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)

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)

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)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (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)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

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)

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)

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)

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

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)

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)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (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)

In this paper I respond to Marcello Di Bello’s criticisms of the ‘normic account’ of the criminal standard of proof. In so doing, I further elaborate on what the normic account predicts about certain significant legal categories of evidence, including DNA and fingerprint evidence and eyewitness identifications.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (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)

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)

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)

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)

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)

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.

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)

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)

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)

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)

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)

Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.

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.

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...) Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries. (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.

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

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)

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)

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

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)

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)

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)

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)

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)

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.

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)

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)

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)