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

This book tells the story of modern ethics, namely the story of a discourse that, after the Renaissance, went through a methodological revolution giving birth to Grotius’s and Pufendorf’s new science of natural law, leaving room for two centuries of explorations of the possible developments and implications of this new paradigm, up to the crisis of the Eighties of the eighteenth century, a crisis that carried a kind of mitosis, the act of birth of both basic paradigms of the two (...) following centuries: Kantian ethics and utilitarianism. The new science of natural law carried a fresh start for ethics, resulting from a mixture of the Old and the New. It was, as suggested by Schneewind, an attempt at rescuing the content of Scholastic and Stoic doctrines on a new methodological basis. The former was the claim of existence of objective and universal moral laws; the latter was the self-aware attempt at justifying a minimal kernel of such laws facing skeptical doubt. What Bentham and Kant did was precisely carrying this strategy further on, even if restructuring it each of them around one out of two alternative basic claims. The nineteenth- and twentieth-century critics of the Enlightenment attacked both not on their alleged failure in carrying out their own projects, but precisely on having adopted Grotius’s and Pufendorf’s project. What counter-enlightenment has been unable to spell out is which alternative project could be carried out facing the modern condition of pluralism, while on the contrary, if we takes a closer look at developments in twentieth-century ethics or at on-going discussions on practical issues, we might feel inclined to believe that Grotius’s and Pufendorf’s project is as up-to-date as ever. -/- Table of Contents -/- Preface I. Fathers of the Reformation and Schoolmen 1.1. Luther: passive justice and the good deeds; 1.2. Calvin: voluntarism and predestination; 1.3. Baroque Scholasticism; 1.4. Casuistry and Institutiones morales -/- II Neo-Platonists, neo-Stoics, neo-Sceptics 2.1. Aristotelian, neo-Platonic, neo-Epicurean and neo-Cynic Humanists; 2.2. Oeconomica and the art of living; 2.3. Neo-Stoics; 2.4. Neo-Sceptics; 2.5. Moralistic literature -/- III Neo-Augustinians 3.l. The Jansenists on natura lapsa, sufficient grace, pure love; 3.2. Nicole on the impossibility of self-knowledge; 3.3. Nicole on self-love and charity; 3.4. Nicole against civic virtue, for Christian civility; 3.5. Malebranche on general laws and necessary evil; 3.6. Malebranche on Neo-Augustinianism and Platonism. -/- IV Grotius, Pufendorf and the new moral science 4.1. Grotius against Aristotle and the sceptics; 4.2. Mersenne and Gassendi; 4.3. Descartes on ethics as the last branch of philosophy’s tree; 4.4. Hobbes on scepticism and the new moral science; 4.5. Spinoza on the new moral science as a descriptive science;4.6. Locke on voluntarism and probabilism; 4.7. Pufendorf on natural law as an exact science; 4.8. Pufendorf on physical and moral entities; 10. Pufendorf on self-preservation -/- V The empiricist version of the new moral science: from Cumberland to Paley 5.1. Cumberland against Hobbesian voluntarism; 5.2. Cumberland and theological consequentialism; 5.3. Cumberland on universal benevolence and self-love; 5.4. Shaftesbury on the moral sense; 5.5. Hutcheson on natural law and moral faculties; 5.6. Gay, Brown, Paley and theological consequentialism. -/- VI The rationalist version of the new moral science: from Cudworth to Price 6.1. The Cambridge Platonists; 6.2. Shaftesbury on the moral sense; 6.3. Butler and a third way between voluntarism and scepticism; 6.4. Price and the rational character of moral truths; -/- VII Leibniz’s compromise between the new moral science and Aristotelianism 1.Leibniz against voluntarism; 2.Leibniz against the division between the physical and the moral good; 3.Leibniz on la