Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

E4BP4, a mammalian basic leucine zipper (bZIP) transcription factor, was first identified through its ability to bind and repress viral promoter sequences. Subsequently, E4BP4 and homologues in other species have been implicated in a diverse range of processes including commitment to cell survival versus apoptosis, the anti‐inflammatory response and, most recently, in the mammalian circadian oscillatory mechanism. In some of these cases at least, E4BP4 appears to act antagonistically with members of the related PAR family of transcription factors with which (...) it shares DNA‐binding specificity. This diversity of function is mirrored by the regulatory pathways impinging on E4BP4, which include regulation by ras via the lymphokine IL‐3 in murine B‐cells, by thyroid hormone during Xenopus tail resorption, by glucocorticoids in murine fibroblasts and by calcium in rat smooth muscle cells. This article will cover the unfolding role/s of and regulation of E4BP4, E4BP4‐like proteins and PAR factors in species as diverse as mouse and C. elegans. BioEssays 24:1023–1029, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

Restoration ecology has recently emerged as a branch of scientific ecology that challenges many of the traditional tenets of environmentalism. Because the restoration of ecosystems, “applied ecology,” has the potential to advance theoretical understanding to such an extent that scientists can extensively manipulate the environment, it encourages increasingly active human participation within ecosystemsand could inhibit the preservation of areas from human influences. Despite the environmentally dangerous possibilities that this form of science and technology present, restoration offers an attractive alternative for (...) human interaction with the environment. I outline the primary claims that have been made for ecological restoration, examine inconsistencies with restorationists’ philosophical position,and propose a reassessment of the definition of restoration that may aid in the clarification and development of a system of environmental ethics that recognizes human relationships with the environment as potentially symbiotic and positive. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

What is inequality? In the late 1990s there was an explosion of interest in the subject that yielded a substantial body of formal tools and results for income-distribution analysis. Nearly all of this is founded on a small set of core assumptions - such as the Principle of Transfers, scale independence, the population principle∑ - that are used to give meaning to specific concepts of inequality measurement, inequality ranking and, indeed, to inequality itself. But does the standard axiomatic structure coincide (...) with public perceptions of inequality? Or is the economist's concept of inequality a thing apart, perpetuated through serial brainwashing in the way the subject is studied and taught? In this 1999 book, Amiel and Cowell examine the evidence from a large international questionnaire experiment using student respondents. Along with basic 'cake-sharing' issues, related questions involving social-welfare rankings, the relationship between inequality and overall income growth and the meaning of poverty comparisons are considered. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

George Kateb's writings have been innovatory in exploring the fundamental quandary of how modern democracy--sovereignty vested in the many--might nevertheless protect, respect, promote, even celebrate the singular, albeit ordinary individual. His essays, often leading to unexpected results, have focused on many inter-related topics: rights, representation, constitutionalism, war, evil, extinction, punishment, privacy, patriotism, and more. This book focuses in particular on his thought in three key areas: Dignity These essays exhibit the breadth and complexity of Kateb's notion of dignity and (...) outline some implications for political theory. Rather than a solely moral approach to the theory of human rights, he elaborates a human-dignity rationale for the very worth of the human species Morality Here Kateb challenges the position that moral considerations are often too demanding to have a place in the rough-and-tumble of modern politics and political analysis. Rejecting common justifications for the propriety of punishment, he insists that state-based punishment is a perplexing moral problem that cannot be allayed by repairing to theories of state legitimacy. Individuality These essays gather some of Kateb's rejoinders and correctives to common conceptions and customary critiques of the theory of democratic individuality. He explains that Locke's hesitations and religious backtracking are instructive, perhaps as precursors for the ways in which vestigial beliefs can still cloud moral reasoning. (shrink)

Georg Aerni is a photographic artist with a particular interest in architecture. Educated as an architect himself, he has been working with the camera on this subject with great precision and consistence for the past fifteen years. Paris, Barcelona, Hon.

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

"Historian Ramsay Cook called George Grant one of Canadas two most important political thinkers in the twentieth century.

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

John Wilson, Barbara Cowell; The Democratic Myth, Journal of Philosophy of Education, Volume 17, Issue 1, 30 May 2006, Pages 111–117, https://doi.org/10.1111/j.

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in the (...) regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Abstract This paper considers the notion of ?social skills? from the viewpoint of analytic philosophy. The authors note first prejudices for and against an approach to human problems in terms of identificable ?skills?. They then stipulate a definition of ?social skills? in terms of techniques ('knowing how'), and point to other essential aspects of change and treatment which fall outside this definition (in particular, the aspects of attitude or desire and judgement). Some generalisations are attempted relevant to the question of (...) what problems are likely to yield to a ?social skills? approach, and what problems are likely to go deeper than such an approach can cure. Attention is drawn to the necessity of defining what is to count as success in such training, and the logical limits of ?social skills? training are clarified. (shrink)

The aim of the Georg Büchner Yearbook, which is published at irregular intervals, is to serve Büchner research as a forum for stock-taking and innovation, reflection and debate, for documenting sources and imparting information swiftly, to support critical debate and understanding, and in so doing to cover the whole range of research findings and discussions in both their substance and their methodology. This mission statement from the foreword to the 1st volume (1981) still guides the Yearbook in all its regular (...) sections (articles debates minor contributions and glosses documents and materials reviews current bibliography). (shrink)

This volume is a direct result of a conference held at Princeton University to honor George A. Miller, an extraordinary psychologist. A distinguished panel of speakers from various disciplines -- psychology, philosophy, neuroscience and artificial intelligence -- were challenged to respond to Dr. Miller's query: "What has happened to cognition? In other words, what has the past 30 years contributed to our understanding of the mind? Do we really know anything that wasn't already clear to William James?" Each participant (...) tried to stand back a little from his or her most recent work, but to address the general question from his or her particular standpoint. The chapters in the present volume derive from that occasion. (shrink)