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 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)

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)

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)

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)

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 National Cancer Institute's (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemen...

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

This second edition of the book contains a new chapter on the notions of natural-kind words and natural kinds.

In Absolute Music: The History of an Idea, author Mark Evan Bonds examines how writers have struggled to isolate the essence of music in ways that account for its profound effects on the human spirit. By carefully tracing the evolution of absolute music from Ancient Greece through the Middle Ages to twentieth-century America, Bonds provides the first comprehensive history of this pivotal concept, and provokes new thoughts on the essence of music and how this essence explains music's effect. A (...) long awaited book from one of the most respected senior scholars in the field. (shrink)

This paper will examine the social and ethical impacts of using artificial intelligence (AI) in the agricultural sector. It will identify what are some of the most prevalent challenges and impacts identified in the literature, how this correlates with those discussed in the domain of AI ethics, and are being implemented into AI ethics guidelines. This will be achieved by examining published articles and conference proceedings that focus on societal or ethical impacts of AI in the agri-food sector, through a (...) thematic analysis of the literature. The thematic analysis will be divided based on the classifications outlined through 11 overarching principles, from an established lexicon (transparency, justice and fairness, non-maleficence, responsibility, privacy, beneficence, freedom and autonomy, trust, dignity, sustainability, and solidarity). While research on AI agriculture is still relatively new, this paper aims to map the debate and illustrate what the literature says in the context of social and ethical impacts. It aim is to analyse these impacts, based on these 11 principles. This research will contrast which impacts are not being discussed in agricultural AI and which issues are not being discussed in AI ethics guidelines, but which are discussed in relation to agricultural AI. The aim of this is to identify gaps within the agricultural literature, and gaps in AI ethics guidelines, that may need to be addressed. (shrink)

A higher order potential analysis of moral status clarifies the issues that divide Human Being Theorists who oppose embryo research from Person Theorists who favor embryo research. Higher order potential personhood is transitive if it is active, identity preserving and morally relevant. If the transition from the Second Order Potential of the embryo to the First Order Potential of an infant is transitive, opponents of embryo research make a powerful case for the moral status of the embryo. If it is (...) intransitive, then the Person Theorist can draw lines between levels of moral status that permit embryo research to proceed. (shrink)

In relation to education, there is in Foucault's approach a double emphasis which constitutes an ordering principle for this work.

Emotion Review, Volume 14, Issue 1, Page 15-30, January 2022. We offer an account of mental health and well-being using the predictive processing framework. According to this framework, the difference between mental health and psychopathology can be located in the goodness of the predictive model as a regulator of action. What is crucial for avoiding the rigid patterns of thinking, feeling and acting associated with psychopathology is the regulation of action based on the valence of affective states. In PPF, valence (...) is modelled as error dynamics—the change in prediction errors over time. Our aim in this paper is to show how error dynamics can account for both momentary happiness and longer term well-being. What will emerge is a new neurocomputational framework for making sense of human flourishing. (shrink)

As the average age of the population increases, so too do the number of people living with chronic illnesses. With limited resources available, the development of dialogue-based e-health systems that provide justified general health advice offers a cost-effective solution to the management of chronic conditions. It is however imperative that such systems are responsible in their approach. We present in this paper two main challenges for the deployment of e-health systems, that have a particular relevance to dialogue and argumentation: collecting (...) and handling health data, and trust. For both challenges, we look at specific issues therein, outlining their importance in general, and describing their relevance to dialogue and argumentation. Finally, we go on to propose six recommendations for handling these issues, towards addressing the main challenges themselves, that act both as general advice for dialogue and argumentation research in the e-health domain, and as a foundation for future work on this topic. (shrink)

This book is a must-read for researchers interested in taking a high-level, non-mechanistic approach to answering age-old fundamental questions in the brain ...

Mark Hearn, pastor of a church in Duluth, Georgia, one of the most diverse counties in America, shares their transition from a monolithic Anglo-American congregation to a cross-cultural community with members from thirty-seven different countries.

A specific issue for argumentation theory is whether information and communication technologies play any role in governing argument — that is, as parties engage in practical activities across space and time via ICTs, does technology matter for the interplay of argumentative content and process in managing disagreement? The case made here is that technologies do matter because they are not merely conduits of communication but have a role in the pragmatics of communication and argumentation. In particular, ICTs should be recognized (...) as communication-information services that are delegated degrees of responsibility for managing disagreements arising from practical activities. These services are organized around practical theories for designing disagreement space. However, recognizing this relationship between argument and technology requires accounting for procedures, techniques, or rules and speech acts that are not argumentative propositions in any strict sense but that are consequential for what becomes argumentation in any setting. An account about designing disagreement space, grounded in Jackson and Jacobs’s theory of Disagreement Management, is put forward to address these issues while more generally contributing to understanding argument in context. (shrink)

The concept of the "unlevel playing field" is critiqued for its tendency to take the prevailing masculinist managerial paradigm for granted. Rather than assume that both men and women should assimilate to corporate masculinity, feminist alternatives are suggested. The pervasiveness of the masculine ethic and the "myth of meritocracy" in organizations are reviewed, with the space shuttle Challenger disaster serving as a focal point to demonstrate the dysfunctionality of masculine management and the rationale for feminist-based organizational transformation to promote not (...) only gender equity, but more effective and ethical organizational behavior. (shrink)

Traditional utilitarianism, when applied, implies a surprising prediction about the future, viz., that all experience of pleasure and pain must end once and for all, or infinitely dwindle. Not only is this implication surprising, it should render utilitarianism unacceptable to persons who hold any of the following theses: that evaluative propositions may not imply descriptive, factual propositions; that evaluative propositions may not imply contingent factual propositions about the future; that there will always exist beings who experience pleasure or pain.