place d’autrui and theological consequentialism; 4.Thomasius, Wolff, Crusius -/- VIII French eighteenth-century philosophers without the new moral science 8.1. The genealogy of our ideas of virtue and vice; 8.2. Maupertuis and moral arithmetic 8.3. The philosophes and the harmony of interests; 8.4. Rousseau on corruption, self-love, and virtue; 8.5. Sade on the merits of vice -/- IX Experimental moral science: Hume and Adam Smith 9.1. Mandeville’s paradox; 9.2. Hutcheson on the law of nature and moral faculties; 9.3. Hume on experimental moral philosophy and the intermediate principles; 9.4. Hume’s Law; 9.5. Hume on the fellow-feeling; 9.6. Hume on natural and artificial virtues and disinterested pleasure for utility; 9.7. Adam Smith’s anti-realist metaethics; 9.8. Adam Smith on self-deception and the paradox of happiness; 9.9. Adam Smith on sympathy and the impartial spectator; 9.10. Adam Smith on the twofold criterion for moral judgement and its paradox; 9.11. Reid on the refutation of scepticism and the self-evidence of duty -/- X Kantian ethics 10.1. Kantian metaethics: moral epistemology; 10.2. Kantian metaethics: moral ontology; 10.3. Kantian metaethics: moral psychology; 10.4. Kantian normative ethics; 10.5. Kant on the impracticability of applied ethics; 10.6. Kantian moral anthropology; 10.7. Civilisation and moralisation; 10.8. Theology on a moral basis and the origins of evil; 10.9. Fichte and the transformation of theoretical philosophy into practical philosophy XI Bentham and utilitarianism 11.1. Bentham’s linguistic theory; 11.2. Bentham’s moral ontology, psychology, and theory of action; 11.3. The principle of greatest happiness; 11.4. The critique of religious ethics; 11.5. The new morality; 11.6. Interest and duty; 11.7. Virtues; 11.8. Private ethics and legislation -/- XII Followers of the Enlightenment: liberal Judaism and Liberal Theology 12.1. Mendelssohn; 12.2. Salomon Maimon; 12.3. Haskalā and liberal Judaism; 12.4. Liberal Theology. -/- XIII Counter-Enlighteners 13.1.Romanticism and the fulfilment of individuality as the Summum Bonum; 13.2. Hegel on history as the making of liberty; 13.3. Hegel on the unhappy consciousness and the beautiful soul; 13.4. Hegel on Morality and Sittlichkeit; 13.5. Marx on ideology, alienation, and praxis; 13.6. Schopenhauer on compassion; 13.7. Kierkegaard on faith beyond ethics. -/- XIV Followers of the Enlightenment: intuitionists and utilitarian 14.1 Whewell‘s criticism of utilitarianism; 14.2 Whewell on morality and the philosophy of morality; 14.3 Whewell on the Supreme Norm; 14.4 Whewell on the conflict between duties; 14.5 Mill and the proof of the principle of utility; 14.6 Mill’s eudemonistic utilitarianism; 14.7 Mill on rules -/- XV Followers of the Enlightenment: neo-Kantians and positivists 15.1. French spiritualism; 15.2. Neo-Kantians: the Marburg school; 15.3. Neo-Kantians: the Marburg school; 15.4. Comte’s positivism and the invention of altruism; 15.5. Social Darwinism; 15.6. Wundt and an ethic of humankind -/- XVI Post-enlighteners: Sidgwick 16.1. Criticism of intuitionism; 16.2. On ethical egoism; 16.3. Criticism of utilitarianism -/- XVII Post-enlighteners: Durkheim 17.1. Sociology as physics of customs; 17.2. Morality as physics of customs and as practical science; 17.3. On Kantian ethics and utilitarianism; 17.4. The variability of moralities;17.5. Social solidarity as end and justification of morality; 17.6. Secular morality as “sociodicy”; XVIII Post-enlighteners: Nietzsche 18.1. On the Dionysian; 18.2. On the deconstruction of the world of values 18.3 On the twofold genealogy of moralities; 18.4. On ascetics and nihilism; 18.5. Normative ethics of self-fulfilment -/- Bibliography / Index of names / Index of concepts -/- . (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)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (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)

