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)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...) always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

This is a short editorial to introduce the double issue of Applied Ontology that celebrates the journal's tenth anniversary. At a time when information technology of all kinds depends on the use of explicit ontologies, our journal addresses the modeling issues that underlie the next generation of computational systems. As the editors of Applied Ontology, we are excited by how far we have come in the past decade and by the opportunities that await our research community.

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

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

In 2005, IOS Press published the first issue of applied Ontology. At the time, we argued that, at the core of the journal, there was “a desire to understand the nature of reality and how people construe their world”. We declared that ontology was both “fundamental to human thought” and “to translating our thoughts into computational artifacts” (Guarino & Musen,2005). With an editorial board of distinguished scholars representing the fields of computer science, informatics, information science, philosophy, linguistics, psychology, and (...) social science, we had the firm belief that applied Ontologywould fulfill an important academic niche, becoming an essential forum for discussion on topics such as ontological analysis, conceptual modeling, and the role of domain models in building and managing information systems. The facts now show that we were correct. (shrink)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as (...) archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The sense of smell occupies a peculiar intermediate position within Aristotle's theory of sense perception: odours, like colours and sounds, are perceived at a distance through an external medium of air or water; yet in their nature they are intimately related to flavours, the proper objects of taste, which for Aristotle is a form of touch. In this paper, I examine Aristotle's claims about odour and smell, especially in De Anima II.9 and De Sensu 5, to see what light they (...) shed on his theory of sense perception more generally. In the first half, I argue that neither of the two most influential recent ways of understanding Aristotle's theory of perception can adequately account for what he says about the sense of smell. In the second half, I offer my own positive account, considering and resolving various puzzles raised by Aristotle's claims about the nature of odour and its relation to flavour. Finally, I conclude that Aristotle's discussions of odour and smell suggest a plausible and interesting way of understanding the relationship, on his view, between ordinary, material changes in the sense organs and the activation of the capacity to perceive, considered merely as such. (shrink)

The Companion begins with a section-by-section overview of Being and Time and a chapter reviewing the genesis of this seminal work. The final chapter situates Being and Time in the context of Heidegger's later work.

National decline is typically blamed on special interests from the demand side of politics corrupting a country's institutions. The usual demand-side suspects include crony capitalists, consumer activists, economic elites, and labor unions. Less attention is given to government insiders on the supply side of politics - rulers, elected officials, bureaucrats, and public employees. In autocracies and democracies, government insiders have the motive, means, and opportunity to co-opt political power for their benefit and at the expense of national well-being. Many storied (...) empires have succumbed to such inside jobs. Today, they imperil countries as different as China and the United States. Democracy - government by the people - does not ensure government for the people. Understanding how government insiders use their power to subvert the public interest - and how these negative consequences can be mitigated - is the topic of this book by Mark A. Zupan. (shrink)

In De Anima II.6, Aristotle divides the objects of perception into three kinds: “special perceptibles" (idia aisthêta) such as colours, sounds and flavours, which can be perceived in their own right by only one sense; “common perceptibles" (koina aisthêta) such as shapes, sizes and movements, which can be perceived in their own right by multiple senses; and “incidental perceptibles,” such as the son of Diares, which can be perceived only “incidentally” (kata sumbebêkos). In this paper, I examine this division of (...) perceptibles and consider what it amounts to. First, I argue that Aristotle’s distinction between perceiving something in its own right (kath' hauto) and perceiving it incidentally marks a causal distinction: what is perceived in its own right causes perception as such, whereas what is perceived incidentally coincides with what is perceived in its own right. Second, I argue that for Aristotle special perceptibles, unlike common perceptibles, belong to homogeneous bodies on account of their chemical composition. Finally, I explain the primacy Aristotle assigns to special perceptibles and his claim that perception of them alone is free from error. I conclude with some brief remarks on Aristotle and the primary/secondary quality distinction. (shrink)