We have used fMRI to measure responses to chromatic and achromatic contrast in retinotopically defined regions of macaque and human visual cortex. We make four observations. Firstly, the relative amplitudes of responses to color and luminance stimuli in macaque area V1 are similar to those previously observed in human fMRI experiments. Secondly, the dorsal and ventral subdivisions of macaque area V4 respond in a similar way to opponent (L j M)-cone chromatic contrast suggesting that they are part of a single (...) functional area. Thirdly, we find that macaque area V4, like area V1, responds preferentially to chromatic contrast compared to luminance contrast and the degree of preference is strongly influenced by the temporal frequency of the stimulus. Finally, we observe that while macaque V4d is a region on the dorsal surface of the macaque visual cortex that responds robustly to chromatic stimuli, human chromatic responses to identical stimuli are largely confined to the ventral surface suggesting a fundamental difference in the topographical organization of higher visual areas between humans and macaques. (shrink)

In his attack on the notion of immediate experience, Hans-Georg Gadamer argues that aesthetic experience should be absorbed into hermeneutics because alone it cannot account for the historical nature of experience ; predicated on an ontological theory of art, the unfathomable, therefore, is the sense we have of these infinite hermeneutic depths. I argue that this account is methodologically and existentially unacceptable: methodologically because it is overly speculative, and existentially because it betrays authentic existence. I critique Gadamer from the perspective (...) of William James’ Pragmatism and argue, inverting Gadamer’s main thesis, that hermeneutics should be reduced to aesthetic experience. The meaning that emerges in aesthetic experience does not ‘rise up’ from the depths but is immanent in what James calls ‘pure experience’. The unfathomable, therefore, is not a glimpse into the metaphysical abyss but a phenomenological insight into the immanent structure of experience. (shrink)

David Steen and co-authors in this journal offer a philosophical argument to support an “Evolutionary Community Concept” to identify what they call “evolutionary communities.” They describe these as “unique collections of species that interact and have co-evolved in a given geographic area” and that include “co-evolved dependencies between different parts of a community.” Steen et al. refer to the coevolution of assemblages, collections, communities, dependencies, interspecific and abiotic interactions, and traits, but they do not define “co-evolution” or provide an example (...) in which co-evolution has been demonstrated. There may be as many ways to explain interactions among species as these interactions themselves; they may result, for example, from ecological fitting and phenotypic plasticity. In this paper, I argue that standard Darwinian Theory explains intraspecific microevolution or descent with modification within an interbreeding and potentially continuous population. The power, mechanism, or force that causes interspecific co-evolution, especially at the community scale, requires further explanation. (shrink)

The focus of this chapter is public policy and consequentialism, especially issues that arise in connection with the environment – i.e. the natural world, including non-human animals. We integrate some of the existing literature on environmental economics, welfare economics, and policy with the literature on environmental values and philosophy. The emphasis on environmental policy is motivated by the fact that it is arguably the most philosophically interesting and challenging application of consequentialism to policy, as it includes all the challenges of (...) valuing the distribution of human wealth and power, and has the further challenge of putting these consequences on the same scale as consequences for human health, non-human animals, and nature. We suggest that standard methods of (economic) policy analysis provide a good approximation of correct welfarist analysis, except that they must be supplemented with methods for valuing animal wellbeing and tradeoffs with human wellbeing. We then provide the needed methods. (shrink)

: This paper develops four related claims: 1. Critical thinking should focus more on decision making, 2. the heuristics and bias literature developed by cognitive psychologists and behavioral economists provides many insights into human irrationality which can be useful in critical thinking instruction, 3. unfortunately the “rational choice” norms used by behavioral economists to identify “biased” decision making narrowly equate rational decision making with the efficient pursuit of individual satisfaction; deviations from these norms should not be treated as an irrational (...) bias, 4. a richer, procedural theory of rational decision making should be the basis for critical thinking instruction in decision making. (shrink)

This paper argues that the type of conscience claims made in last decade’s spate of cases involving pharmacists’ objections to filling birth control prescriptions and cases such as Ms. Means and Mercy Health Partners of Michigan, and even the Affordable Care Act and the Little Sisters of the Poor, as different as they appear to be from each other, share a common element that ties them together and makes them fundamentally different in kind from traditional claims of conscience about which (...) a practical consensus emerged in the 1980s and 1990s. This difference in kind is profoundly significant; so much so, we contend, that it puts them at odds with the normative basis for protecting conscience claims in United States health care settings in the first place, making them illegitimate. Finally, we argue that, given the illegitimacy of these contemporary claims of conscience, physicians and other health professionals must honor their well-established standing obligations to provide informed consent and refer or transfer care even if the service requested or needed is at odds with their own core moral beliefs—a requirement that is in line with the aforementioned practical consensus on traditional claims of conscience. (shrink)