In a world of partially overlapping and partially conflicting interests there is good reason to doubt that self-seeking behaviour at the micro-level will spontaneously lead to desirable social outcomes at the macro-level. Nevertheless, some sophisticated economic writers advocating a laissez-faire policy prescription have proposed various 'invisible hand' mechanisms which can supposedly be relied upon to 'educe good from ill'. Smith defended the 'simple system of natural liberty' as giving the greatest scope to the unfolding of God's will and the (...) working out of 'natural' providential processes free of interference by 'artificial' state intervention - the expression not of divine order but of fallible human reason. Hayek, adopting a similar policy stance, based it in an evolutionary process in which those institutional forms best adapted to reconciling individual interests would, he believed, spontaneously be selected for in the inter-group struggle for survival. Keynes shares the holistic approach of Smith and Hayek, but without their reliance on invisible hand mechanisms. If spontaneous processes cannot be relied upon to generate desirable social outcomes then we have to take responsibility for achieving this ourselves by establishing the appropriate institutional framework. Keynes takes a historical view of the role of capitalism and analyses its pathology as rooted in what we would now refer to as a multi-player prisoners' dilemma. The paper draws out the significance of his methodological standpoint here. Keynes's policy standpoint assigns a critical role to his own class, the 'educated bourgeoisie' in the reform process he maps out. A distinction, but also an intimate connection, is highlighted between, on the one hand, micro-level individualism (the 'Manchester System, and, on the other, the macro-level collective action ('planning') required to preserve it. Finally Keynes is considered in relation to the themes of laissez-faire, holism, reductionism, providentialism and the invisible hand. (shrink)

This thesis argues for the fundamental importance of the opposition between holistic and reductionistic world-views in economics. Both reductionism and holism may nevertheless underpin laissez-faire policy prescriptions. Scrutiny of the nature of the articulation between micro and macro levels in the writings of economists suggests that invisible hand theories play a key role in reconciling reductionist policy prescriptions with a holistic world. An examination of the prisoners' dilemma in game theory and Arrow's impossibility theorem in social choice theory sets the (...) scene. The prisoners' dilemma epitomises the collective irrationality coordination problems lead to. The source of the dilemma is identified as the combination of interdependence in content and independence in form of the decision making process. Arrovian impossibility has been perceived as challenging traditional views of the relationship between micro and macro levels in economics. Conservative arguments against the possibility in principle of a social welfare function are criticised here as depending on an illicit dualism. The thesis then reviews the standpoints of Smith, Hayek and Keynes. For Smith, the social desirability of individual self-seeking activity is ensured by the 'invisible hand' of a god who has moulded us so to behave, that the quantity of happiness in the world is always maximised. Hayek seeks to re-establish the invisible hand in a secular age, replacing the agency of a deity with an evolutionary mechanism. Hayek's evolutionary theory, criticised here as being based on the exploded notion of group selection, cannot underpin the desirability of spontaneous outcomes. I conclude by arguing that Keynes shares the holistic approach of Smith and Hayek, but without their reliance on invisible hand mechanisms. If spontaneous processes cannot be relied upon to generate desirable social outcomes then we have to take responsibility for achieving this ourselves by establishing the appropriate institutional framework to eliminate macroeconomic prisoners' dilemmas. (shrink)

Bunge (2000) distinguishes two main methodological approaches of holism and individualism, and associates with them policy prescriptions of centralism and laissez-faire. He identifies systemism as a superior approach to both the study and management of society. The present paper, seeking to correct and develop this line of thought, suggests a more complex relation between policy and methodology. There are two possible methodological underpinnings for laissez-faire: while writers such as Friedman and Lucas fit Bunge’s pattern, more sophisticated advocates of laissez-faire, such (...) as Smith and Hayek, base their policy prescription in a methodology quite divergent from the individualism Bunge describes. (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)

Hohwy (Hohwy 2016, Hohwy 2017) argues there is a tension between the free energy principle and leading depictions of mind as embodied, enactive, and extended (so-called ‘EEE1 cognition’). The tension is traced to the importance, in free energy formulations, of a conception of mind and agency that depends upon the presence of a ‘Markov blanket’ demarcating the agent from the surrounding world. In what follows I show that the Markov blanket considerations do not, in fact, lead to the kinds of (...) tension that Hohwy depicts. On the contrary, they actively favour the EEE story. This is because the Markov property, as exemplified in biological agents, picks out neither a unique nor a stationary boundary. It is this multiplicity and mutability– rather than the absence of agent-environment boundaries as such - that EEE cognition celebrates. (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)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...) and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (shrink)