This paper examines how people think about aiding others in a way that can inform both theory and practice. It uses data gathered from Kiva, an online, non-profit organization that allows individuals to aid other individuals around the world, to isolate intuitions that people find broadly compelling. The central result of the paper is that people seem to give more priority to aiding those in greater need, at least below some threshold. That is, the data strongly suggest incorporating both a (...) threshold and a prioritarian principle into the analysis of what principles for aid distribution people accept. This conclusion should be of broad interest to aid practitioners and policy makers. It may also provide important information for political philosophers interested in building, justifying, and criticizing theories about meeting needs using empirical evidence. (shrink)

Various authors debate the question of whether neuroscience is relevant to criminal responsibility. However, a plethora of different techniques and technologies, each with their own abilities and drawbacks, lurks beneath the label “neuroscience”; and in criminal law responsibility is not a single, unitary and generic concept, but it is rather a syndrome of at least six different concepts. Consequently, there are at least six different responsibility questions that the criminal law asks—at least one for each responsibility concept—and, I will suggest, (...) a multitude of ways in which the techniques and technologies that comprise neuroscience might help us to address those diverse questions. In a way, on my account neuroscience is relevant to criminal responsibility in many ways, but I hesitate to state my position like this because doing so obscures two points which I would rather highlight: one, neither neuroscience nor criminal responsibility are as unified as that; and two, the criminal law asks many different responsibility questions and not just one generic question. (shrink)

Garrath Williams claims that truly responsible people must possess a “capacity … to respond [appropriately] to normative demands” (2008:462). However, there are people whom we would normally praise for their responsibility despite the fact that they do not yet possess such a capacity (e.g. consistently well-behaved young children), and others who have such capacity but who are still patently irresponsible (e.g. some badly-behaved adults). Thus, I argue that to qualify for the accolade “a responsible person” one need not possess such (...) a capacity, but only to be earnestly willing to do the right thing and to have a history that testifies to this willingness. Although we may have good reasons to prefer to have such a capacity ourselves, and to associate ourselves with others who have it, at a conceptual level I do not think that such considerations support the claim that having this capacity is a necessary condition of being a responsible person in the virtue sense. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Luck egalitarians think that considerations of responsibility can excuse departures from strict equality. However critics argue that allowing responsibility to play this role has objectionably harsh consequences. Luck egalitarians usually respond either by explaining why that harshness is not excessive, or by identifying allegedly legitimate exclusions from the default responsibility-tracking rule to tone down that harshness. And in response, critics respectively deny that this harshness is not excessive, or they argue that those exclusions would be ineffective or lacking in justification. (...) Rather than taking sides, after criticizing both positions I also argue that this way of carrying on the debate – i.e. as a debate about whether the harsh demands of responsibility outweigh other considerations, and about whether exclusions to responsibility-tracking would be effective and/or justified – is deeply problematic. On my account, the demands of responsibility do not – in fact, they can not – conflict with the demands of other normative considerations, because responsibility only provides a formal structure within which those other considerations determine how people may be treated, but it does not generate its own practical demands. (shrink)

It has become standard for feminist philosophers of language to analyze Catherine MacKinnon's claim in terms of speech act theory. Backed by the Austinian observation that speech can do things and the legal claim that pornography is speech, the claim is that the speech acts performed by means of pornography silence women. This turns upon the notion of illocutionary silencing, or disablement. In this paper I observe that the focus by feminist philosophers of language on the failure to achieve uptake (...) for illocutionary acts serves to group together different kinds of illocutionary silencing which function in very different ways. (shrink)

In this paper I argue that Beall and Restall's claim that there is one true logic of metaphysical modality is incompatible with the formulation of logical pluralism that they give. I investigate various ways of reconciling their pluralism with this claim, but conclude that none of the options can be made to work.

