Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

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)

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)

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)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

Introduction: the age of Paine -- Portrait of a failure -- The great American cause -- The peculiar honor of France -- The Age of Reason -- An honest and useful life.

Die MISCELLANEA MEDIAEVALIA präsentieren seit ihrer Gründung durch Paul Wilpert im Jahre 1962 Arbeiten des Thomas-Instituts der Universität zu Köln. Das Kernstück der Publikationsreihe bilden die Akten der im zweijährigen Rhythmus stattfindenden Kölner Mediaevistentagungen, die vor über 50 Jahren von Josef Koch, dem Gründungsdirektor des Instituts, ins Leben gerufen wurden. Der interdisziplinäre Charakter dieser Kongresse prägt auch die Tagungsakten: Die MISCELLANEA MEDIAEVALIA versammeln Beiträge aus allen mediävistischen Disziplinen - die mittelalterliche Geschichte, die Philosophie, die Theologie sowie die Kunst- und Literaturwissenschaften (...) sind Teile einer Gesamtbetrachtung des Mittelalters. (shrink)

Die MISCELLANEA MEDIAEVALIA präsentieren seit ihrer Gründung durch Paul Wilpert im Jahre 1962 Arbeiten des Thomas-Instituts der Universität zu Köln. Das Kernstück der Publikationsreihe bilden die Akten der im zweijährigen Rhythmus stattfindenden Kölner Mediaevistentagungen, die vor über 50 Jahren von Josef Koch, dem Gründungsdirektor des Instituts, ins Leben gerufen wurden. Der interdisziplinäre Charakter dieser Kongresse prägt auch die Tagungsakten: Die MISCELLANEA MEDIAEVALIA versammeln Beiträge aus allen mediävistischen Disziplinen - die mittelalterliche Geschichte, die Philosophie, die Theologie sowie die Kunst- und Literaturwissenschaften (...) sind Teile einer Gesamtbetrachtung des Mittelalters. (shrink)

Après un effort de remise à jour des concepts temps, matière, vie, hasard et personne, cet essai les utilise pour décrire de façon aussi précise que possible la réalité de la Terre, "bouleversée au rythme effréné des agissements des hommes". Un nouveau regard sur l'histoire des sciences, pour mieux prendre conscience "que nous vivons tous, désormais, dans un même monde fini, que ce qui touche les uns ne peut que concerner les autres", tel est donc l'itinéraire suivi ici par (...) class='Hi'>Albert Jacq. (shrink)

Economics as a science of human behavior has been grounded in a remarkably parsimonious postulate: that of the self-interested, isolated individual who chooses freely and rationally between alternative courses of action after computing their prospective costs and benefits. In recent decades, a group of economists has shown considerable industry and ingenuity in applying this way of interpreting the social world to a series of ostensibly noneconomic phenomena, from crime to the family, and from collective action to democracy. The “economic” or (...) “rational-actor” approach has yielded some important insights, but its onward sweep has also revealed some of its intrinsic weaknesses. As a result, it has become possible to mount a critique which, ironically, can be carried all the way back to the heartland of the would-be conquering discipline. That the economic approach presents us with too simpleminded an account of even such fundamental economic processes as consumption and production is the basic thesis of the present paper. (shrink)

Introduction Watching the Doctor In some cultures, it is said, villagers cluster around a healer and a patient, eagerly listening to their conversation and ...

Albert Dzur proposes an approach he calls "democratic professionalism" to build bridges between specialists in domains like law, medicine, and journalism and the lay public in such a way as to enable and enhance broader public engagement ...

L’Union Européenne vit sous un régime de démocratie représentative de type fédéral dont la particularité est d’être en vigueur dans un État qui n’est pas fédéral. Les critiques qui l’accablent aujourd’hui sont en grande partie liées aux ambiguïtés et aux impasses qu’engendre l’enchevêtrement, pas toujours très clair, des pouvoirs actuellement exercés par le Parlement, la Commission et le Conseil. Une autre partie de la critique est plus tranchante : elle récuse le principe même de la construction européenne en l’accusant d’instituer (...) un déni de démocratie. Trois arguments étayent ce réquisitoire : le premier pointe la perte de souveraineté nationale ; le second le manque de représentativité des élus ; le troisième le déficit de légitimité des autorités en place. Des révisions apportées à chacun de ces trois facteurs permettraient-elles de conforter la démocratie dans le cadre européen? (shrink)

Sartre importe à l'histoire vivante de la philosophie sous plusieurs angles. Héritier de Hegel qui le hante, il conteste celui-ci dans sa conviction « totaliste ». S'il reste fidèle au dynamisme hégélien, à l'interrogation constante du vécu, il les traduit pourtant par nos langages présents.