A very simple contextualist treatment of a sentence containing an epistemic modal, e.g. a might be F, is that it is true iff for all the contextually salient community knows, a is F. It is widely agreed that the simple theory will not work in some cases, but the counterexamples produced so far seem amenable to a more complicated contextualist theory. We argue, however, that no contextualist theory can capture the evaluations speakers naturally make of sentences containing epistemic modals. If (...) we want to respect these evaluations, our best option is a relativist theory of epistemic modals. On a relativist theory, an utterance of a might be F can be true relative to one context of evaluation and false relative to another. We argue that such a theory does better than any rival approach at capturing all the behaviour of epistemic modals. (shrink)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

The moral status of animals is a subject of controversy both within and beyond academic philosophy, especially regarding the question of whether and when it is ethical to eat meat. A commitment to animal rights and related notions of animal protection is often thought to entail a plant-based diet, but recent philosophical work challenges this view by arguing that, even if animals warrant a high degree of moral standing, we are permitted - or even obliged - to eat meat. (...) class='Hi'>Andy Lamey provides critical analysis of past and present dialogues surrounding animal rights, discussing topics including plant agriculture, animal cognition, and in vitro meat. He documents the trend toward a new kind of omnivorism that justifies meat-eating within a framework of animal protection, and evaluates for the first time which forms of this new omnivorism can be ethically justified, providing crucial guidance for philosophers as well as researchers in culture and agriculture. (shrink)

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

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

What should we make of systems that behave just like conscious creatures but operate via mechanisms that are profoundly different from our own? How should we even think about mechanistic similarity and difference in this context? To answer these questions, I take a closer look at the inferential machinery that allows us to justifiably draw conclusions about consciousness in others. I argue that inferences about consciousness in others are best viewed as involving analogical inferences grounded in explanatory considerations. I conclude (...) that profound mechanistic difference severs the evidential link between behavioural evidence and subjective experience. I then draw on recent developments within the mechanistic philosophy of science to motivate a conception of mechanistic similarity that is not wedded to similarity of physical substrate and outline a strategy for resolving disputes about whether it is cognitive similarity or neural similarity that matters for inferences about consciousness. (shrink)

During long-term refugee displacements, it is common for the refugees’ country of origin to be called on to recognize a right of return. A long-standing tradition of philosophical theorizing is sceptical of such a right. Howard Adelman and Elazar Barkan are contemporary proponents of this view. They argue that, in many cases, it is not feasible for entire refugee populations to return home, and so the notion of a right of return is no right at all. We can call Adelman (...) and Barkan’s view the feasibility objection. Many defenders of rights will deny that empirical facts such as the kind to which Adelman and Barkan appeal are relevant to determining whether a moral entitlement amounts to a right. In contrast, I offer a response to the feasibility objection that does admit the relevance of facts. In my view, considerations of feasibility do matter when determining what rights human beings possess. Nevertheless, the feasibility objection is undone by its failure to acknowledge a distinction between two different kinds of feasibility constraints. ‘Hard’ constraints include logical, nomological and biological considerations. ‘Soft’ constraints include political, cultural and institutional factors. A necessary condition of a moral entitlement achieving the status of a right, I argue, is that it be feasible in the hard sense. Crucially, however, a right need not always be feasible in the soft sense. Refugees can have rights that it is not currently possible to implement politically. (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)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

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)

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

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

This article brings animal protection theory to bear on Temple Grandin’s work, in her capacity both as a designer of slaughter facilities and as an advocate for omnivorism. Animal protection is a better term for what is often termed animal rights, given that many of the theories grouped under the animal rights label do not extend the concept of rights to animals. I outline the nature of Grandin’s system of humane slaughter as it pertains to cattle. I then outline four (...) arguments Grandin has made defending meat-eating. On a protection-based approach, I argue, Grandin’s system of slaughter is superior to its traditional counterpart. Grandin’s success as a designer of humane slaughterhouses however is not matched by any corresponding success in offering a moral defence of meat-eating. Despite, or perhaps because of, the popularity of her work, Grandin’s arguments for continuing to eat animals are noteworthy only in how disappointing and rudimentary they are. If we can thank Grandin for making a difference in the lives of millions of farm animals, her work can also be criticized for not engaging the moral status of animals with the depth and rigor that it deserves. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

