the concept of time was subordinated to the concept of movement: time was a ‘measure’ of movement. In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an autonomy of its own: time becomes "the pure and empty form" of everything that moves and changes. What is essential in the theory of time is not the distinction between objective ‘clock (...) time’ (or physical time) and the subjective experience of ‘time consciousness,’ since both of them measure movements, whether the movement of extensive objects or intensive states. What is fundamental is rather the relation between time and movement, since time can only assume its own concept when it ceases to be subordinate to movement, whether that movement is objective or subjective. This article examines how Kant inverted the relation between time and movement, and how Deleuze’s own theory of time builds on Kant’s revolution and extends it further. (shrink)

In this paper I defend an eudaimonistic reading of Spinoza’s ethical philosophy. Eudaimonism refers to the mainstream ethical tradition of the ancient Greeks, which considers happiness a naturalistic, stable, and exclusively intrinsic good. Within this tradition, we can also draw a distinction between weak eudaimonists and strong eudaimonists. Weak eudaimonists do not ground their ethical conceptions of happiness in complete theories of metaphysics, epistemology, or psychology. Strong eudaimonists, conversely, build their conceptions of happiness around an overall philosophical system that extends (...) far beyond ethics, while nevertheless being directed at the promotion of a happy life. I will show that Spinozistic happiness is not only naturalistic, stable, and exclusively intrinsically good, but that Spinoza is also a strong eudaimonist because his ethical account of happiness is incomprehensible without appeal to metaphysical, epistemological, and psychological doctrines. As well, I will explain how the apparent subjective and relativistic features of Spinoza’s ethics do not undermine the eudaimonistic reading, because both Spinoza and the ancient eudaimonists grant that the beliefs/feelings of the subject play a necessary (but insufficient) role in happiness as the highest good. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.