This article is an amendment to Drengson (2011) that offers examples from fieldwork and reporting of practices influenced by the technocratic paradigm. Specifically (1) Krippner's work with Brazilian shamans and the theft of their tribal knowledge by the biotechnology industry that Krippner refers to as ecopiratism. (2) Hitchcock's field research with indigenous populations in the northwestern Kalahari Desert region of southern Africa and his documented assault of these indigenous peoples by private companies that Hitchcock refers to as developmental genocide. And (...) (3) Walker's summary of Monsanto's patenting of seeds, and her warning of the health and environmental problems associated with genetically modified organisms. These examples offer support for the hypothesis that the eco-crisis is born of conscious agency. Beyond documenting and diagnosing these symptoms of the eco-crisis, this article puts forth the thesis that a transformation of consciousness would change the conditions of our present situation by providing the opportunity for different solutions to be found through the creation of a new mind set to make the necessary decisions for change. Many refer to the emerging field concerned with developing approaches to this transformation of consciousness as ecopsychology that Schroll prefers to call transpersonal ecosophy. (shrink)

Exploring mysteries that have evoked wonder and consternation for millennia, this handbook covers topics such as the nature of divinity and humanity, the legitimacy of religious experience, the possibility of miracles, and idea of life after death. As a reference volume and introductory text, this is an essential resource for students and scholars.

An innocent form of emergence—what I call "weak emergence"—is now a commonplace in a thriving interdisciplinary nexus of scientific activity—sometimes called the "sciences of complexity"—that include connectionist modelling, non-linear dynamics (popularly known as "chaos" theory), and artificial life.1 After defining it, illustrating it in two contexts, and reviewing the available evidence, I conclude that the scientific and philosophical prospects for weak emergence are bright.

Abstract:Moral imagination is a reasoning process thought to counter the organizational factors that corrupt ethical judgment. We describe the psychology of moral imagination as composed of the four decision processes identified by Rest (1986), i.e., moral sensitivity, moral judgment, moral intention, and moral behavior. We examine each process in depth, distilling extant psychological research and indicating organizational implications. The conclusion offers suggestions for future research.The majority of men are subjective toward themselves and objective toward all others—terribly objective sometimes—but the real (...) task is in fact to be objective toward one’s self and subjective toward all others. (shrink)

Weak emergence has been offered as an explication of the ubiquitous notion of emergence used in complexity science (Bedau 1997). After outlining the problem of emergence and comparing weak emergence with the two other main objectivist approaches to emergence, this paper explains a version of weak emergence and illustrates it with cellular automata. Then it explains the sort of downward causation and explanatory autonomy involved in weak emergence.

Weak emergence is the view that a system’s macro properties can be explained by its micro properties but only in an especially complicated way. This paper explains a version of weak emergence based on the notion of explanatory incompressibility and “crawling the causal web.” Then it examines three reasons why weak emergence might be thought to be just in the mind. The first reason is based on contrasting mere epistemological emergence with a form of ontological emergence that involves irreducible downward (...) causation. The second reason is based on the idea that attributions of emergence are always a reflection of our ignorance of non-emergent explanations. The third reason is based on the charge that complex explanations are anthropocentric. Rather than being just in the mind, weak emergence is seen to involve a distinctive kind of complex, macro-pattern in the mind-independent objective micro-causal structure that exists in nature. The paper ends by addressing two further questions. One concerns whether weak emergence applies only or mainly to computer simulations and computational systems. The other concerns the respect in which weak emergence is dynamic rather than static. (shrink)

Deep-seated intellectual problems lie at the root of explaining religious change in the sixteenth century. The idea of reformatio denoted a return to an original, pristine order. It was about recov...

Therehasbeenevidencefortheverybrief,temporalquantizationofperceptualexperienceatregularintervalsbelo w100msforseveraldecades.Webrieflydescribehowearlierstudiesledtotheconceptof“psychologicalmoment”ofbe tween50and60msduration.Accordingtohistoricaltheories,withinthepsychologicalmomentalleventswouldbepro cessedasco-temporal.Morerecently,alinkwithphysiologicalmechanismshasbeenproposed,accordingtowhichthe 50–60mspsychologicalmomentwouldbedefinedbytheupperlimitrequiredbyneuralmechanismstosynchronizeandthe rebyrepresentasnapshotofcurrentperceptualeventstructure.However,ourownexperimentaldevelopmentsalsoid entifyamorefine-scaled,serializedprocessstructurewithinthepsychologicalmoment.Ourdatasuggeststhatnot alleventsareprocessedasco-temporalwithinthepsychologicalmomentandinstead,someareprocessedsuccessivel y.Thisevidencequestionstheanalogrelationshipbetweensynchronizedprocessandsimultaneousexperienceandop ensdebateontheontologyandfunctionof“moments”inpsychologicalexperience.