Fred Adams and collaborators advocate a view on which empty-name sentences semantically encode incomplete propositions, but which can be used to conversationally implicate descriptive propositions. This account has come under criticism recently from Marga Reimer and Anthony Everett. Reimer correctly observes that their account does not pass a natural test for conversational implicatures, namely, that an explanation of our intuitions in terms of implicature should be such that we upon hearing it recognize it to be roughly correct. Everett argues that (...) the implicature view provides an explanation of only some of our intuitions, and is in fact incompatible with others, especially those concerning the modal profile of sentences containing empty names. I offer a pragmatist treatment of empty names based upon the recognition that the Gricean distinction between what is said and what is implicated is not exhaustive, and argue that such a solution avoids both Everett's and Reimer's criticisms. (shrink)

In this paper, we locate a general rhetorical strategy employed in theoretical discourse wherein philosophers argue from the mere existence of internalized oppression to some kind of epistemic, moral, political, or cognitive deficiency of oppressed people. We argue that this strategy has harmful consequences for oppressed people, breaking down our analysis in terms of individual and structural harms within both epistemic and moral domains. These harms include attempting to undermine the self-trust of oppressed people, reinforcing unjust epistemic power hierarchies, undermining (...) the moral agency of oppressed people, and obscuring real issues of oppression. In light of these many harms, we conclude that there are pro tanto reasons not to employ this strategy, and instead offer a series of suggestions for those considering adopting such a rhetorical move. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

According to a captivating picture, epistemic justification is essentially a matter of epistemic or evidential likelihood. While certain problems for this view are well known, it is motivated by a very natural thought—if justification can fall short of epistemic certainty, then what else could it possibly be? In this paper I shall develop an alternative way of thinking about epistemic justification. On this conception, the difference between justification and likelihood turns out to be akin to the more widely recognised difference (...) between ceteris paribus laws and brute statistical generalisations. I go on to discuss, in light of this suggestion, issues such as classical and lottery-driven scepticism as well as the lottery and preface paradoxes. (shrink)

This thesis considers two allegations which conservatives often level at no-fault systems — namely, that responsibility is abnegated under no-fault systems, and that no-fault systems under- and over-compensate. I argue that although each of these allegations can be satisfactorily met – the responsibility allegation rests on the mistaken assumption that to properly take responsibility for our actions we must accept liability for those losses for which we are causally responsible; and the compensation allegation rests on the mistaken assumption that tort (...) law’s compensatory decisions provide a legitimate norm against which no-fault’s decisions can be compared and criticized – doing so leads in a direction which is at odds with accident law reform advocates’ typical recommendations. On my account, accident law should not just be reformed in line with no-fault’s principles, but rather it should be completely abandoned since the principles that protect no- fault systems from the conservatives’ two allegations are incompatible with retaining the category of accident law, they entail that no-fault systems are a form of social welfare and not accident law systems, and that under these systems serious deprivation – and to a lesser extent causal responsibility – should be conditions of eligibility to claim benefits. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (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 study aims to investigate the relationship between job burnout and employee performance in the feed industry during the ASF outbreak. Further, the researchers employed a descriptive-correlational research design in order to analyze the acquired data and produce pertinent findings. Thus, the researchers gathered data from one hundred two (102) feed industry employees. The Maslach Burnout Inventory (MBI) and Individual Work Performance Questionnaire (IWPQ) were employed to ascertain the extent of job burnout experienced by the respondents and evaluate employee performance, (...) respectively. Based on the statistical analysis, there is a significant relationship between job burnout and employee performance. Moreover, the study's findings were thoroughly analyzed and discussed. (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)

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)

Many jurisdictions prohibit or severely restrict the use of evidence about a defendant’s character to prove legal culpability. Situationists, who argue that conduct is largely determined by situational features rather than by character, can easily defend this prohibition. According to situationism, character evidence is misleading or paltry. -/- Proscriptions on character evidence seem harder to justify, however, on virtue ethical accounts. It appears that excluding character evidence either denies the centrality of character for explaining conduct—the situationist position—or omits probative evidence. (...) Situationism is, after all, presented as antithetical to virtue ethics. -/- This essay provides a virtue ethical defense of character evidence exclusion rules. We show that existing virtue ethical rebuttals to situationism themselves support prohibitions on character evidence; even if behavior arises from stable character traits, character evidence should be prohibited. In building our case, we provide a taxonomy of kinds of character judgment and reconcile the ubiquity and reasonableness of character judgments in ordinary life with the epistemic legitimacy of character evidence prohibitions in law. (shrink)

