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.

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)

One of the most influential works of this century, The Myth of Sisyphus and Other Essays is a crucial exposition of existentialist thought. Influenced by works such as Don Juan and the novels of Kafka, these essays begin with a meditation on suicide; the question of living or not living in a universe devoid of order or meaning. With lyric eloquence, Albert Camus brilliantly posits a way out of despair, reaffirming the value of personal existence, and the possibility of (...) life lived with dignity and authenticity. (shrink)

An extraordinary horde of aberrant, deformed, and grotesque beings inhabits the writings collected in the Zhuangzi. Crippled, malformed, hideous, foolish, eccentric, and even outlawed individuals conquer the central place of philosophical narration, traditionally proscribed for them, and create one of the most important and intriguing voices echoing through the text. Yet, for all their undeniably significant presence, scholars of ancient Chinese philosophy have paid surprisingly little attention to the topic of monsters. Structured into three sections and adopting a critical, strictly (...) philosophical standpoint, this paper aims to draw attention to the crucial role played by monsters in the Zhuangzi. The first section underlines the essential characteristics of these monsters and, most particularly, their disruptive dimension together with the challenge they pose to philosophical thinking. The second section offers a detailed review of the recent bibliography on the Zhuangzi with regard to analysis of these aberrant figures. Finally, based on contributions in the work of Jacques Rancière, the third section highlights the political scope embodied by the monstrous beings of the Zhuangzi. (shrink)

Hans Albert is the leading critical rationalist in the German-speaking world and the main critic of the hermeneutic tradition. He is well-known for applying the idea of critical reason to various kinds of human practice, including economics, politics, and law. But he has also improved on Popper's methodology by introducing the idea of rational heuristics. This collection of essays presents the core of his work on epistemology, philosophy of the social sciences, philosophy of religion, and philosophy of law. Most (...) of Albert's works have not been available in English. It is enormously useful to have these articles collected in a single volume. (shrink)

Comment faire de l’existence un thème anthropologique? Faisons l’hypothèse que Heidegger peut nous aider dans cet objectif d’une anthropologie empirique et théorique de l’existence. Il ne s’agit pas de paraître heideggérien ou anti-heideggérien. Il ne s’agit pas non plus d’expliciter la pensée de Heidegger, ni de l’accepter mais d’aider à comprendre, avec celle-ci et aussi contre celle-ci, cette possible anthropologie, sa spécificité et son thème de travail, la condition humaine. Heidegger,...

The paradox is brought out of blondel's philosophy's claim to be at once a true philosophy respecting the autonomy of human reason in investigating the problem of human destiny with full objectivity, Without being prejudiced ahead of time by the christian answer, And at the same time its openness to the christian answer as one that must necessarily be considered by reason itself. This was quite contrary to the rationalistic temper of the university philosophical world in blondel's time and awakened (...) strong resistance. His claim that action itself is an essential ingredient for the clarification of thought and the revelation of truth was also contrary to and ahead of the spirit of his time. The author shows how the combination of intellectual rigor with openness and respect for the role of action go hand in hand throughout this unique type of philosophy. (shrink)

The key difference between the two concepts is that power acts directly on the actions of others by providing incentives and penalties for action, whereas influence operates on beliefs. From this distinction it follows that the exercise of influence is not simply a sub-class of instances of the exercise of power. It can be perfectly reasonable to attribute influence where there is no power, as in the example of the influence of Cervantes on subsequent writers.

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.

This is a reproduction of a book published before 1923. This book may have occasional imperfections such as missing or blurred pages, poor pictures, errant marks, etc. that were either part of the original artifact, or were introduced by the scanning process. We believe this work is culturally important, and despite the imperfections, have elected to bring it back into print as part of our continuing commitment to the preservation of printed works worldwide. We appreciate your understanding of the imperfections (...) in the preservation process, and hope you enjoy this valuable book. (shrink)

In den sozialwissenschaftlichen und sozialtheoretischen Diskussionen ruckt nach einer langeren Interimszeit wieder zunehmend die Frage nach den Konstitutionsbedingungen des Sozialen, von Sozialitat bzw. sozialen Gebilden in den Vordergrund.

In this paper it is shown that the attempt by Gerhard Seel to give a positive solution to the problem of absolute justification of socalled practical sentences has failed. His attempts to explicate his central concepts and the conditions of adequacy of his fundamental practical sentence are analyzed in detail. And his proposals for the formulation of a sentence of this kind are shown to lead to absurd consequences, so that consistent fallibilism is saved from his attack.