Mobile devices with health apps, direct-to-consumer genetic testing, crowd-sourced information, and other data sources have enabled research by new classes of researchers. Independent researchers, citizen scientists, patient-directed researchers, self-experimenters, and others are not covered by federal research regulations because they are not recipients of federal financial assistance or conducting research in anticipation of a submission to the FDA for approval of a new drug or medical device. This article addresses the difficult policy challenge of promoting the welfare and interests of (...) research participants, as well as the public, in the absence of regulatory requirements and without discouraging independent, innovative scientific inquiry. The article recommends a series of measures, including education, consultation, transparency, self-governance, and regulation to strike the appropriate balance. (shrink)

Huston Smith has argued that the universal source of wholeness, which he refers to as the primordial tradition, is essential to a meaningful life. Indeed embracing this tradition is, said Smith, an act of rejoining the human race. Our current forms of organized religion offer us ritualized expressions of this tradition, yet often fail to provide us with transpersonal growth; it is this transpersonal growth that reconnects us with the source of religion. This essay differentiates mainstream religion from a way (...) that we can begin to construct a physical theory of the primordial tradition–a necessary first step toward reclaiming the source of religion. (shrink)

Aristotle sometimes claims that the perception of special perceptibles by their proper sense is unerring. This claim is striking, since it might seem that we quite often misperceive things like colours, sounds and smells. Aristotle also claims that the perception of common perceptibles is more prone to error than the perception of special perceptibles. This is puzzling in its own right, and also places constraints on the interpretation of. I argue that reading Alexander of Aphrodisias on perceptual error can help (...) to make good sense of both of Aristotle’s claims. (shrink)

This book includes ten essays that trace the notion of unconcealment as it develops from Heidegger's early writings to his later work, shaping his philosophy of truth, language and history. 'Unconcealment' is the idea that what entities are depends on the conditions that allow them to manifest themselves. This concept, central to Heidegger's work, also applies to worlds in a dual sense: first, a condition of entities manifesting themselves is the existence of a world; and second, worlds themselves are disclosed. (...) The unconcealment or disclosure of a world is the most important historical event, and Heidegger believes there have been a number of quite distinct worlds that have emerged and disappeared in history. Heidegger's thought as a whole can profitably be seen as working out the implications of the original understanding of unconcealment. (shrink)

Prompted by the development of the Theory of Challenge and Threat States in Athletes (Jones et al, 2009), recent years has witnessed a considerable increase in research examining challenge and threat in sport. This manuscript provides a critical review of the literature examining challenge and threat in sport, tracing its historical development and some of the current empirical ambiguities. In an attempt to reconcile some of these ambiguities, and utilising neurobiological evidence associated with approach- and avoidance-motivation (cf. Elliot & Covington, (...) 2001), this paper draws upon the Evaluative Space Model (ESM: Cacioppo et al., 1997) and considers the implications for understanding challenge and threat in sport. For example, rather than see challenge and threat as opposite ends of a single bipolar continuum, the ESM implies that individuals could be (1) challenged, (2) threatened, (3) challenged and threatened, or (4) neither challenged or threatened by a particular stimulus. From this perspective it could be argued that the appraisal of some sport situations as both challenging and threatening could be advantageous, whereas the current literature seems to imply that the appraisal of stress as a threat is maladaptive for performance. In drawing upon the ESM, we outline the Evaluative Space Approach to Challenge and Threat and provide several testable hypotheses for advancing understanding of challenge and threat (in sport). We also outline a number of cardiovascular and experiential measures that can be used to examine these hypotheses. In sum, this paper provides a significant theoretical, empirical and practical contribution to our understanding of challenge and threat (in sport). (shrink)

Public health is a dynamic field. Outbreaks of new diseases, as well as changing patterns of population growth, economic development, and lifestyle trends all may threaten public health and thus demand a public health response. As the practice of public health evolves, there is an ongoing need to reassess its scientific, ethical, legal, and social underpinnings. Such a reappraisal must consider the disagreement among public health officials, public health scholars, elected officials, and the public about the proper role of public (...) health and the distinctions, for example, between public health and clinical care, and public health and health promotion.In this article I will attempt to characterize the main points of contention as well as offer my own views regarding the proper scope of public health. Greater clarity and consensus on the meaning of public health are likely to lead to more efficient and effective public health interventions as well as increased public and political support for public health activities. (shrink)