What constitutes illocutionary silencing? This is the key question underlying much recent work on Catherine MacKinnon's claim that pornography silences women. In what follows I argue that the focus of the literature on the notion of audience `uptake' serves to mischaracterize the phenomena. I defend a broader interpretation of what it means for an illocutionary act to succeed, and show how this broader interpretation provides a better characterization of the kinds of silencing experienced by women.

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Egalitarians must address two questions: i. What should there be an equality of, which concerns the currency of the ‘equalisandum’; and ii. How should this thing be allocated to achieve the so-called equal distribution? A plausible initial composite answer to these two questions is that resources should be allocated in accordance with choice, because this way the resulting distribution of the said equalisandum will ‘track responsibility’ — responsibility will be tracked in the sense that only we will be responsible for (...) the resources that are available to us, since our allocation of resources will be a consequence of our own choices. But the effects of actual choices should not be preserved until the prior effects of luck in constitution and circumstance are first eliminated. For instance, people can choose badly because their choice-making capacity was compromised due to a lack of intelligence (i.e. due to constitutional bad luck), or because only bad options were open to them (i.e. due to circumstantial bad luck), and under such conditions we are not responsible for our choices. So perhaps a better composite answer to our two questions (from the perspective of tracking responsibility) might be that resources should be allocated so as to reflect people’s choices, but only once those choices have been corrected for the distorting effects of constitutional and circumstantial luck, and on this account choice preservation and luck elimination are two complementary aims of the egalitarian ideal. Nevertheless, it is one thing to say that luck’s effects should be eliminated, but quite another to figure out just how much resource redistribution would be required to achieve this outcome, and so it was precisely for this purpose that in 1981 Ronald Dworkin developed the ingenuous hypothetical insurance market argumentative device (HIMAD), which he then used in conjunction with the talent slavery (TS) argument, to arrive at an estimate of the amount of redistribution that would be required to reduce the extent of luck’s effects. However recently Daniel Markovits has cast doubt over Dworkin’s estimates of the amount of redistribution that would be required, by pointing out flaws with his understanding of how the hypothetical insurance market would function. Nevertheless, Markovits patched it up and he used this patched-up version of Dworkin’s HIMAD together with his own version of the TS argument to reach his own conservative estimate of how much redistribution there ought to be in an egalitarian society. Notably though, on Markovits’ account once the HIMAD is patched-up and properly understood, the TS argument will also allegedly show that the two aims of egalitarianism are not necessarily complementary, but rather that they can actually compete with one another. According to his own ‘equal-agent’ egalitarian theory, the aim of choice preservation is more important than the aim of luck elimination, and so he alleges that when the latter aim comes into conflict with the former aim then the latter will need to be sacrificed to ensure that people are not subordinated to one another as agents. I believe that Markovits’ critique of Dworkin is spot on, but I also think that his own positive thesis — and hence his conclusion about how much redistribution there ought to be in an egalitarian society — is flawed. Hence, this paper will begin in Section I by explaining how Dworkin uses the HIMAD and his TS argument to estimate the amount of redistribution that there ought to be in an egalitarian society — this section will be largely expository in content. Markovits’ critique of Dworkin will then be outlined in Section II, as will be his own positive thesis. My critique of Markovits, and my own positive thesis, will then make a fleeting appearance in Section III. Finally, I will conclude by rejecting both Dworkin’s and Markovits’ estimates of the amount of redistribution that there ought to be in an egalitarian society, and by reaffirming the responsibility-tracking egalitarian claim that choice preservation and luck elimination are complementary and not competing egalitarian aims. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