I argue against two of the most influential contemporary theories of moral responsibility: those of Harry Frankfurt and John Martin Fischer. Both propose conditions which are supposed to be sufficient for direct moral responsibility for actions. (By the term direct moral responsibility, I mean moral responsibility which is not traced from an earlier action.) Frankfurt proposes a condition of 'identification'; Fischer, writing with Mark Ravizza, proposes conditions for 'guidance control'. I argue, using counterexamples, that neither is sufficient for direct moral (...) responsibility. -/- My counterexample cases are based on recent research in psychology which reveals many surprising causes of our actions. Some of this research comes from the field of situationist social psychology; some from experiments which reveal the influence of automatic processes in our actions. Broadly, I call such causes 'subverting' when the agent would not identify with her action, if she knew all the causes of the action. When an action has subverting causes, the agent is not directly morally responsible for it, even though she may meet the conditions specified by Frankfurt and Fischer. -/- I also criticise the theories of Eddy Nahmias and John Doris, who have both engaged specifically with the threats posed to moral responsibility by situationist research. Against Doris and Nahmias, I argue that their conditions are neither necessary nor sufficient for direct moral responsibility. -/- My final objective is to argue that there are many everyday actions for which we mistakenly hold agents morally responsible. I review evidence that there are many everyday actions which have subverting causes. Many of those are actions for which we currently hold agents morally responsible. But I argue that, in many of those same actions, the agents are not in fact morally responsible – they bear neither direct nor traced moral responsibility. (shrink)

One of the starting assumptions in the debate over the ethical status of animals is that someone who is committed to reducing animal suffering should not eat meat. Steven Davis has recently advanced a novel criticism of this view. He argues that individuals who are committed to reducing animal suffering should not adopt a vegetarian or vegan diet, as Tom Regan an other animal rights advocates claim, but one containing free-range beef. To make his case Davis highlights an overlooked form (...) of animal harm, that done to field animals in crop production. Yet while Davis's argument is ingenious and thought-provoking, it is not a successful challenge to vegetarianism and veganism's status as the diets that most advance animal rights. Scientific studies of crop production that Davis draws on document two different forms of harm done to field animals: those that are directly killed by harvesting equipment and those that are killed by other animals. Once this distinction is made explicit, the degree to which such studies pose a problem for animal protection theory considerably weakens. Davis also overlooks philosophically significant forms of harm to human beings that are present in beef production but not crop harvesting. Finally, he bases his argument on the controversial assumption that there is no difference between deliberate and accidental killing - either of animals or people. Although these problems defeat Davis's attempt to offer an immanent critique of Regan's animal rights position, his analysis does have important dietary ramifications that animal advocates should take into account. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...) performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (shrink)

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)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (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)

J.M. Coetzee’s book, 'Elizabeth Costello' is one of the stranger works to appear in recent years. Yet if we focus our attention on the book’s two chapters dealing with animals, two preoccupations emerge. The first sees Coetzee use animals to evoke a particular conception of ethics, one similar to that of the philosopher Mary Midgley. Coetzee’s second theme connects animals to the phenomena of scapegoating, as it has been characterized by the philosophical anthropologist René Girard. While both themes involve human (...) interactions with animals, each transcends application to that particular issue and raises deeper questions, respectively concerning the foundations of morality and the therapeutic allure of political violence. Making explicit these two preoccupations enhances our understanding of Coetzee’s fiction, particularly Disgrace. However, when Coetzee’s two philosophical strands are analyzed in their own terms, the ethics of sympathy is shown to be a more coherent notion than the understanding of politics he takes over from Girard. (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)

Some philosophers (Duff, Hampton) conceive of punishment as a way of communicating a message to the punished and argue that this communicative function justifies the harm of punishment. I object to communicative theories because punishment seems intuitively justified in cases in which it fails as a method of communication. Punishment fails as communication when the punished ignores the intended message or fails to understand it. Among those most likely to ignore or fail to understand the message of punishment are the (...) most hardened criminals, whom we typically think are appropriate targets of punishment. I suggest that an alternative justificatory strategy, one that focuses not on the successful receipt of the message of punishment by the wrongdoer but on the expression of condemnation by the community, is not subject to the same worry. The norms of successful expression are more easily met than those of communication, so that expressing condemnation toward a criminal might be justified even if he is unreceptive in the face of the expression. (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.