In this paper, I offer a new solution to the old problem of how best to understand the meaning of the word ‘logos’ in the extant writings of Heraclitus, especially in fragments DK B1, B2 and B50. On the view I defend, Heraclitus was neither using the word in a perfectly ordinary way in these fragments, as some have maintained, nor denoting by it some kind of general principle or law governing change in the cosmos, as many have claimed. Rather, (...) I argue, Heraclitus deliberately traded on the ordinary use of the word in his time (to refer to a written or spoken presentation of things as ‘thus and so’) to denote the world’s constant presentation of itself as ‘thus and so’ to all of us in our experience – a kind of cosmic self-revelation. I show how this captures the sense in which ‘the logos’ is said to be ‘common’ (xunos) and to be the kind of thing most people fail to comprehend even before hearing Heraclitus’ own account, all without detaching Heraclitus’ use of the word from its ordinary contemporary meaning. This interpretation suggests Heraclitus was a thinker more centrally concerned with human (mis)understanding than with speculative cosmology. (shrink)

Calling for an expanded framework of EuroAmerican science's methodology whose perspective acknowledges both quantitative/etic and qualitative/emic orientations is the broad focus of this article. More specifically this article argues that our understanding of shamanic and/or other related states of consciousness has been greatly enhanced through ethnographic methods, yet in their present form these methods fail to provide the means to fully comprehend these states. They fail, or are limited, because this approach is only a “cognitive interpretation” or “metanarrative” of the (...) actual experience and not the experience itself. Consequently this perspective is also limited because the researcher continues to assess his or her data through the lens of their symbolic constructs, thereby preventing them from truly experiencing shamanic and psi/spirit approaches to knowing since the data collection process does not “in and of itself” affect the observer. We, therefore, need expanded ethnographic methods that include within their approaches an understanding of methods and techniques to experientially encounter these states of consciousness—and become transformed by them. Our becoming transformed and then recollecting our ethnoautobiographical experiences is the means toward a new kind of science and its methods of inquiry that this article seeks to encourage. (shrink)

Public health is a dynamic field. Outbreaks of new diseases, as well as changing patterns of population growth, economic development, and lifestyle trends all may threaten public health and thus demand a public health response. As the practice of public health evolves, there is an ongoing need to reassess its scientific, ethical, legal, and social underpinnings. Such a reappraisal must consider the disagreement among public health officials, public health scholars, elected officials, and the public about the proper role of public (...) health and the distinctions, for example, between public health and clinical care, and public health and health promotion.In this article I will attempt to characterize the main points of contention as well as offer my own views regarding the proper scope of public health. Greater clarity and consensus on the meaning of public health are likely to lead to more efficient and effective public health interventions as well as increased public and political support for public health activities. (shrink)

This book explores the making of health care rationing decisions through the analysis of three alternative decision makers: patients paying out of pocket; officials setting limits on treatments and coverage; and physicians at the bedside. Hall develops this analysis along three dimensions: political economics, ethics, and law. The economic dimension addresses the practical feasibility of each method. The ethical dimension discusses the moral aspects of these methods, while the legal dimension traces the most recent developments in jurisprudence and health law.

Huston Smith has argued that the universal source of wholeness, which he refers to as the primordial tradition, is essential to a meaningful life. Indeed embracing this tradition is, said Smith, an act of rejoining the human race. Our current forms of organized religion offer us ritualized expressions of this tradition, yet often fail to provide us with transpersonal growth; it is this transpersonal growth that reconnects us with the source of religion. This essay differentiates mainstream religion from a way (...) that we can begin to construct a physical theory of the primordial tradition–a necessary first step toward reclaiming the source of religion. (shrink)

This paper describes and defends the view that minimal chemical life essentially involves the chemical integration of three chemical functionalities: containment, metabolism, and program (Rasmussen et al. in Protocells: bridging nonliving and living matter, 2009a ). This view is illustrated and explained with the help of CMP and Rasmussen diagrams (Rasmussen et al. In: Rasmussen et al. (eds.) in Protocells: bridging nonliving and living matter, 71–100, 2009b ), both of which represent the key chemical functional dependencies among containment, metabolism, and (...) program. The CMP model of minimal chemical life gains some support from the broad view of life as open-ended evolution, which I have defended elsewhere (Bedau in The philosophy of artificial life, 1996 ; Bedau in Artificial Life, 4:125–140, 1998 ). Further support comes from the natural way the CMP model resolves the puzzle about whether life is a matter of degree. (shrink)