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

It could be argued that tort law is failing, and arguably an example of this failure is the recent public liability and insurance (‘PL&I’) crisis. A number of solutions have been proposed, but ultimately the chosen solution should address whatever we take to be the cause of this failure. On one account, the PL&I crisis is a result of an unwarranted expansion of the scope of tort law. Proponents of this position sometimes argue that the duty of care owed by (...) defendants to plaintiffs has expanded beyond reasonable levels, such that parties who were not really responsible for another’s misfortune are successfully sued, while those who really were to blame get away without taking any responsibility. However people should take responsibility for their actions, and the only likely consequence of allowing them to shirk it is that they and others will be less likely to exercise due care in the future, since the deterrents of liability and of no compensation for accidentally self-imposed losses will not be there. Others also argue that this expansion is not warranted because it is inappropriately fueled by ‘deep pocket’ considerations rather than by considerations of fault. They argue that the presence of liability insurance sways the judiciary to award damages against defendants since they know that insurers, and not the defendant personally, will pay for it in the end anyway. But although it may seem that no real person has to bear these burdens when they are imposed onto insurers, in reality all of society bears them collectively when insurers are forced to hike their premiums to cover these increasing damages payments. In any case, it seems unfair to force insurers to cover these costs simply because they can afford to do so. If such an expansion is indeed the cause of the PL&I crisis, then a contraction of the scope of tort liability, and a pious return to the fault principle, might remedy the situation. However it could also be argued that inadequate deterrence is the cause of this crisis. On this account the problem would lie not with the tort system’s continued unwarranted expansion, but in the fact that defendants really have been too careless. If prospective injurers were appropriately deterred from engaging in unnecessarily risky activities, then fewer accidents would ever occur in the first place, and this would reduce the need for litigation at its very source. If we take this to be the cause of tort law’s failure then our solution should aim to improve deterrence. Glen Robinson has argued that improved deterrence could be achieved if plaintiffs were allowed to sue defendants for wrongful exposure to ongoing risks of future harm, even in the absence of currently materialized losses. He argues that at least in toxic injury type cases the tortious creation of risk [should be seen as] an appropriate basis of liability, with damages being assessed according to the value of the risk, as an alternative to forcing risk victims to abide the outcome of the event and seek damages only if and when harm materializes. In a sense, Robinson wishes to treat newly-acquired wrongful risks as de-facto wrongful losses, and these are what would be compensated in liability for risk creation (‘LFRC’) cases. Robinson argues that if the extent of damages were fixed to the extent of risk exposure, all detected unreasonable risk creators would be forced to bear the costs of their activities, rather than only those who could be found responsible for another’s injuries ‘on the balance of probabilities’. The incidence of accidents should decrease as a result of improved deterrence, reduce the ‘suing fest’, and so resolve the PL&I crisis. So whilst the first solution involves contracting the scope of tort liability, Robinson’s solution involves an expansion of its scope. However Robinson acknowledges that LFRC seems prima facie incompatible with current tort principles which in the least require the presence of plaintiff losses, defendant fault, and causation to be established before making defendants liable for plaintiffs’ compensation. Since losses would be absent in LFRC cases by definition, the first evidentiary requirement would always be frustrated, and in its absence proof of defendant fault and causation would also seem scant. If such an expansion of tort liability were not supported by current tort principles then it would be no better than proposals to switch accident law across to no-fault, since both solutions would require comprehensive legal reform. However Robinson argues that the above three evidentiary requirements could be met in LFRC cases to the same extent that they are met in other currently accepted cases, and hence that his solution would therefore be preferable to no-fault solutions as it would only require incremental but not comprehensive legal reform. Although I believe that actual losses should be present before allowing plaintiffs to seek compensation, I will not present a positive argument for this conclusion. My aim in this paper is not to debate the relative merits of Robinson’s solution as compared to no-fault solutions, nor to determine which account of the cause of the PL&I crisis is closer to the truth, but rather to find out whether Robinson’s solution would indeed require less radical legal reform than, for example, proposed no-fault solutions. I will argue that Robinson fails to show that current tort principles would support his proposed solution, and hence that his solution is at best on an even footing with no-fault solutions since both would require comprehensive legal reform. (shrink)