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

The Handmaid’s Tale depicts a United States taken over by a fundamentalist dictatorship called Gilead that also resembles Plato’s ideal city. Attempts to explain Gilead’s debt to Plato face two challenges. First, aspects of Gilead that recall Plato also contain features that differ, at times dramatically, from the Platonic original. Second, Gilead invokes distorted versions of ideas from philosophies other than Plato’s. I explore two ways of making sense of Gilead’s distorted philosophical appropriations. The explanations differ over whether such distortions (...) are best explained by the nature of the philosophies they misrepresent, or by the nature of Gilead. The explanation that emphasizes Gilead’s own agency is ultimately best able to make sense of how illiberal regimes misappropriate philosophical concepts, both in the novel and in reality, in order to limit the political imagination of their subjects. (shrink)

Detecting introspective errors about consciousness presents challenges that are widely supposed to be difficult, if not impossible, to overcome. This is a problem for consciousness science because many central questions turn on when and to what extent we should trust subjects’ introspective reports. This has led some authors to suggest that we should abandon introspection as a source of evidence when constructing a science of consciousness. Others have concluded that central questions in consciousness science cannot be answered via empirical investigation. (...) I argue that on closer inspection, the challenges associated with detecting introspective errors can be overcome. I demonstrate how natural kind reasoning—the iterative application of inference to the best explanation to home in on and leverage regularities in nature—can allow us to detect introspective errors even in difficult cases such as judgments about mental imagery, and I conclude that worries about intractable methodological challenges in consciousness science are misguided. (shrink)

This study aims to describe the cultural strategy of the Buginese people of Pagatan (one of ethnic group in Indonesia) in preserving their local wisdom living in a multicultural society. This research was conducted using qualitative descriptive method through three methods of data collection i.e. in-depth interview, observation and literature involving community leaders and ordinary people as informants. The historical-interpretative method was used to analyze the Data. The findings from this study indicate that the people of Buginese-Pagatan use two strategies (...) to preserve their Buginese identity in a pluralistic society i.e. the strategy of interaction patterns and the use of ethnic symbols. In the strategy of interaction patterns, they implement adaptive and inclusive interaction patterns. This strategy is represented by the mastery and the use of regional languages in addition to the Buginese language, cross-ethnic marriages, and participation in social activities. While in the strategy of using ethnic symbols, they form a distinct identity from the one existing in Sulawesi. This strategy is represented by the use of ethnic symbols such as wearing Bodo clothes, bone cap in the rituals of marriage and moving in new houses, preserving the ancient model of Buginese house for settlement, and forming a new cultural identity called Maccera Tasi. This research has identified local values preserved and held by its people as cultural strategies in building a harmonious society. We believe that the cultural strategies are useful not only to form a united, dignified and civilized local community of Indonesia, but also to serve as a model for other cultures to preserve their local wisdom. (shrink)

This study aims to evaluate whether the idea of ultimate reality in world religions contributes to the characteristics of the world religion paradigm, which is hierarchical cosmology or “subject-object cosmology.” Several research on this topic claims that one of the characteristics of the world religion paradigm is its hierarchical perspective. Discussing this issue is important to distinguish the world religions as the paradigm and the world religions as the most widely embraced religion. This study argues that the hierarchical perspective of (...) the world religion paradigm can be rooted in the idea of ultimate reality, that there is a supreme, foremost, and most principal reality in the continuity of this universe, namely the supernatural or God. The hierarchical cosmology consists of three main domains: supernatural/God, culture/human, and nature. This study uses a literature study methodology, relying on books, journals, and texts related to research questions. This study finds that the world religion paradigm or hierarchical cosmology or “subject-object cosmology” is prominent, especially in Abrahamic religions such as Islam, Christianity, and Judaism, even though the concept of ultimate reality in these three religions is different. (shrink)

1. The Situation in Cognition 2. Situated Cognition: A Potted Recent History 3. Extensions in Biology, Computation, and Cognition 4. Articulating the Idea of Cognitive Extension 5. Are Some Resources Intrinsically Non-Cognitive? 6. Is Cognition Extended or Only Embedded? 7. Letting Nature Take Its Course.