Holding On to Reality is a brilliant history of information, from its inception in the natural world to its role in the transformation of culture to the current Internet mania and is attendant assets and liabilities. Drawing on the history of ideas, the details of information technology, and the boundaries of the human condition, Borgmann illuminates the relationship between things and signs, between reality and information. "[Borgmann] has offered a stunningly clear definition of information in Holding On to Reality.... He (...) leaves room for little argument, unless one wants to pose the now vogue objection: I guess it depends on what you mean by nothing."—Paul Bennett, Wired "A superb anecdotal analysis of information for a hype-addled age."—New Scientist "This insightful and poetic reflection on the changing nature of information is a wonderful antidote to much of the current hype about the 'information revolution.' Borgmann reminds us that whatever the reality of our time, we need 'a balance of signs and things' in our lives."—Margaret Wertheim, LA Weekly. (shrink)

Focusing democratic theory on the pressing issue of punishment, Punishment, Participatory Democracy, and the Jury argues for participatory institutional designs as antidotes to the American penal state. Citizen action in institutions like the jury and restorative justice programs can foster the attunement, reflectiveness, and full-bodied communication needed as foundations for widespread civic responsibility for criminal justice.

America is a wonderful and magnificent country that affords its citizens the broadest freedoms and the greatest prosperity in the world. But it also has its share of warts. It is embroiled in a war that many of its citizens consider unjust and even illegal. It continues to ravage the natural environment and ignore poverty both at home and abroad, and its culture is increasingly driven by materialism and consumerism. But America, for better or for worse, is still a nation (...) that we have built. So why then, asks Albert Borgmann in this most timely and urgent work, are we failing to take responsibility for it? In Real American Ethics , Borgmann asks us to reevaluate our role in the making of American values. Taking his cue from Winston Churchill—who once observed that we shape our buildings, and then our buildings shape us—Borgmann considers the power of our most enduring institutions and the condition of our present moral makeup to propose inspired new ways in which we, as ordinary citizens, can act to improve our country. This, he shows, includes everything from where we choose to live and what we spend our money on to daunting tasks like the reshaping of our cities—habits and actions that can guide us to more accomplished and virtuous lives. Using prose that is easy and direct throughout, Borgmann’s position is grounded neither by conservative nor liberal ideology, but in his understanding that he is a devoted citizen among many. In an age in which the blame game is the only game in town, this patriotic book is an eloquent reminder of the political strength we all wield when we work together. (shrink)

Bringing expert knowledge to bear in an open and deliberative way to help solve pressing social problems is a major concern today, when technocratic and bureaucratic decision making often occurs with little or no input from the general public. Albert Dzur proposes an approach he calls “democratic professionalism” to build bridges between specialists in domains like law, medicine, and journalism and the lay public in such a way as to enable and enhance broader public engagement with and deliberation about (...) major social issues. Sparking a critical and constructive dialogue among social theories of the professions, professional ethics, and political theories of deliberative democracy, Dzur reveals interests, motivations, strengths, and vulnerabilities in conventional professional roles that provide guideposts for this new approach. He then applies it in examining three practical arenas in which experiments in collaboration and power-sharing between professionals and citizens have been undertaken: public journalism, restorative justice, and the bioethics movement. Finally, he draws lessons from these cases to refine this innovative theory and identify the kinds of challenges practitioners face in being both democratic and professional. (shrink)

Die MISCELLANEA MEDIAEVALIA präsentieren seit ihrer Gründung durch Paul Wilpert im Jahre 1962 Arbeiten des Thomas-Instituts der Universität zu Köln. Das Kernstück der Publikationsreihe bilden die Akten der im zweijährigen Rhythmus stattfindenden Kölner Mediaevistentagungen, die vor über 50 Jahren von Josef Koch, dem Gründungsdirektor des Instituts, ins Leben gerufen wurden. Der interdisziplinäre Charakter dieser Kongresse prägt auch die Tagungsakten: Die MISCELLANEA MEDIAEVALIA versammeln Beiträge aus allen mediävistischen Disziplinen - die mittelalterliche Geschichte, die Philosophie, die Theologie sowie die Kunst- und Literaturwissenschaften (...) sind Teile einer Gesamtbetrachtung des Mittelalters. (shrink)