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

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

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some (...) of its anticipated uses. (shrink)

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the (...) body fluids ontology initiative may provide support to basic and translational science. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Theories of epistemic justification are commonly assessed by exploring their predictions about particular hypothetical cases – predictions as to whether justification is present or absent in this or that case. With a few exceptions, it is much less common for theories of epistemic justification to be assessed by exploring their predictions about logical principles. The exceptions are a handful of ‘closure’ principles, which have received a lot of attention, and which certain theories of justification are well known to invalidate. But (...) these closure principles are only a small sample of the logical principles that we might consider. In this paper, I will outline four further logical principles that plausibly hold for justification and two which plausibly do not. While my primary aim is just to put these principles forward, I will use them to evaluate some different approaches to justification and (tentatively) conclude that a ‘normic’ theory of justification best captures its logic. (shrink)

BioéthiqueOnline was launched in March 2012 as a non-peer reviewed journal with the aim of providing a platform to facilitate and encourage the development of a bilingual bioethics community in Canada and internationally. In light of discussions amongst the Editorial Committee over the past few months regarding the growth of the journal, we have decided to move to a peer-reviewed process for articles submitted to the journal.

Third-party property insurance (TPPI) protects insured drivers who accidentally damage an expensive car from the threat of financial ruin. Perhaps more importantly though, TPPI also protects the victims whose losses might otherwise go uncompensated. Ought responsible drivers therefore take out TPPI? This paper begins by enumerating some reasons for why a rational person might believe that they have a moral obligation to take out TPPI. It will be argued that if what is at stake in taking responsibility is the ability (...) to compensate our possible future victims for their losses, then it might initially seem that most people should be thankful for the availability of relatively inexpensive TPPI because without it they may not have sufficient funds to do the right thing and compensate their victims in the event of an accident. But is the ability to compensate one's victims really what is at stake in taking responsibility? The second part of this paper will critically examine the arguments for the above position, and it will argue that these arguments do not support the conclusion that injurers should compensate their victims for their losses, and hence that drivers need not take out TPPI in order to be responsible. Further still, even if these arguments did support the conclusion that injurers should compensate their victims for their losses, then (perhaps surprisingly) nobody should to be allowed to take out TPPI because doing so would frustrate justice. (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)

A de minimis risk is defined as a risk that is so small that it may be legitimately ignored when making a decision. While ignoring small risks is common in our day-to-day decision making, attempts to introduce the notion of a de minimis risk into the framework of decision theory have run up against a series of well-known difficulties. In this paper, I will develop an enriched decision theoretic framework that is capable of overcoming two major obstacles to the modelling (...) of de minimis risk. The key move is to introduce, into decision theory, a non-probabilistic conception of risk known as normic risk. (shrink)

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)

Self-esteem can influence educational success, and educational success can also be influenced by self-esteem. Hence, high self-esteem has been recognized as a key predictor of academic success in students. Thus, this study investigates the relationship between self-esteem and anxiety of senior high school students. Employing descriptive-correlational design with 194 senior high school students enrolled in private schools during the school year 2021-2022. Based on the statistical analysis, there is a correlation between self-esteem and anxiety (r.=.125).

Our understanding of subjunctive conditionals has been greatly enhanced through the use of possible world semantics and, more precisely, by the idea that they involve variably strict quantification over possible worlds. I propose to extend this treatment to ceteris paribus conditionals – that is, conditionals that incorporate a ceteris paribus or ‘other things being equal’ clause. Although such conditionals are commonly invoked in scientific theorising, they traditionally arouse suspicion and apprehensiveness amongst philosophers. By treating ceteris paribus conditionals as a species (...) of variably strict conditional I hope to shed new light upon their content and their logic. (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.