Hannah Arendt argued that refugees pose a major problem for liberalism. Most liberal theorists endorse the idea of human rights. At the same time, liberalism takes the existence of sovereign states for granted. When large numbers of people petition a liberal state for asylum, Arendt argued, these two commitments will come into conflict. An unwavering respect for human rights would mean that no refugee is ever turned away. Being sovereign, however, allows states to control their borders. States supposedly committed to (...) human rights will thus often violate the rights of refugees by denying them entry. I attempt to defend liberalism from Arendt’s criticism by outlining a rights-based model of asylum that is enforceable by sovereign states. This approach avoids the question of what border-enforcement measures, if any, are defensible at the level of ideal justice, and instead seeks to outline a framework of refugee rights that can be realized in a world in which migration controls are a fact of life. Central to my argument is a distinction between the place where a person is recognized as a rights-bearing agent and the potentially different place where he or she exercises those rights. (shrink)

How, as Caldwell puts it, does one choose between rival systems all of which claim to rest on a priori foundations? On the nonfallibilistic conception it is difficult to make sense even of the possibility of rival systems of this sort. On the conception here defended, in contrast, the existence of such rival systems can be seen to be a perfectly natural and acceptable consequence of the just-mentioned difficulties we will often fact in coming to know even the intelligible traits (...) of reality: one adjudicates between such systems in the same way in which one adjudicates between all rival scientific hypotheses, namely via a complex mixture of empirical and a priori considerations. (shrink)

A central project for the neuroscience of consciousness is to reveal the neural basis of consciousness. For the past 20-odd years, this project has been conceptualized in terms of minimal sufficiency. Recently, a number of authors have suggested that the project is better conceived in mechanistic terms as the search for difference-makers. In this paper, I (i) motivate this mechanistic alternative to minimal sufficiency, (ii) develop it further by clarifying debates about the prospects of leveraging mutual manipulability to distinguish constitutive (...) difference-makers from those that are merely causal, and (iii) explore the implications this has for recent debates concerning the status of the prefrontal cortex. I argue that adopting a mechanistic approach to the neuroscience of consciousness suggests that the prefrontal cortex is part of the neural mechanisms underlying consciousness even if it is not strictly speaking a necessary part. (shrink)

The phenomenon of abbreviation used on Instagram is an interesting thing since the users modify the abbreviation form of expansion words making deviation from the original meaning. The principle of meaning relation between abbreviations and their expansions is used to make a change to the purposes of Instagram users. This research was aimed to describe the principle of abbreviation used in Instagram. An exploitation method was used by the technique of making screenshots and recording the abbreviation data. The results of (...) research indicate that the principle of abbreviation consists of three forms namely inclusion, contact, and complementary. The results of this research can be very effective in understanding as well as how to use abbreviations, especially on Instagram. The Novelty of the study is in investigating the abbreviation used in Instagram. (shrink)

The thesis that an analysis of property rights is essential to an adequate analysis of the state is a mainstay of political philosophy. The contours of the type of government a society has are shaped by the system regulating the property rights prevailing in that society. Views of this sort are widespread. They range from Locke to Nozick and encompass pretty much everything else in between. Defenders of this sort of view accord to property rights supreme importance. A state that (...) does not sufficiently respect property rights is likely to be a totalitarian state, and will also be likely to fail to respect rights of other sorts. (shrink)

Philosophers have highlighted a dilemma for the criminal law. Unjust, racist policies in the United States have produced conditions in which the dispossessed are more likely to commit crime. This complicity undermines the standing of the state to blame their offenses. Nevertheless, the state has reason to punish those crimes in order to deter future offenses. Tommie Shelby proposes a way out of this dilemma. He separates the state’s right to condemn from its right to punish. I raise doubts about (...) Shelby’s proposed resolution. So long as punishment is widely and reasonably understood to condemn crime, Shelby’s proposal does not resolve the dilemma. Moreover, there is reason to think the blaming aspect of punishment plays a role in the justification of its hard treatment. I conclude by considering some other ways out of the dilemma, focusing especially on how the United States might take responsibility for its complicity. (shrink)

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